4V5C

Structure of the Thermus thermophilus 70S ribosome in complex with mRNA, paromomycin, acylated A-site tRNA, deacylated P-site tRNA, and E-site tRNA.

• PDB DOI: https://doi.org/10.2210/pdb4V5C/pdb
• Entry: 4V5C supersedes: 2WDG, 2WDH, 2WDI, 2WDJ
• NAKB: 4V5C

• Classification: RIBOSOME
• Organism(s): Thermus thermophilus HB8, Escherichia coli K-12, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-24 Released: 2014-07-09 
• Deposition Author(s): Voorhees, R.M., Weixlbaumer, A., Loakes, D., Kelley, A.C., Ramakrishnan, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.272 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 

Starting Model: experimental

Literature

Insights Into Substrate Stabilization from Snapshots of the Peptidyl Transferase Center of the Intact 70S Ribosome

Voorhees, R.M., Weixlbaumer, A., Loakes, D., Kelley, A.C., Ramakrishnan, V.

(2009) Nat Struct Mol Biol 16: 528-533

• PubMed: 19363482 
• DOI: https://doi.org/10.1038/nsmb.1577
• Primary Citation of Related Structures:  
  4V5C, 4V5D


• PubMed Abstract: 
  

  Protein synthesis is catalyzed in the peptidyl transferase center (PTC), located in the large (50S) subunit of the ribosome. No high-resolution structure of the intact ribosome has contained a complete active site including both A- and P-site tRNAs. In addition, although past structures of the 50S subunit have found no ordered proteins at the PTC, biochemical evidence suggests that specific proteins are capable of interacting with the 3' ends of tRNA ligands. Here we present structures, at 3.6-A and 3.5-A resolution respectively, of the 70S ribosome in complex with A- and P-site tRNAs that mimic pre- and post-peptidyl-transfer states. These structures demonstrate that the PTC is very similar between the 50S subunit and the intact ribosome. They also reveal interactions between the ribosomal proteins L16 and L27 and the tRNA substrates, helping to elucidate the role of these proteins in peptidyl transfer.

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Organizational Affiliation: 

Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 50-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 50-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 50-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 50-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 4,519.39 kDa 
• Atom Count: 296,168 
• Modelled Residue Count: 21,250 
• Deposited Residue Count: 22,004 
• Unique protein chains: 50
• Unique nucleic acid chains: 7

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S2	B [auth AB], GB [auth CB]	256	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P80371

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S3	C [auth AC], HB [auth CC]	239	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80372 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P80372

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S4	D [auth AD], IB [auth CD]	209	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80373 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P80373

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S5	E [auth AE], JB [auth CE]	162	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHQ5

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S6	F [auth AF], KB [auth CF]	101	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SLP8

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S7	G [auth AG], LB [auth CG]	156	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P17291

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S8	H [auth AH], MB [auth CH]	138	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S9	I [auth AI], NB [auth CI]	128	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P62669 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Go to UniProtKB:  P62669

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S10	J [auth AJ], OB [auth CJ]	105	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHN7

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S11	K [auth AK], PB [auth CK]	129	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P80376

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S12	L [auth AL], QB [auth CL]	135	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHN3

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S13	M [auth AM], RB [auth CM]	126	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80377 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P80377

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S14	N [auth AN], SB [auth CN]	61	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S15	O [auth AO], TB [auth CO]	89	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SJ76

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S16	P [auth AP], UB [auth CP]	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SJH3

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S17	Q [auth AQ], VB [auth CQ]	105	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S18	R [auth AR], WB [auth CR]	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SLQ0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S19	S [auth AS], XB [auth CS]	93	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHP2

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S20	T [auth AT], YB [auth CT]	106	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P80380

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN THX	U [auth AU], ZB [auth CU]	27	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SIH3

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L27	EC [auth D0], Z [auth B0]	85	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60493 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P60493

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L28	AA [auth B1], FC [auth D1]	98	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60494 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P60494

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L29	BA [auth B2], GC [auth D2]	72	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHP6

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L30	CA [auth B3], HC [auth D3]	60	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHQ6

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L31	DA [auth B4], IC [auth D4]	71	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SJE1

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L32	EA [auth B5], JC [auth D5]	60	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P80339

