7XVM

Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment)

Adhireksan, Z.Qiuye, B.Lee, P.L.Sharma, D.Padavattan, S.Davey, C.A.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
A, E, K, O
138Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
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PHAROS:  P68431
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UniProt GroupP68431
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F, L, P
105Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
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PHAROS:  P62805
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UniProt GroupP62805
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E
C, G, M, Q
132Homo sapiensMutation(s): 0 
Gene Names: H2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
UniProt & NIH Common Fund Data Resources
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PHAROS:  P04908
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-J
D, H, N, R
128Homo sapiensMutation(s): 0 
Gene Names: H2BC11H2BFRHIST1H2BJ
UniProt & NIH Common Fund Data Resources
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PHAROS:  P06899
GTEx:  ENSG00000124635 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H5
U, V
190Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (169-MER)
I, S
169synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (169-MER)
J, T
169synthetic construct
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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AA [auth I]
BA [auth I]
CA [auth I]
DA [auth I]
EA [auth I]
AA [auth I],
BA [auth I],
CA [auth I],
DA [auth I],
EA [auth I],
FA [auth I],
GA [auth I],
IA [auth J],
JA [auth J],
KA [auth J],
MA [auth S],
NA [auth S],
OA [auth S],
PA [auth S],
QA [auth T],
RA [auth T],
W [auth C],
Z [auth I]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
HA [auth I],
SA [auth T]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
LA [auth M],
X [auth C],
Y [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.16α = 90
b = 103.758β = 100.97
c = 212.955γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Singapore)SingaporeMOE2015-T2-2-089
Ministry of Education (MoE, Singapore)SingaporeMOE2012-T3-1-001

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description