5ZBU

Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub

• PDB DOI: https://doi.org/10.2210/pdb5ZBU/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-02-12 Released: 2019-02-27 
• Deposition Author(s): Datta, A.B., Sarkar, S.
• Funding Organization(s): Wellcome Trust-DBT India Alliance

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.262 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Literature

Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub

Sarkar, S., Datta, A.B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 60.2 kDa 
• Atom Count: 4,163 
• Modelled Residue Count: 517 
• Deposited Residue Count: 524 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 D2	A [auth C], B	148	Homo sapiens	Mutation(s): 1  Gene Names: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P62837 (Homo sapiens) Explore P62837  Go to UniProtKB:  P62837
PHAROS:  P62837 GTEx:  ENSG00000131508

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RNF13	C [auth A], D	76	Homo sapiens	Mutation(s): 0  Gene Names: RNF13, RZF EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for O43567 (Homo sapiens) Explore O43567  Go to UniProtKB:  O43567
PHAROS:  O43567 GTEx:  ENSG00000082996

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	E	76	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	F [auth A], G [auth A], H [auth D], I [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.262 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.559	α = 90
b = 105.74	β = 115.49
c = 60.79	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-02-27 
Deposition Author(s): Datta, A.B., Sarkar, S.

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Funding Organization	Location	Grant Number
Wellcome Trust-DBT India Alliance	India	500241/Z/11/Z

Revision History  

• Version 1.0: 2019-02-27
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description