6CVZ

Crystal structure of the WD40-repeat of RFWD3

• PDB DOI: https://doi.org/10.2210/pdb6CVZ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2018-03-29 Released: 2018-06-27 
• Deposition Author(s): DONG, A., LOPPNAU, P., SEITOVA, A., HUTCHINSON, A., TEMPEL, W., WEI, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J., TONG, Y., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.214 
• R-Value Observed: 0.215 

Starting Model: other

Literature

Target highlights in CASP13: Experimental target structures through the eyes of their authors.

Lepore, R., Kryshtafovych, A., Alahuhta, M., Veraszto, H.A., Bomble, Y.J., Bufton, J.C., Bullock, A.N., Caba, C., Cao, H., Davies, O.R., Desfosses, A., Dunne, M., Fidelis, K., Goulding, C.W., Gurusaran, M., Gutsche, I., Harding, C.J., Hartmann, M.D., Hayes, C.S., Joachimiak, A., Leiman, P.G., Loppnau, P., Lovering, A.L., Lunin, V.V., Michalska, K., Mir-Sanchis, I., Mitra, A.K., Moult, J., Phillips Jr., G.N., Pinkas, D.M., Rice, P.A., Tong, Y., Topf, M., Walton, J.D., Schwede, T.

(2019) Proteins 87: 1037-1057

• PubMed: 31442339 
• DOI: https://doi.org/10.1002/prot.25805
• Primary Citation of Related Structures:  
  6CVZ, 6SD8, 6SDA


• PubMed Abstract: 
  

  The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.

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Organizational Affiliation: 

BSC-CNS Barcelona Supercomputing Center, Barcelona, Spain.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 116.47 kDa 
• Atom Count: 8,013 
• Modelled Residue Count: 1,001 
• Deposited Residue Count: 1,053 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RFWD3	A, B, C	351	Homo sapiens	Mutation(s): 0  Gene Names: RFWD3, RNF201 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PCD5 (Homo sapiens) Explore Q6PCD5  Go to UniProtKB:  Q6PCD5
PHAROS:  Q6PCD5 GTEx:  ENSG00000168411

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth A], E [auth B], F [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.214 
• R-Value Observed: 0.215 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.991	α = 90
b = 91.991	β = 90
c = 110.738	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-27 
Deposition Author(s): DONG, A., LOPPNAU, P., SEITOVA, A., HUTCHINSON, A., TEMPEL, W., WEI, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J., TONG, Y., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2018-06-27
  Type: Initial release
  
• Version 1.1: 2021-09-22
  Changes: Database references, Derived calculations
• Version 1.2: 2024-04-03
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary