4X64

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

• PDB DOI: https://doi.org/10.2210/pdb4X64/pdb
• NAKB: 4X64

• Classification: Ribosome/antibiotic
• Organism(s): Thermus thermophilus HB8
• Mutation(s): No 


• Deposited: 2014-12-06 Released: 2015-11-18 
• Deposition Author(s): Demirci, H., Chen, J., Choi, J., Soltis, M., Puglisi, J.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 
  0.205 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics.

Choi, J., Ieong, K.W., Demirci, H., Chen, J., Petrov, A., Prabhakar, A., O'Leary, S.E., Dominissini, D., Rechavi, G., Soltis, S.M., Ehrenberg, M., Puglisi, J.D.

(2016) Nat Struct Mol Biol 23: 110-115

• PubMed: 26751643 
• DOI: https://doi.org/10.1038/nsmb.3148
• Primary Citation of Related Structures:  
  4X62, 4X64, 4X65, 4X66


• PubMed Abstract: 
  

  N(6)-methylation of adenosine (forming m(6)A) is the most abundant post-transcriptional modification within the coding region of mRNA, but its role during translation remains unknown. Here, we used bulk kinetic and single-molecule methods to probe the effect of m(6)A in mRNA decoding. Although m(6)A base-pairs with uridine during decoding, as shown by X-ray crystallographic analyses of Thermus thermophilus ribosomal complexes, our measurements in an Escherichia coli translation system revealed that m(6)A modification of mRNA acts as a barrier to tRNA accommodation and translation elongation. The interaction between an m(6)A-modified codon and cognate tRNA echoes the interaction between a near-cognate codon and tRNA, because delay in tRNA accommodation depends on the position and context of m(6)A within codons and on the accuracy level of translation. Overall, our results demonstrate that chemical modification of mRNA can change translational dynamics.

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Organizational Affiliation: 

Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 20-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 785.87 kDa 
• Atom Count: 52,825 
• Modelled Residue Count: 3,922 
• Deposited Residue Count: 3,932 
• Unique protein chains: 20
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	B	236	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80371  Go to UniProtKB:  P80371

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	C	207	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80372 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80372  Go to UniProtKB:  P80372

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	D	208	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80373 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80373  Go to UniProtKB:  P80373

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	E	151	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ5  Go to UniProtKB:  Q5SHQ5

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6	F	101	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP8  Go to UniProtKB:  Q5SLP8

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	G	155	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P17291  Go to UniProtKB:  P17291

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	H	138	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY9  Go to UniProtKB:  P0DOY9

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	I	127	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80374 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80374  Go to UniProtKB:  P80374

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	J	99	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN7  Go to UniProtKB:  Q5SHN7

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	K	119	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80376  Go to UniProtKB:  P80376

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	L	125	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN3  Go to UniProtKB:  Q5SHN3

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	M	118	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80377 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80377  Go to UniProtKB:  P80377

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14 type Z	N	60	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY6  Go to UniProtKB:  P0DOY6

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	O	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ76  Go to UniProtKB:  Q5SJ76

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	P	84	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJH3  Go to UniProtKB:  Q5SJH3

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	Q	99	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY7  Go to UniProtKB:  P0DOY7

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	R	73	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ0  Go to UniProtKB:  Q5SLQ0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	S	81	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP2  Go to UniProtKB:  Q5SHP2

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	T	99	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80380  Go to UniProtKB:  P80380

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein Thx	U	25	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIH3  Go to UniProtKB:  Q5SIH3

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S rRNA	A	1,522	Thermus thermophilus HB8

Entity ID: 22
Molecule	Chains	Length	Organism	Image
RNA (5'-D(*(MA6)P*AP*AP*UP*UP*U)-3')	V [auth a]	6	Thermus thermophilus HB8

