5ZB2 | pdb_00005zb2

Crystal structure of Rad7 and Elc1 complex in yeast

PDB DOI: https://doi.org/10.2210/pdb5ZB2/pdb

Classification: DNA BINDING PROTEIN/LIGASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-02-09 Released: 2019-02-27
Deposition Author(s): Jiang, T., Liu, L., Huo, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.224 (Depositor), 0.228 (DCC)
R-Value Work:
0.195 (Depositor), 0.197 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the yeast Rad7-Elc1 complex and assembly of the Rad7-Rad16-Elc1-Cul3 complex.

Liu, L., Huo, Y., Li, J., Jiang, T.

(2019) DNA Repair (Amst) 77: 1-9

PubMed: 30840920 Search on PubMed
DOI: https://doi.org/10.1016/j.dnarep.2019.02.012
Primary Citation Related Structures:
5ZB2

PubMed Abstract:
Nucleotide excision repair (NER) is a versatile system that deals with various bulky and helix-distorting DNA lesions caused by UV and environmental mutagens. Based on how lesion recognition occurs, NER has been separated into global genome repair (GGR) and transcription-coupled repair (TCR). The yeast Rad7-Rad16 complex is indispensable for the GGR sub-pathway. Rad7-Rad16 binds to UV-damaged DNA in a synergistic fashion with Rad4, the main lesion recognizer, to achieve efficient recognition of lesions. In addition, Rad7-Rad16 associates with Elc1 and Cul3 to form an EloC-Cul-SOCS-box (ECS)-type E3 ubiquitin ligase complex that ubiquitinates Rad4 in response to UV radiation. However, the structure and architecture of the Rad7-Rad16-Elc1-Cul3 complex remain unsolved. Here, we determined the structure of the Rad7-Elc1 complex and revealed key interaction regions responsible for the formation of the Rad7-Rad16-Elc1-Cul3 complex. These results provide new insights into the assembly of the Rad7-Rad16-Elc1-Cul3 complex and structural framework for further studies.

Organizational Affiliation

National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; School of Medicine, Sun Yat-Sen University, Guangzhou 510275, China.

Macromolecule Content

Total Structure Weight: 59.27 kDa
Atom Count: 4,171
Modeled Residue Count: 480
Deposited Residue Count: 508
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD7	A	405	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: RAD7, YJR052W, J1665
UniProt
Find proteins for P06779 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06779 Go to UniProtKB: P06779
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06779
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	B	103	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: ELC1, YPL046C
UniProt
Find proteins for Q03071 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03071 Go to UniProtKB: Q03071
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q03071
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9FO Query on 9FO Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57-nonadecaoxanonapentacontane-1,59-diol C₄₀ H₈₂ O₂₁ ZHMUMDLGQBRJIW-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
P33 Query on P33 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
PG0 Query on PG0 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	2-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.224 (Depositor), 0.228 (DCC)
R-Value Work: 0.195 (Depositor), 0.197 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.921	α = 90
b = 67.764	β = 90
c = 69.015	γ = 90

Software Package:

Software Name	Purpose
phenix.refine	refinement
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
SHELXCD	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-02-27

Deposition Author(s):

Jiang, T.

Liu, L.

Huo, Y.

Revision History (Full details and data files)

Version 1.0: 2019-02-27
Type: Initial release
Version 1.1: 2019-03-20
Changes: Data collection, Database references
Version 1.2: 2024-03-27
Changes: Data collection, Database references, Structure summary