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L33	FA [auth B6], KC [auth D6]	54	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P35871 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P35871

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L34	GA [auth B7], LC [auth D7]	49	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80340 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P80340

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L35	HA [auth B8], MC [auth D8]	65	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SKU1

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L36	IA [auth B9], NC [auth D9]	37	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHR2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHR2

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L1	LA [auth BC], QC [auth DC]	229	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SLP7

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L2	MA [auth BD], RC [auth DD]	276	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60405 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P60405

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L3	NA [auth BE], SC [auth DE]	206	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHN8

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L4	OA [auth BF], TC [auth DF]	210	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHN9

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L5	PA [auth BG], UC [auth DG]	182	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHQ0

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L6	QA [auth BH], VC [auth DH]	180	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L9	RA [auth BI], WC [auth DI]	148	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLQ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SLQ1

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L13	SA [auth BN], XC [auth DN]	140	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60488 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P60488

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L14	TA [auth BO], YC [auth DO]	122	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHP8

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L15	UA [auth BP], ZC [auth DP]	150	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHQ7

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L16	AD [auth DQ], VA [auth BQ]	141	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60489 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P60489

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L17	BD [auth DR], WA [auth BR]	118	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q9Z9H5

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L18	CD [auth DS], XA [auth BS]	112	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHQ4

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L19	DD [auth DT], YA [auth BT]	146	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60490 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P60490

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L20	ED [auth DU], ZA [auth BU]	118	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60491 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P60491

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L21	AB [auth BV], FD [auth DV]	101	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60492 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  P60492

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L22	BB [auth BW], GD [auth DW]	113	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHP3

Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L23	CB [auth BX], HD [auth DX]	96	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHP0

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L24	DB [auth BY], ID [auth DY]	110	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHP9

Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L25	EB [auth BZ], JD [auth DZ]	206	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHZ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Go to UniProtKB:  Q5SHZ1

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S ribosomal RNA	A [auth AA], FB [auth CA]	1,522	Thermus thermophilus HB8

Entity ID: 22
Molecule	Chains	Length	Organism	Image
P-SITE TRNA FMET	AC [auth CV], V [auth AV]	77	Escherichia coli K-12

Entity ID: 23
Molecule	Chains	Length	Organism	Image
E-SITE TRNA PHE	BC [auth CW], W [auth AW]	76	Escherichia coli K-12

Entity ID: 24
Molecule	Chains	Length	Organism	Image
MRNA	CC [auth CX], X [auth AX]	10	synthetic construct

Entity ID: 25
Molecule	Chains	Length	Organism	Image
A-SITE PHE-TRNA PHE	DC [auth CY], Y [auth AY]	77	Escherichia coli K-12

Entity ID: 36
Molecule	Chains	Length	Organism	Image
23S Ribosomal RNA	JA [auth BA], OC [auth DA]	2,822	Thermus thermophilus HB8

