1IW7

Crystal structure of the RNA polymerase holoenzyme from Thermus thermophilus at 2.6A resolution

• PDB DOI: https://doi.org/10.2210/pdb1IW7/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus
• Mutation(s): No 


• Deposited: 2002-04-22 Released: 2002-06-26 
• Deposition Author(s): RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.274 
• R-Value Work: 0.228 
• R-Value Observed: 0.232 

Starting Model: experimental

Literature

Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution

Vassylyev, D.G., Sekine, S., Laptenko, O., Lee, J., Vassylyeva, M.N., Borukhov, S., Yokoyama, S.

(2002) Nature 417: 712-719

• PubMed: 12000971 
• DOI: https://doi.org/10.1038/nature752
• Primary Citation of Related Structures:  
  1IW7


• PubMed Abstract: 
  

  In bacteria, the binding of a single protein, the initiation factor sigma, to a multi-subunit RNA polymerase core enzyme results in the formation of a holoenzyme, the active form of RNA polymerase essential for transcription initiation. Here we report the crystal structure of a bacterial RNA polymerase holoenzyme from Thermus thermophilus at 2.6 A resolution. In the structure, two amino-terminal domains of the sigma subunit form a V-shaped structure near the opening of the upstream DNA-binding channel of the active site cleft. The carboxy-terminal domain of sigma is near the outlet of the RNA-exit channel, about 57 A from the N-terminal domains. The extended linker domain forms a hairpin protruding into the active site cleft, then stretching through the RNA-exit channel to connect the N- and C-terminal domains. The holoenzyme structure provides insight into the structural organization of transcription intermediate complexes and into the mechanism of transcription initiation.

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Organizational Affiliation: 

Cellular Signaling Laboratory, RIKEN Harima Institute at Spring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B1C1D1E1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B1C1D1E1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 865.89 kDa 
• Atom Count: 59,529 
• Modelled Residue Count: 6,818 
• Deposited Residue Count: 7,590 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase alpha subunit	A, B, G [auth K], H [auth L]	315	Thermus thermophilus	Mutation(s): 0  EC: 2.7.7.6
UniProt
Find proteins for Q9Z9H6 (Thermus thermophilus) Explore Q9Z9H6  Go to UniProtKB:  Q9Z9H6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase beta subunit	C, I [auth M]	1,119	Thermus thermophilus	Mutation(s): 0  EC: 2.7.7.6
UniProt
Find proteins for Q8RQE9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q8RQE9  Go to UniProtKB:  Q8RQE9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase beta subunit	D, J [auth N]	1,524	Thermus thermophilus	Mutation(s): 0  EC: 2.7.7.6
UniProt
Find proteins for Q8RQE8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q8RQE8  Go to UniProtKB:  Q8RQE8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase omega subunit	E, K [auth O]	99	Thermus thermophilus	Mutation(s): 0  EC: 2.7.7.6
UniProt
Find proteins for Q8RQE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q8RQE7  Go to UniProtKB:  Q8RQE7

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma-70 subunit	F, L [auth P]	423	Thermus thermophilus	Mutation(s): 0  EC: 2.7.7.6
UniProt
Find proteins for Q72L95 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72L95  Go to UniProtKB:  Q72L95

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PB	ND [auth D], NN [auth N], OD [auth D], ON [auth N]	LEAD (II) ION Pb RVPVRDXYQKGNMQ-UHFFFAOYSA-N
MG	AA [auth A], AB [auth B], AC [auth C], AD [auth C], AE [auth D], AF [auth D], AG [auth D], AH [auth D], AI [auth D], AJ [auth F], AK [auth K], AL [auth L], AM [auth M], AN [auth M], AO [auth N], AP [auth N], AQ [auth N], AR [auth N], AS [auth P], BA [auth A], BB [auth B], BC [auth C], BD [auth C], BE [auth D], BF [auth D], BG [auth D], BH [auth D], BI [auth D], BJ [auth F], BK [auth K], BL [auth M], BM [auth M], BN [auth M], BO [auth N], BP [auth N], BQ [auth N], BR [auth N], BS [auth P], CA [auth A], CB [auth C], CC [auth C], CD [auth C], CE [auth D], CF [auth D], CG [auth D], CH [auth D], CI [auth D], CJ [auth F], CK [auth K], CL [auth M], CM [auth M], CN [auth M], CO [auth N], CP [auth N], CQ [auth N], CR [auth N], CS [auth P], DA [auth A], DB [auth C], DC [auth C], DD [auth C], DE [auth D], DF [auth D], DG [auth D], DH [auth D], DI [auth E], DJ [auth F], DK [auth K], DL [auth M], DM [auth M], DN [auth M], DO [auth N], DP [auth N], DQ [auth N], DR [auth O], DS [auth P], EA [auth B], EB [auth C], EC [auth C], ED [auth C], EE [auth D], EF [auth D], EG [auth D], EH [auth D], EI [auth E], EJ [auth F], EK [auth K], EL [auth M], EM [auth M], EN [auth M], EO [auth N], EP [auth N], EQ [auth N], ER [auth O], ES [auth P], FA [auth B], FB [auth C], FC [auth C], FD [auth C], FE [auth D], FF [auth D], FG [auth D], FH [auth D], FI [auth E], FJ [auth F], FK [auth K], FL [auth M], FM [auth M], FN [auth M], FO [auth N], FP [auth N], FQ [auth N], FR [auth O], FS [auth P], GA [auth B], GB [auth C], GC [auth C], GD [auth C], GE [auth D], GF [auth D], GG [auth D], GH [auth D], GI [auth E], GJ [auth F], GK [auth K], GL [auth M], GM [auth M], GN [auth M], GO [auth N], GP [auth N], GQ [auth N], GR [auth O], GS [auth P], HA [auth B], HB [auth C], HC [auth C], HD [auth C], HE [auth D], HF [auth D], HG [auth D], HH [auth D], HI [auth E], HJ [auth F], HK [auth K], HL [auth M], HM [auth M], HN [auth M], HO [auth N], HP [auth N], HQ [auth N], HR [auth O], IA [auth B], IB [auth C], IC [auth C], ID [auth C], IE [auth D], IF [auth D], IG [auth D], IH [auth D], II [auth E], IJ [auth F], IK [auth L], IL [auth M], IM [auth M], IN [auth M], IO [auth N], IP [auth N], IQ [auth N], IR [auth O], JA [auth B], JB [auth C], JC [auth C], JD [auth C], JE [auth D], JF [auth D], JG [auth D], JH [auth D], JI [auth F], JJ [auth F], JK [auth L], JL [auth M], JM [auth M], JN [auth M], JO [auth N], JP [auth N], JQ [auth N], JR [auth O], KA [auth B], KB [auth C], KC [auth C], KD [auth C], KE [auth D], KF [auth D], KG [auth D], KH [auth D], KI [auth F], KJ [auth F], KK [auth L], KL [auth M], KM [auth M], KN [auth M], KO [auth N], KP [auth N], KQ [auth N], KR [auth O], LA [auth B], LB [auth C], LC [auth C], LD [auth C], LE [auth D], LF [auth D], LG [auth D], LH [auth D], LI [auth F], LJ [auth F], LK [auth L], LL [auth M], LM [auth M], LN [auth M], LO [auth N], LP [auth N], LQ [auth N], LR [auth P], M [auth A], MA [auth B], MB [auth C], MC [auth C], MD [auth C], ME [auth D], MF [auth D], MG [auth D], MH [auth D], MI [auth F], MJ [auth F], MK [auth L], ML [auth M], MM [auth M], MN [auth M], MO [auth N], MP [auth N], MQ [auth N], MR [auth P], N [auth A], NA [auth B], NB [auth C], NC [auth C], NE [auth D], NF [auth D], NG [auth D], NH [auth D], NI [auth F], NJ [auth F], NK [auth L], NL [auth M], NM [auth M], NO [auth N], NP [auth N], NQ [auth N], NR [auth P], O [auth A], OA [auth B], OB [auth C], OC [auth C], OE [auth D], OF [auth D], OG [auth D], OH [auth D], OI [auth F], OJ [auth K], OK [auth L], OL [auth M], OM [auth M], OO [auth N], OP [auth N], OQ [auth N], OR [auth P], P [auth A], PA [auth B], PB [auth C], PC [auth C], PD [auth D], PE [auth D], PF [auth D], PG [auth D], PH [auth D], PI [auth F], PJ [auth K], PK [auth L], PL [auth M], PM [auth M], PN [auth N], PO [auth N], PP [auth N], PQ [auth N], PR [auth P], Q [auth A], QA [auth B], QB [auth C], QC [auth C], QD [auth D], QE [auth D], QF [auth D], QG [auth D], QH [auth D], QI [auth F], QJ [auth K], QK [auth L], QL [auth M], QM [auth M], QN [auth N], QO [auth N], QP [auth N], QQ [auth N], QR [auth P], R [auth A], RA [auth B], RB [auth C], RC [auth C], RD [auth D], RE [auth D], RF [auth D], RG [auth D], RH [auth D], RI [auth F], RJ [auth K], RK [auth L], RL [auth M], RM [auth M], RN [auth N], RO [auth N], RP [auth N], RQ [auth N], RR [auth P], S [auth A], SA [auth B], SB [auth C], SC [auth C], SD [auth D], SE [auth D], SF [auth D], SG [auth D], SH [auth D], SI [auth F], SJ [auth K], SK [auth L], SL [auth M], SM [auth M], SN [auth N], SO [auth N], SP [auth N], SQ [auth N], SR [auth P], T [auth A], TA [auth B], TB [auth C], TC [auth C], TD [auth D], TE [auth D], TF [auth D], TG [auth D], TH [auth D], TI [auth F], TJ [auth K], TK [auth L], TL [auth M], TM [auth M], TN [auth N], TO [auth N], TP [auth N], TQ [auth N], TR [auth P], U [auth A], UA [auth B], UB [auth C], UC [auth C], UD [auth D], UE [auth D], UF [auth D], UG [auth D], UH [auth D], UI [auth F], UJ [auth K], UK [auth L], UL [auth M], UM [auth M], UN [auth N], UO [auth N], UP [auth N], UQ [auth N], UR [auth P], V [auth A], VA [auth B], VB [auth C], VC [auth C], VD [auth D], VE [auth D], VF [auth D], VG [auth D], VH [auth D], VI [auth F], VJ [auth K], VK [auth L], VL [auth M], VM [auth M], VN [auth N], VO [auth N], VP [auth N], VQ [auth N], VR [auth P], W [auth A], WA [auth B], WB [auth C], WC [auth C], WD [auth D], WE [auth D], WF [auth D], WG [auth D], WH [auth D], WI [auth F], WJ [auth K], WK [auth L], WL [auth M], WM [auth M], WN [auth N], WO [auth N], WP [auth N], WQ [auth N], WR [auth P], X [auth A], XA [auth B], XB [auth C], XC [auth C], XD [auth D], XE [auth D], XF [auth D], XG [auth D], XH [auth D], XI [auth F], XJ [auth K], XK [auth L], XL [auth M], XM [auth M], XN [auth N], XO [auth N], XP [auth N], XQ [auth N], XR [auth P], Y [auth A], YA [auth B], YB [auth C], YC [auth C], YD [auth D], YE [auth D], YF [auth D], YG [auth D], YH [auth D], YI [auth F], YJ [auth K], YK [auth L], YL [auth M], YM [auth M], YN [auth N], YO [auth N], YP [auth N], YQ [auth N], YR [auth P], Z [auth A], ZA [auth B], ZB [auth C], ZC [auth C], ZD [auth D], ZE [auth D], ZF [auth D], ZG [auth D], ZH [auth D], ZI [auth F], ZJ [auth K], ZK [auth L], ZL [auth M], ZM [auth M], ZN [auth N], ZO [auth N], ZP [auth N], ZQ [auth N], ZR [auth P]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.274 
• R-Value Work: 0.228 
• R-Value Observed: 0.232 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 236.35	α = 90
b = 236.35	β = 90
c = 249.04	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-06-26 
Deposition Author(s): RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2002-06-26
  Type: Initial release
  
• Version 1.1: 2008-04-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description