5G5L

RNA polymerase I-Rrn3 complex at 4.8 A resolution

PDB DOI: https://doi.org/10.2210/pdb5G5L/pdb
EM Map EMD-3439: EMDB EMDataResource

Classification: RNA POLYMERASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-05-26 Released: 2016-07-27
Deposition Author(s): Engel, C., Plitzko, J., Cramer, P.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

RNA Polymerase I-Rrn3 Complex at 4.8 A Resolution

Engel, C., Plitzko, J., Cramer, P.

(2016) Nat Commun 7: 12129

PubMed: 27418309 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/ncomms12129
Primary Citation of Related Structures:
5G5L

PubMed Abstract:
Transcription of ribosomal DNA by RNA polymerase I (Pol I) requires the initiation factor Rrn3. Here we report the cryo-EM structure of the Pol I-Rrn3 complex at 4.8 Å resolution. The structure reveals how Rrn3 binding converts an inactive Pol I dimer into an initiation-competent monomeric complex and provides insights into the mechanisms of Pol I-specific initiation and regulation.

Organizational Affiliation

Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.

Macromolecule Content

Total Structure Weight: 663.19 kDa
Atom Count: 37,349
Modelled Residue Count: 4,686
Deposited Residue Count: 5,863
Unique protein chains: 15

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190	A	1,664	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P10964 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P10964 Go to UniProtKB: P10964
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10964
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135	B	1,203	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P22138 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22138 Go to UniProtKB: P22138
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22138
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1	C	335	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P07703 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07703 Go to UniProtKB: P07703
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07703
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14	D	137	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P50106 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P50106 Go to UniProtKB: P50106
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50106
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1	E	215	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20434 Go to UniProtKB: P20434
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20434
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2	F	155	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20435 Go to UniProtKB: P20435
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20435
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43	G	326	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P46669 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P46669 Go to UniProtKB: P46669
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P46669
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3	H	146	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20436 Go to UniProtKB: P20436
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20436
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12	I	125	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32529 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32529 Go to UniProtKB: P32529
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32529
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5	J	70	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22139 Go to UniProtKB: P22139
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22139
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2	K	142	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P28000 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P28000 Go to UniProtKB: P28000
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28000
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4	L	70	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40422 Go to UniProtKB: P40422
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40422
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49	M	415	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q01080 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q01080 Go to UniProtKB: Q01080
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q01080
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34	N	233	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P47006 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47006 Go to UniProtKB: P47006
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P47006
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA POLYMERASE I-SPECIFIC TRANSCRIPTION INITIATION FACTOR RRN3	O	627	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36070 Go to UniProtKB: P36070
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P36070
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain R [auth B] SDF format, chain S [auth I] SDF format, chain T [auth I] SDF format, chain U [auth J] SDF format, chain V [auth L] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth I] MOL2 format, chain T [auth I] MOL2 format, chain U [auth J] MOL2 format, chain V [auth L]	P [auth A] Q [auth A] R [auth B] S [auth I] T [auth I] P [auth A], Q [auth A], R [auth B], S [auth I], T [auth I], U [auth J], V [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth I] Focus chain T [auth I] Focus chain U [auth J] Focus chain V [auth L] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth I] Focus chain T [auth I] Focus chain U [auth J] Focus chain V [auth L]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-07-27

Deposition Author(s):

Engel, C.

Plitzko, J.

Cramer, P.

Revision History (Full details and data files)

Version 1.0: 2016-07-27
Type: Initial release
Version 1.1: 2017-08-02
Changes: Data collection
Version 1.2: 2018-06-20
Changes: Advisory, Data collection, Derived calculations
Version 1.3: 2018-10-24
Changes: Advisory, Data collection, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.

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Help and Resources

5G5L

RNA polymerase I-Rrn3 complex at 4.8 A resolution

RNA Polymerase I-Rrn3 Complex at 4.8 A Resolution

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Entity ID: 15

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)