7Q42 | pdb_00007q42

Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of chromatin reader BAZ2B

PDB DOI: https://doi.org/10.2210/pdb7Q42/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-10-29 Released: 2022-11-16
Deposition Author(s): Demenge, A., Howard, E., Cousido-Siah, A., Mitschler, A., Podjarny, A., McEwen, A.G., Trave, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.206 (Depositor), 0.209 (DCC)
R-Value Work:
0.168 (Depositor), 0.170 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7Q42

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of chromatin reader BAZ2B

Demenge, A., Howard, E., Cousido-Siah, A., Mitschler, A., Podjarny, A., McEwen, A.G., Trave, G.

To be published.

Macromolecule Content

Total Structure Weight: 134.08 kDa
Atom Count: 9,343
Modeled Residue Count: 1,132
Deposited Residue Count: 1,260
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase HERC2	A, B [auth C], C [auth E]	405	Homo sapiens	Mutation(s): 0 Gene Names: HERC2 EC: 2.3.2.26
UniProt & NIH Common Fund Data Resources
Find proteins for O95714 (Homo sapiens) Explore O95714 Go to UniProtKB: O95714
PHAROS: O95714 GTEx: ENSG00000128731
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O95714
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain adjacent to zinc finger domain protein 2B	D, E [auth B], F	15	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIF8 (Homo sapiens) Explore Q9UIF8 Go to UniProtKB: Q9UIF8
PHAROS: Q9UIF8 GTEx: ENSG00000123636
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UIF8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain I [auth E] SDF format, chain H [auth E] SDF format, chain G [auth C] MOL2 format, chain I [auth E] MOL2 format, chain H [auth E] MOL2 format, chain G [auth C] mmCIF format, chain I [auth E] mmCIF format, chain H [auth E] mmCIF format, chain G [auth C]	G [auth C], H [auth E], I [auth E]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Focus chain H [auth E] Focus chain I [auth E] Interactions & Density Focus chain G [auth C] Focus chain H [auth E] Focus chain I [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.206 (Depositor), 0.209 (DCC)
R-Value Work: 0.168 (Depositor), 0.170 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.98	α = 90
b = 107.98	β = 90
c = 241.56	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-16

Deposition Author(s):

Cousido-Siah, A.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-11-16
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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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.