8YJF | pdb_00008yjf

Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and an H2A-H2B dimer

• PDB DOI: https://doi.org/10.2210/pdb8YJF/pdb

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


• Deposited: 2024-03-01 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.40 Å
• R-Value Free: 
  0.312 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.293 (Depositor), 0.290 (DCC) 
• R-Value Observed: 
  0.357 (Depositor) 

Starting Models: experimental

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 67: 1305-1307

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

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A2B2C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A5B1C1D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 121.37 kDa 
• Atom Count: 6,797 
• Modelled Residue Count: 846 
• Deposited Residue Count: 1,073 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FACT complex subunit SPT16	A	350	Homo sapiens	Mutation(s): 0  Gene Names: SUPT16H, FACT140, FACTP140
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5B9 (Homo sapiens) Explore Q9Y5B9  Go to UniProtKB:  Q9Y5B9
PHAROS:  Q9Y5B9 GTEx:  ENSG00000092201

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 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, 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 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 ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 2-E	G	126	Homo sapiens	Mutation(s): 0  Gene Names: HIST2H2BE
UniProt & NIH Common Fund Data Resources
Find proteins for Q16778 (Homo sapiens) Explore Q16778  Go to UniProtKB:  Q16778
PHAROS:  Q16778 GTEx:  ENSG00000184678

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-D	H	136	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2AD
UniProt & NIH Common Fund Data Resources
Find proteins for P20671 (Homo sapiens) Explore P20671  Go to UniProtKB:  P20671
PHAROS:  P20671 GTEx:  ENSG00000196866

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.40 Å
• R-Value Free:  0.312 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.293 (Depositor), 0.290 (DCC) 
• R-Value Observed: 0.357 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.405	α = 90
b = 190.405	β = 90
c = 79.832	γ = 120

Software Package:

Software Name	Purpose
autoPX	data processing
PHENIX	phasing
PHENIX	refinement
autoPX	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-20 
Deposition Author(s): Gan, S.L., Yang, W.S., Xu, R.M.

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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

Revision History  

• Version 1.0: 2024-03-20
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Database references
• Version 1.2: 2024-06-19
  Changes: Database references