Entity ID: 37
Molecule	Chains	Length	Organism	Image
5S RIBOSOMAL RNA	KA [auth BB], PC [auth DB]	122	Thermus thermophilus HB8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PAR	JOA [auth CA], PL [auth AA]	PAROMOMYCIN C23 H45 N5 O14 UOZODPSAJZTQNH-LSWIJEOBSA-N
ZN	DQA [auth D9], IN [auth B9], KOA [auth CD], OOA [auth CN], RL [auth AD], UL [auth AN]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	AAA [auth BA], AAB [auth DA], ABA [auth BA], ABB [auth DA], ACA [auth BA], ACB [auth DA], ADA [auth BA], ADB [auth DA], AE [auth AA], AEA [auth BA], AEB [auth DA], AF [auth AA], AFA [auth BB], AFB [auth DA], AG [auth AA], AGA [auth BX], AGB [auth DA], AH [auth AA], AHA [auth CA], AHB [auth DA], AI [auth AA], AIA [auth CA], AIB [auth DB], AJ [auth AA], AJA [auth CA], AK [auth AA], AKA [auth CA], AL [auth AA], ALA [auth CA], AM [auth AV], AMA [auth CA], AN [auth AX], ANA [auth CA], AO [auth BA], AOA [auth CA], AP [auth BA], APA [auth CW], AQ [auth BA], AQA [auth D5], AR [auth BA], ARA [auth DA], AS [auth BA], ASA [auth DA], AT [auth BA], ATA [auth DA], AU [auth BA], AUA [auth DA], AV [auth BA], AVA [auth DA], AW [auth BA], AWA [auth DA], AX [auth BA], AXA [auth DA], AY [auth BA], AYA [auth DA], AZ [auth BA], AZA [auth DA], BAA [auth BA], BAB [auth DA], BBA [auth BA], BBB [auth DA], BCA [auth BA], BCB [auth DA], BDA [auth BA], BDB [auth DA], BE [auth AA], BEA [auth BA], BEB [auth DA], BF [auth AA], BFA [auth BB], BFB [auth DA], BG [auth AA], BGA [auth CA], BGB [auth DA], BH [auth AA], BHA [auth CA], BHB [auth DA], BI [auth AA], BIA [auth CA], BIB [auth DB], BJ [auth AA], BJA [auth CA], BK [auth AA], BKA [auth CA], BL [auth AA], BLA [auth CA], BM [auth AV], BMA [auth CA], BN [auth AX], BNA [auth CA], BO [auth BA], BOA [auth CA], BP [auth BA], BPA [auth CW], BQ [auth BA], BQA [auth D7], BR [auth BA], BRA [auth DA], BS [auth BA], BSA [auth DA], BT [auth BA], BTA [auth DA], BU [auth BA], BUA [auth DA], BV [auth BA], BVA [auth DA], BW [auth BA], BWA [auth DA], BX [auth BA], BXA [auth DA], BY [auth BA], BYA [auth DA], BZ [auth BA], BZA [auth DA], CAA [auth BA], CAB [auth DA], CBA [auth BA], CBB [auth DA], CCA [auth BA], CCB [auth DA], CDA [auth BA], CDB [auth DA], CE [auth AA], CEA [auth BA], CEB [auth DA], CF [auth AA], CFA [auth BB], CFB [auth DA], CG [auth AA], CGA [auth CA], CGB [auth DA], CH [auth AA], CHA [auth CA], CHB [auth DA], CI [auth AA], CIA [auth CA], CIB 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BA], VOA [auth CV], VP [auth BA], VPA [auth D1], VQ [auth BA], VQA [auth DA], VR [auth BA], VRA [auth DA], VS [auth BA], VSA [auth DA], VT [auth BA], VTA [auth DA], VU [auth BA], VUA [auth DA], VV [auth BA], VVA [auth DA], VW [auth BA], VWA [auth DA], VX [auth BA], VXA [auth DA], VY [auth BA], VYA [auth DA], VZ [auth BA], VZA [auth DA], WAA [auth BA], WAB [auth DA], WBA [auth BA], WBB [auth DA], WCA [auth BA], WCB [auth DA], WD [auth AA], WDA [auth BA], WDB [auth DA], WE [auth AA], WEA [auth BB], WEB [auth DA], WF [auth AA], WFA [auth BV], WFB [auth DA], WG [auth AA], WGA [auth CA], WGB [auth DA], WH [auth AA], WHA [auth CA], WHB [auth DB], WI [auth AA], WIA [auth CA], WJ [auth AA], WJA [auth CA], WK [auth AA], WKA [auth CA], WL [auth AV], WLA [auth CA], WM [auth AW], WMA [auth CA], WN [auth BA], WNA [auth CA], WO [auth BA], WOA [auth CV], WP [auth BA], WPA [auth D1], WQ [auth BA], WQA [auth DA], WR [auth BA], WRA [auth DA], WS [auth BA], WSA [auth DA], WT [auth BA], WTA [auth DA], WU [auth BA], WUA [auth DA], WV [auth BA], WVA [auth