Entity ID: 23
Molecule	Chains	Length	Organism	Image
RNA (5'-D(P*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*C)-3')	W [auth b]	11	Thermus thermophilus HB8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PAR	AA [auth A], BA [auth A], CA [auth A], X [auth A], Y [auth A], Z [auth A]	PAROMOMYCIN C23 H45 N5 O14 UOZODPSAJZTQNH-LSWIJEOBSA-N
ZN	DN [auth N], OM [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	AL [auth A], AM [auth A], BL [auth A], BM [auth A], CL [auth A], CM [auth A], CN [auth M], DL [auth A], DM [auth A], EL [auth A], EM [auth A], FL [auth A], FM [auth A], GL [auth A], GM [auth A], HL [auth A], HM [auth A], IL [auth A], IM [auth A], JL [auth A], JM [auth A], KL [auth A], KM [auth A], LL [auth A], LM [auth A], ML [auth A], NL [auth A], OL [auth A], PL [auth A], QL [auth A], RL [auth A], RM [auth E], SL [auth A], TL [auth A], UL [auth A], VL [auth A], VM [auth G], WL [auth A], XL [auth A], YL [auth A], ZL [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	AB [auth A], AC [auth A], AD [auth A], AE [auth A], AF [auth A], AG [auth A], AH [auth A], AI [auth A], AJ [auth A], AK [auth A], AN [auth L], BB [auth A], BC [auth A], BD [auth A], BE [auth A], BF [auth A], BG [auth A], BH [auth A], BI [auth A], BJ [auth A], BK [auth A], BN [auth L], CB [auth A], CC [auth A], CD [auth A], CE [auth A], CF [auth A], CG [auth A], CH [auth A], CI [auth A], CJ [auth A], CK [auth A], DA [auth A], DB [auth A], DC [auth A], DD [auth A], DE [auth A], DF [auth A], DG [auth A], DH [auth A], DI [auth A], DJ [auth A], DK [auth A], EA [auth A], EB [auth A], EC [auth A], ED [auth A], EE [auth A], EF [auth A], EG [auth A], EH [auth A], EI [auth A], EJ [auth A], EK [auth A], EN [auth N], FA [auth A], FB [auth A], FC [auth A], FD [auth A], FE [auth A], FF [auth A], FG [auth A], FH [auth A], FI [auth A], FJ [auth A], FK [auth A], FN [auth P], GA [auth A], GB [auth A], GC [auth A], GD [auth A], GE [auth A], GF [auth A], GG [auth A], GH [auth A], GI [auth A], GJ [auth A], GK [auth A], GN [auth P], HA [auth A], HB [auth A], HC [auth A], HD [auth A], HE [auth A], HF [auth A], HG [auth A], HH [auth A], HI [auth A], HJ [auth A], HK [auth A], HN [auth P], IA [auth A], IB [auth A], IC [auth A], ID [auth A], IE [auth A], IF [auth A], IG [auth A], IH [auth A], II [auth A], IJ [auth A], IK [auth A], IN [auth P], JA [auth A], JB [auth A], JC [auth A], JD [auth A], JE [auth A], JF [auth A], JG [auth A], JH [auth A], JI [auth A], JJ [auth A], JK [auth A], JN [auth Q], KA [auth A], KB [auth A], KC [auth A], KD [auth A], KE [auth A], KF [auth A], KG [auth A], KH [auth A], KI [auth A], KJ [auth A], KK [auth A], KN [auth Q], LA [auth A], LB [auth A], LC [auth A], LD [auth A], LE [auth A], LF [auth A], LG [auth A], LH [auth A], LI [auth A], LJ [auth A], LK [auth A], LN [auth S], MA [auth A], MB [auth A], MC [auth A], MD [auth A], ME [auth A], MF [auth A], MG [auth A], MH [auth A], MI [auth A], MJ [auth A], MK [auth A], MM [auth A], MN [auth S], NA [auth A], NB [auth A], NC [auth A], ND [auth A], NE [auth A], NF [auth A], NG [auth A], NH [auth A], NI [auth A], NJ [auth A], NK [auth A], NM [auth C], NN [auth S], OA [auth A], OB [auth A], OC [auth A], OD [auth A], OE [auth A], OF [auth A], OG [auth A], OH [auth A], OI [auth A], OJ [auth A], OK [auth A], ON [auth T], PA [auth A], PB [auth A], PC [auth A], PD [auth A], PE [auth A], PF [auth A], PG [auth A], PH [auth A], PI [auth A], PJ [auth A], PK [auth A], PM [auth D], PN [auth a], QA [auth A], QB [auth A], QC [auth A], QD [auth A], QE [auth A], QF [auth A], QG [auth A], QH [auth A], QI [auth A], QJ [auth A], QK [auth A], QM [auth E], QN [auth a], RA [auth A], RB [auth A], RC [auth A], RD [auth A], RE [auth A], RF [auth A], RG [auth A], RH [auth A], RI [auth A], RJ [auth A], RK [auth A], RN [auth b], SA [auth A], SB [auth A], SC [auth A], SD [auth A], SE [auth A], SF [auth A], SG [auth A], SH [auth A], SI [auth A], SJ [auth A], SK [auth A], SM [auth F], SN [auth b], TA [auth A], TB [auth A], TC [auth A], TD [auth A], TE [auth A], TF [auth A], TG [auth A], TH [auth A], TI [auth A], TJ [auth A], TK [auth A], TM [auth G], UA [auth A], UB [auth A], UC [auth A], UD [auth A], UE [auth A], UF [auth A], UG [auth A], UH [auth A], UI [auth A], UJ [auth A], UK [auth A], UM [auth G], VA [auth A], VB [auth A], VC [auth A], VD [auth A], VE [auth A], VF [auth A], VG [auth A], VH [auth A], VI [auth A], VJ [auth A], VK [auth A], WA [auth A], WB [auth A], WC [auth A], WD [auth A], WE [auth A], WF [auth A], WG [auth A], WH [auth A], WI [auth A], WJ [auth A], WK [auth A], WM [auth H], XA [auth A], XB [auth A], XC [auth A], XD [auth A], XE [auth A], XF [auth A], XG [auth A], XH [auth A], XI [auth A], XJ [auth A], XK [auth A], XM [auth H], YA [auth A], YB [auth A], YC [auth A], YD [auth A], YE [auth A], YF [auth A], YG [auth A], YH [auth A], YI [auth A], YJ [auth A], YK [auth A], YM [auth H], ZA [auth A], ZB [auth A], ZC [auth A], ZD [auth A], ZE [auth A], ZF [auth A], ZG [auth A], ZH [auth A], ZI [auth A], ZJ [auth A], ZK [auth A], ZM [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
0TD	L	L-PEPTIDE LINKING	C5 H9 N O4 S		ASP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free:  0.205 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 400.496	α = 90
b = 400.496	β = 90
c = 175.534	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Demirci, H., Chen, J., Choi, J., Soltis, M., Puglisi, J.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM51266
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM099687

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2016-01-13
  Changes: Database references
• Version 1.2: 2016-01-27
  Changes: Database references
• Version 1.3: 2016-02-10
  Changes: Database references
• Version 1.4: 2017-09-06
  Changes: Author supporting evidence, Derived calculations
• Version 1.5: 2019-12-25
  Changes: Author supporting evidence
• Version 1.6: 2025-02-19
  Changes: Data collection, Database references, Derived calculations, Structure summary