7WI7 | pdb_00007wi7

Crystal structure of human MCM8/9 complex

• PDB DOI: https://doi.org/10.2210/pdb7WI7/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2022-01-03 Released: 2023-01-25 
• Deposition Author(s): Li, J., Liu, Y.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 6.60 Å
• R-Value Free: 
  0.398 (Depositor), 0.399 (DCC) 
• R-Value Work: 
  0.321 (Depositor), 0.323 (DCC) 
• R-Value Observed: 
  0.329 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of human MCM8/9 complex

Li, J., Liu, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Cyclic - C6  (Explore in 3D)
Pseudo Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 164.8 kDa 
• Atom Count: 8,839 
• Modeled Residue Count: 1,131 
• Deposited Residue Count: 1,471 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA helicase MCM8	A	787	Homo sapiens	Mutation(s): 0  Gene Names: MCM8, C20orf154 EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJA3 (Homo sapiens) Explore Q9UJA3  Go to UniProtKB:  Q9UJA3
PHAROS:  Q9UJA3 GTEx:  ENSG00000125885

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA helicase MCM9	B	684	Homo sapiens	Mutation(s): 0  Gene Names: MCM9, C6orf61, MCMDC1 EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXL9 (Homo sapiens) Explore Q9NXL9  Go to UniProtKB:  Q9NXL9
PHAROS:  Q9NXL9 GTEx:  ENSG00000111877

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 6.60 Å
• R-Value Free:  0.398 (Depositor), 0.399 (DCC) 
• R-Value Work:  0.321 (Depositor), 0.323 (DCC) 
• R-Value Observed: 0.329 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.616	α = 90
b = 185.616	β = 90
c = 185.616	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-25 
Deposition Author(s): Li, J., Liu, Y.

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Funding Organization	Location	Grant Number
Other government	China	2019ZT08Y464
Other government	China	JCYJ20200109142412265

Revision History  

• Version 1.0: 2023-01-25
  Type: Initial release
  
• Version 1.1: 2023-07-26
  Changes: Other
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description