8D30

Crystal structure of the human COPB2 WD-domains

• PDB DOI: https://doi.org/10.2210/pdb8D30/pdb

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


• Deposited: 2022-05-31 Released: 2022-11-16 
• Deposition Author(s): Zeng, H., Dong, A., Hutchinson, A., Seitova, A., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.247 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

Starting Model: experimental

Literature

Crystal structure of the human COPB2 WD-domains

Zeng, H., Dong, A., Hutchinson, A., Seitova, A., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

To be published.

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.

Macromolecule Content

• Total Structure Weight: 140.07 kDa 
• Atom Count: 8,563 
• Modelled Residue Count: 1,136 
• Deposited Residue Count: 1,230 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coatomer subunit beta'	A, B	615	Homo sapiens	Mutation(s): 0  Gene Names: COPB2
UniProt & NIH Common Fund Data Resources
Find proteins for P35606 (Homo sapiens) Explore P35606  Go to UniProtKB:  P35606
PHAROS:  P35606 GTEx:  ENSG00000184432

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.247 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.074	α = 90
b = 134.062	β = 90
c = 144.27	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Zeng, H., Dong, A., Hutchinson, A., Seitova, A., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2022-11-16
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description