4AYB | pdb_00004ayb

RNAP at 3.2Ang

PDB DOI: https://doi.org/10.2210/pdb4AYB/pdb

Classification: TRANSFERASE
Organism(s): Saccharolobus shibatae
Mutation(s): No

Deposited: 2012-06-19 Released: 2012-08-08
Deposition Author(s): Wojtas, M.N., Mogni, M., Millet, O., Bell, S.D., Abrescia, N.G.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.300 (Depositor), 0.294 (DCC)
R-Value Work:
0.242 (Depositor), 0.236 (DCC)
R-Value Observed:
0.245 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Structural and Functional Analyses of the Interaction of Archaeal RNA Polymerase with DNA.

Wojtas, M.N., Mogni, M., Millet, O., Bell, S.D., Abrescia, N.G.A.

(2012) Nucleic Acids Res 40: 9941

PubMed: 22848102 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/nar/gks692
Primary Citation Related Structures:
4AYB, 4V8S

PubMed Abstract:
Multi-subunit RNA polymerases (RNAPs) in all three domains of life share a common ancestry. The composition of the archaeal RNAP (aRNAP) is not identical between phyla and species, with subunits Rpo8 and Rpo13 found in restricted subsets of archaea. While Rpo8 has an ortholog, Rpb8, in the nuclear eukaryal RNAPs, Rpo13 lacks clear eukaryal orthologs. Here, we report crystal structures of the DNA-bound and free form of the aRNAP from Sulfolobus shibatae. Together with biochemical and biophysical analyses, these data show that Rpo13 C-terminus binds non-specifically to double-stranded DNA. These interactions map on our RNAP-DNA binary complex on the downstream DNA at the far end of the DNA entry channel. Our findings thus support Rpo13 as a RNAP-DNA stabilization factor, a role reminiscent of eukaryotic general transcriptional factors. The data further yield insight into the mechanisms and evolution of RNAP-DNA interaction.

Organizational Affiliation

Structural Biology Unit, CIC bioGUNE, CIBERehd, 48160 Derio, Spain.

Macromolecule Content

Total Structure Weight: 406.67 kDa
Atom Count: 27,121
Modeled Residue Count: 3,412
Deposited Residue Count: 3,585
Unique protein chains: 13

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE	A	880	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB53 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB53 Go to UniProtKB: B8YB53
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB53
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE	B	1,131	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB55 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB55 Go to UniProtKB: B8YB55
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB55
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE	C	395	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB54 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB54 Go to UniProtKB: B8YB54
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB54
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE	D	265	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB56 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB56 Go to UniProtKB: B8YB56
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB56
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE	E	180	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB57 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB57 Go to UniProtKB: B8YB57
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB57
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE	F	113	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB58 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB58 Go to UniProtKB: B8YB58
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB58
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE	G	132	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB59 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB59 Go to UniProtKB: B8YB59
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB59
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE	H	84	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB60 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB60 Go to UniProtKB: B8YB60
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB60
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE	I [auth K]	95	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB61 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB61 Go to UniProtKB: B8YB61
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB61
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE	J [auth L]	92	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB62 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB62 Go to UniProtKB: B8YB62
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB62
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE	K [auth N]	66	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB63 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB63 Go to UniProtKB: B8YB63
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB63
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE	L [auth P]	48	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB64 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB64 Go to UniProtKB: B8YB64
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB64
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE	M [auth Q]	104	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB65 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB65 Go to UniProtKB: B8YB65
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB65
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain W [auth D] MOL2 format, chain W [auth D] mmCIF format, chain W [auth D]	W [auth D]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain W [auth D] Interactions & Density Focus chain W [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Y [auth P] SDF format, chain X [auth N] SDF format, chain V [auth C] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] MOL2 format, chain Y [auth P] MOL2 format, chain X [auth N] MOL2 format, chain V [auth C] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] mmCIF format, chain Y [auth P] mmCIF format, chain X [auth N] mmCIF format, chain V [auth C] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A]	N [auth A] O [auth A] P [auth A] Q [auth A] S [auth B] N [auth A], O [auth A], P [auth A], Q [auth A], S [auth B], T [auth B], U [auth B], V [auth C], X [auth N], Y [auth P]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth C] Focus chain X [auth N] Focus chain Y [auth P] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth C] Focus chain X [auth N] Focus chain Y [auth P]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.300 (Depositor), 0.294 (DCC)
R-Value Work: 0.242 (Depositor), 0.236 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 195.725	α = 90
b = 212.415	β = 90
c = 128.757	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-08-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-08
Type: Initial release
Version 1.1: 2012-08-15
Changes: Atomic model, Derived calculations, Non-polymer description, Other
Version 1.2: 2012-09-05
Changes: Atomic model
Version 1.3: 2012-11-07
Changes: Database references
Version 1.4: 2019-11-20
Changes: Advisory, Derived calculations, Other
Version 1.5: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.6: 2024-10-23
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

4AYB | pdb_00004ayb

RNAP at 3.2Ang

Literature

Structural and Functional Analyses of the Interaction of Archaeal RNA Polymerase with DNA.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)