8X19

Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into histone exchange by human SRCAP complex.

Yu, J.Sui, F.Gu, F.Li, W.Yu, Z.Wang, Q.He, S.Wang, L.Xu, Y.

(2024) Cell Discov 10: 15-15

  • DOI: https://doi.org/10.1038/s41421-023-00640-1
  • Primary Citation of Related Structures:  
    8X15, 8X19, 8X1C

  • PubMed Abstract: 

    Histone variant H2A.Z is found at promoters and regulates transcription. The ATP-dependent chromatin remodeler SRCAP complex (SRCAP-C) promotes the replacement of canonical histone H2A-H2B dimer with H2A.Z-H2B dimer. Here, we determined structures of human SRCAP-C bound to H2A-containing nucleosome at near-atomic resolution. The SRCAP subunit integrates a 6-subunit actin-related protein (ARP) module and an ATPase-containing motor module. The ATPase-associated ARP module encircles half of the nucleosome along the DNA and may restrain net DNA translocation, a unique feature of SRCAP-C. The motor module adopts distinct nucleosome binding modes in the apo (nucleotide-free), ADP-bound, and ADP-BeF x -bound states, suggesting that ATPase-driven movement destabilizes H2A-H2B by unwrapping the entry DNA and pulls H2A-H2B out of nucleosome through the ZNHIT1 subunit. Structure-guided chromatin immunoprecipitation sequencing analysis confirmed the requirement of H2A-contacting ZNHIT1 in maintaining H2A.Z occupancy on the genome. Our study provides structural insights into the mechanism of H2A-H2A.Z exchange mediated by SRCAP-C.


  • Organizational Affiliation

    Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-C
A, E
130Homo sapiensMutation(s): 0 
Gene Names: H2AC6H2AFLHIST1H2AC
UniProt & NIH Common Fund Data Resources
Find proteins for Q93077 (Homo sapiens)
Explore Q93077 
Go to UniProtKB:  Q93077
PHAROS:  Q93077
GTEx:  ENSG00000180573 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93077
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-C/E/F/G/I
B, F
126Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62807 (Homo sapiens)
Explore P62807 
Go to UniProtKB:  P62807
PHAROS:  P62807
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62807
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
C, G
136Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68431
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
D, H
103Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
PHAROS:  P62805
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62805
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Helicase SRCAP3,230Homo sapiensMutation(s): 0 
Gene Names: SRCAPKIAA0309
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZRS2 (Homo sapiens)
Explore Q6ZRS2 
Go to UniProtKB:  Q6ZRS2
PHAROS:  Q6ZRS2
GTEx:  ENSG00000080603 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ZRS2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 72 homolog364Homo sapiensMutation(s): 0 
Gene Names: VPS72TCFL1YL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15906 (Homo sapiens)
Explore Q15906 
Go to UniProtKB:  Q15906
PHAROS:  Q15906
GTEx:  ENSG00000163159 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15906
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 6396Homo sapiensMutation(s): 0 
Gene Names: ACTR6CDA12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZN1 (Homo sapiens)
Explore Q9GZN1 
Go to UniProtKB:  Q9GZN1
PHAROS:  Q9GZN1
GTEx:  ENSG00000075089 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GZN1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger HIT domain-containing protein 1154Homo sapiensMutation(s): 0 
Gene Names: ZNHIT1CGBP1ZNFN4A1
UniProt & NIH Common Fund Data Resources
Find proteins for O43257 (Homo sapiens)
Explore O43257 
Go to UniProtKB:  O43257
PHAROS:  O43257
GTEx:  ENSG00000106400 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43257
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like 1
M, O, Q
456Homo sapiensMutation(s): 0 
Gene Names: RUVBL1INO80HNMP238TIP49TIP49A
EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y265 (Homo sapiens)
Explore Q9Y265 
Go to UniProtKB:  Q9Y265
PHAROS:  Q9Y265
GTEx:  ENSG00000175792 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y265
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like 2
N, P, R
463Homo sapiensMutation(s): 0 
Gene Names: RUVBL2INO80JTIP48TIP49BCGI-46
EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y230 (Homo sapiens)
Explore Q9Y230 
Go to UniProtKB:  Q9Y230
PHAROS:  Q9Y230
GTEx:  ENSG00000183207 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y230
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1
S, U
375Homo sapiensMutation(s): 0 
Gene Names: ACTB
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P60709 (Homo sapiens)
Explore P60709 
Go to UniProtKB:  P60709
PHAROS:  P60709
GTEx:  ENSG00000075624 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60709
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-like protein 6A429Homo sapiensMutation(s): 0 
Gene Names: ACTL6ABAF53BAF53AINO80K
UniProt & NIH Common Fund Data Resources
Find proteins for O96019 (Homo sapiens)
Explore O96019 
Go to UniProtKB:  O96019
PHAROS:  O96019
GTEx:  ENSG00000136518 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO96019
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA methyltransferase 1-associated protein 1467Homo sapiensMutation(s): 0 
Gene Names: DMAP1KIAA1425
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPF5 (Homo sapiens)
Explore Q9NPF5 
Go to UniProtKB:  Q9NPF5
PHAROS:  Q9NPF5
GTEx:  ENSG00000178028 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NPF5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
YEATS domain-containing protein 4227Homo sapiensMutation(s): 0 
Gene Names: YEATS4GAS41
UniProt & NIH Common Fund Data Resources
Find proteins for O95619 (Homo sapiens)
Explore O95619 
Go to UniProtKB:  O95619
PHAROS:  O95619
GTEx:  ENSG00000127337 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95619
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains LengthOrganismImage
DNA (147-MER)147Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains LengthOrganismImage
DNA (147-MER)147Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
IA [auth T],
JA [auth U]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
CA [auth M]
DA [auth N]
EA [auth O]
FA [auth P]
GA [auth Q]
CA [auth M],
DA [auth N],
EA [auth O],
FA [auth P],
GA [auth Q],
HA [auth R],
Z [auth I]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF (Subject of Investigation/LOI)
Query on BEF

Download Ideal Coordinates CCD File 
BA [auth I]BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth I]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references