8YJM

Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and a single chain H2B-H2A chimera

PDB DOI: https://doi.org/10.2210/pdb8YJM/pdb

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

Deposited: 2024-03-02 Released: 2024-03-20
Deposition Author(s): Gan, S.L., Yang, W.S., Xu, R.M.
Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.15 Å
R-Value Free: 0.286
R-Value Work: 0.263
R-Value Observed: 0.374

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure of a histone hexamer bound by the chaperone domains of SPT16 and MCM2.

Gan, S., Yang, W.S., Wei, L., Zhang, Z., Xu, R.M.

(2024) Sci China Life Sci

PubMed: 38478295 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1007/s11427-024-2560-8
Primary Citation of Related Structures:
8YJF, 8YJM

Organizational Affiliation

Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

Macromolecule Content

Total Structure Weight: 116.12 kDa
Atom Count: 6,879
Modelled Residue Count: 854
Deposited Residue Count: 1,024
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FACT complex subunit SPT16	A	350	Homo sapiens	Mutation(s): 0 Gene Names: SUPT16H
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5B9 (Homo sapiens) Explore Q9Y5B9 Go to UniProtKB: Q9Y5B9
PHAROS: Q9Y5B9 GTEx: ENSG00000092201
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y5B9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM2	B	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49736
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	C, E	81	Homo sapiens	Mutation(s): 0 Gene Names: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB... H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68431
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	D, F	103	Homo sapiens	Mutation(s): 0
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62805
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1/2/3/4/6,Histone H2A type 1-D	G	213	Homo sapiens	Mutation(s): 0 Gene Names: H2B-I, H2B-II, H2B-III, H2B-IV, H2B-VI, H2AC7, H2AFG, HIST1H2AD
UniProt & NIH Common Fund Data Resources
Find proteins for P20671 (Homo sapiens) Explore P20671 Go to UniProtKB: P20671
PHAROS: P20671 GTEx: ENSG00000196866
Find proteins for P0C1H3 (Gallus gallus) Explore P0C1H3 Go to UniProtKB: P0C1H3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P0C1H3P20671
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.15 Å
R-Value Free: 0.286
R-Value Work: 0.263
R-Value Observed: 0.374
Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 191.337	α = 90
b = 191.337	β = 90
c = 80.094	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-20

Deposition Author(s):

Gan, S.L.

Yang, W.S.

Xu, R.M.

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2019YFA0508900
National Natural Science Foundation of China (NSFC)	China	32330021
National Natural Science Foundation of China (NSFC)	China	31991162