5GT0

Crystal structure of nucleosome complex with human testis-specific histone variants, Th2a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural analyses of the nucleosome complexes with human testis-specific histone variants, hTh2a and hTh2b

Padavattan, S.Thiruselvam, V.Shinagawa, T.Hasegawa, K.Kumasaka, T.Ishii, S.Kumarevel, T.

(2017) Biophys Chem 221: 41-48

  • DOI: https://doi.org/10.1016/j.bpc.2016.11.013
  • Primary Citation of Related Structures:  
    5GSU, 5GT0, 5GT3

  • PubMed Abstract: 

    Th2a and Th2b are the testis-specific histone variants highly expressed during spermatogenesis. Approximately 4% of the genome is retained in nucleosomes in mature human sperm, which is enriched at loci of developmental importance. Our recent studies revealed that the mouse histone variant homologs TH2a and TH2b are involved in reprogramming. In the present work, we report three nucleosome structures (NCPs) with human testis-specific histone variants hTh2a and hTh2b, [hGcH (hTh2a-hTh2b-H3-H4), hGcHV1 (hTh2a-H2b-H3-H4) and hGcHV2 (H2a-hTh2b-H3-H4)] and a 146-base pair (bp) duplex DNA fragment at ~3.0Å resolutions. These crystal structures revealed two major changes within the nucleosomes, either with hTh2a, hTh2b or both variants, as compared to the canonical counterpart. First, the H-bonding interactions between the L1-L1' interfaces mediated by the hTh2a/hTh2a' L1-loops are lost. Second, the histone dimer-DNA contacts are considerably reduced, and these changes are localized around ±31 to 35-bp from the nucleosome entry/exit sites. Thus, the modified functional residues at the N- and C-terminal ends of histone variants are responsible for the observed structural changes and regulate the gene expression through specific structural alterations in the chromatin by modulating the chromatin-associated binding proteins.


  • Organizational Affiliation

    RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1A,
B [auth E]
135Homo 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4C [auth B],
D [auth F]
102Homo 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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-AE [auth C],
F [auth G]
130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2AAH2AFR
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QV6 (Homo sapiens)
Explore Q96QV6 
Go to UniProtKB:  Q96QV6
PHAROS:  Q96QV6
GTEx:  ENSG00000164508 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96QV6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-JG [auth D],
H
125Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFR
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 nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (146-MER)
I, J
146Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
AA [auth J]
BA [auth J]
CA [auth J]
K [auth E]
M [auth C]
AA [auth J],
BA [auth J],
CA [auth J],
K [auth E],
M [auth C],
N [auth I],
O [auth I],
P [auth I],
Q [auth I],
R [auth I],
S [auth I],
X [auth J],
Y [auth J],
Z [auth J]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
DA [auth J]
L [auth E]
T [auth I]
U [auth I]
V [auth I]
DA [auth J],
L [auth E],
T [auth I],
U [auth I],
V [auth I],
W [auth I]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.788α = 90
b = 108.966β = 90
c = 170.951γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data scaling
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Advisory, Data collection
  • Version 1.2: 2022-04-27
    Changes: Database references, Derived calculations
  • Version 1.3: 2022-05-04
    Changes: Advisory
  • Version 1.4: 2024-05-29
    Changes: Data collection