5C3I | pdb_00005c3i

Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2

PDB DOI: https://doi.org/10.2210/pdb5C3I/pdb

Classification: REPLICATION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3), Escherichia coli
Mutation(s): No

Deposited: 2015-06-17 Released: 2015-07-29
Deposition Author(s): Wang, H., Wang, M., Yang, N., Xu, R.M.
Funding Organization(s): National Natural Science Foundation of China, MOST

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.253 (Depositor), 0.262 (DCC)
R-Value Work:
0.216 (Depositor)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2

Wang, H., Wang, M., Yang, N., Xu, R.M.

(2015) Protein Cell 6: 693-697

PubMed: 26186914 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1007/s13238-015-0190-0
Primary Citation Related Structures:
5C3I

Organizational Affiliation

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

Macromolecule Content

Total Structure Weight: 347.73 kDa
Atom Count: 17,655
Modeled Residue Count: 2,198
Deposited Residue Count: 3,120
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone chaperone ASF1A	A, E, I, M, Q A, E, I, M, Q, U	188	Homo sapiens	Mutation(s): 0 Gene Names: ASF1A, CGI-98, HSPC146
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y294 (Homo sapiens) Explore Q9Y294 Go to UniProtKB: Q9Y294
PHAROS: Q9Y294 GTEx: ENSG00000111875
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y294
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	B, F, J, N, R B, F, J, N, R, V	136	Homo sapiens	Mutation(s): 0 Gene Names: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD... HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431 Go to UniProtKB: P68431
PHAROS: P68431 GTEx: ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68431
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	C, G, K, O, S C, G, K, O, S, W	103	Homo sapiens	Mutation(s): 0 Gene Names: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D... HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805 Go to UniProtKB: P62805
PHAROS: P62805 GTEx: ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62805
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM2,MCM2	D, H, L, P, T D, H, L, P, T, X	93	Homo sapiens	Mutation(s): 0 Gene Names: MCM2, BM28, CCNL1, CDCL1, KIAA0030 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P49736 (Homo sapiens) Explore P49736 Go to UniProtKB: P49736
PHAROS: P49736 GTEx: ENSG00000073111
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49736
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.253 (Depositor), 0.262 (DCC)
R-Value Work: 0.216 (Depositor)
R-Value Observed: 0.217 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.704	α = 90
b = 147.704	β = 90
c = 261.796	γ = 120

Software Package:

Software Name	Purpose
DENZO	data collection
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2015-07-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31210103914
National Natural Science Foundation of China	China	34130018
MOST	China	2015CB856202

Revision History (Full details and data files)

Version 1.0: 2015-07-29
Type: Initial release
Version 1.1: 2015-09-02
Changes: Database references
Version 1.2: 2017-10-18
Changes: Author supporting evidence, Derived calculations
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-10-16
Changes: Structure summary