6M4I | pdb_00006m4i

Structure of CENP-E motor domain at 1.9 angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6M4I/pdb

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


• Deposited: 2020-03-07 Released: 2021-03-10 
• Deposition Author(s): Shibuya, A., Yokoyama, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Structure and comparison of the motor domain ofcentromere-associated protein E

Shibuya, A., Ogo, N., Sawada, J., Asai, A., Yokoyama, H.

(2021) Acta Crystallogr D Biol Crystallogr 77: 280-287

• DOI: https://doi.org/10.1107/S2059798321000176

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: 80.5 kDa 
• Atom Count: 5,120 
• Modeled Residue Count: 609 
• Deposited Residue Count: 706 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Centromere-associated protein E	A, B	353	Homo sapiens	Mutation(s): 0  Gene Names: CENPE
UniProt & NIH Common Fund Data Resources
Find proteins for Q02224 (Homo sapiens) Explore Q02224  Go to UniProtKB:  Q02224
PHAROS:  Q02224 GTEx:  ENSG00000138778

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	C [auth A], E [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.825	α = 90
b = 82.839	β = 100.85
c = 49.372	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
Coot	model building
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-10 
Deposition Author(s): Shibuya, A., Yokoyama, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2021-03-10
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description