5ZC4 | pdb_00005zc4

Crystal Structure of RNF13 RING domain

• PDB DOI: https://doi.org/10.2210/pdb5ZC4/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-02-14 Released: 2019-02-27 
• Deposition Author(s): Datta, A.B., Sarkar, S.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Crystal Structure of RNF13 RING domain

Sarkar, S., Datta, A.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.94 kDa 
• Atom Count: 1,294 
• Modeled Residue Count: 145 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RNF13	A, B [auth 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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.338	α = 90
b = 90.338	β = 90
c = 45.445	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
SHELXD	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	India	500241/Z/11/Z

Revision History  

• Version 1.0: 2019-02-27
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references