DA], WW [auth BA], WWA [auth DA], WX [auth BA], WXA [auth DA], WY [auth BA], WYA [auth DA], WZ [auth BA], WZA [auth DA], XAA [auth BA], XAB [auth DA], XBA [auth BA], XBB [auth DA], XCA [auth BA], XCB [auth DA], XD [auth AA], XDA [auth BA], XDB [auth DA], XE [auth AA], XEA [auth BB], XEB [auth DA], XF [auth AA], XFA [auth BV], XFB [auth DA], XG [auth AA], XGA [auth CA], XGB [auth DA], XH [auth AA], XHA [auth CA], XHB [auth DB], XI [auth AA], XIA [auth CA], XJ [auth AA], XJA [auth CA], XK [auth AA], XKA [auth CA], XL [auth AV], XLA [auth CA], XM [auth AW], XMA [auth CA], XN [auth BA], XNA [auth CA], XO [auth BA], XOA [auth CW], XP [auth BA], XPA [auth D2], XQ [auth BA], XQA [auth DA], XR [auth BA], XRA [auth DA], XS [auth BA], XSA [auth DA], XT [auth BA], XTA [auth DA], XU [auth BA], XUA [auth DA], XV [auth BA], XVA [auth DA], XW [auth BA], XWA [auth DA], XX [auth BA], XXA [auth DA], XY [auth BA], XYA [auth DA], XZ [auth BA], XZA [auth DA], YAA [auth BA], YAB [auth DA], YBA [auth BA], YBB [auth DA], YCA [auth BA], YCB [auth DA], YD [auth AA], YDA [auth BA], YDB [auth DA], YE [auth AA], YEA [auth BB], YEB [auth DA], YF [auth AA], YFA [auth BW], YFB [auth DA], YG [auth AA], YGA [auth CA], YGB [auth DA], YH [auth AA], YHA [auth CA], YHB [auth DB], YI [auth AA], YIA [auth CA], YJ [auth AA], YJA [auth CA], YK [auth AA], YKA [auth CA], YL [auth AV], YLA [auth CA], YM [auth AX], YMA [auth CA], YN [auth BA], YNA [auth CA], YO [auth BA], YOA [auth CW], YP [auth BA], YPA [auth D2], YQ [auth BA], YQA [auth DA], YR [auth BA], YRA [auth DA], YS [auth BA], YSA [auth DA], YT [auth BA], YTA [auth DA], YU [auth BA], YUA [auth DA], YV [auth BA], YVA [auth DA], YW [auth BA], YWA [auth DA], YX [auth BA], YXA [auth DA], YY [auth BA], YYA [auth DA], YZ [auth BA], YZA [auth DA], ZAA [auth BA], ZAB [auth DA], ZBA [auth BA], ZBB [auth DA], ZCA [auth BA], ZCB [auth DA], ZD [auth AA], ZDA [auth BA], ZDB [auth DA], ZE [auth AA], ZEA [auth BB], ZEB [auth DA], ZF [auth AA], ZFA [auth BX], ZFB [auth DA], ZG [auth AA], ZGA [auth CA], ZGB [auth DA], ZH [auth AA], ZHA [auth CA], ZHB [auth DB], ZI [auth AA], ZIA [auth CA], ZJ [auth AA], ZJA [auth CA], ZK [auth AA], ZKA [auth CA], ZL [auth AV], ZLA [auth CA], ZM [auth AX], ZMA [auth CA], ZN [auth BA], ZNA [auth CA], ZO [auth BA], ZOA [auth CW], ZP [auth BA], ZPA [auth D2], ZQ [auth BA], ZQA [auth DA], ZR [auth BA], ZRA [auth DA], ZS [auth BA], ZSA [auth DA], ZT [auth BA], ZTA [auth DA], ZU [auth BA], ZUA [auth DA], ZV [auth BA], ZVA [auth DA], ZW [auth BA], ZWA [auth DA], ZX [auth BA], ZXA [auth DA], ZY [auth BA], ZYA [auth DA], ZZ [auth BA], ZZA [auth DA]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PHA	DC [auth CY], Y [auth AY]	L-PEPTIDE LINKING	C9 H11 N O		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.272 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 212.132	α = 90
b = 450.802	β = 90
c = 629.616	γ = 90

Software Package:

Software Name	Purpose
CNS	model building
CNS	refinement
XDS	data reduction
XDS	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Voorhees, R.M., Weixlbaumer, A., Loakes, D., Kelley, A.C., Ramakrishnan, V.
• This entry supersedes: 2WDG, 2WDH, 2WDI, 2WDJ

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release
  
• Version 1.1: 2014-12-10
  Changes: Other
• Version 1.2: 2018-03-14
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2018-04-18
  Changes: Data collection, Source and taxonomy
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.5: 2024-10-23
  Changes: Structure summary