7Q46

Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of pericentriolar material 1 protein

• PDB DOI: https://doi.org/10.2210/pdb7Q46/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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.245 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 

Starting Model: experimental

Literature

Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of pericentriolar material 1 protein

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 133.86 kDa 
• Atom Count: 8,894 
• Modelled Residue Count: 1,128 
• Deposited Residue Count: 1,260 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase HERC2	A, B [auth C], D [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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pericentriolar material 1 protein	C [auth D], E [auth F], F [auth B]	15	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15154 (Homo sapiens) Explore Q15154  Go to UniProtKB:  Q15154
PHAROS:  Q15154 GTEx:  ENSG00000078674

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	G [auth E]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.245 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.66	α = 90
b = 107.66	β = 90
c = 241.21	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Demenge, A., Howard, E., Cousido-Siah, A., Mitschler, A., Podjarny, A., McEwen, A.G., Trave, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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