7XX7

Crystal Structure of Nucleosome-H1x Linker Histone Assembly (sticky-169a DNA fragment)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Diversity in Linker Histone-Nucleosome Interactions Between and Within Variants

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: 
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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: 
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PHAROS:  P62805
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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
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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
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GTEx:  ENSG00000124635 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H1.10
U, V
214Homo sapiensMutation(s): 0 
Gene Names: H1-10H1FX
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GTEx:  ENSG00000184897 
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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

Download Ideal Coordinates CCD File 
AC [auth S]
BA [auth C]
CB [auth L]
DA [auth G]
DC [auth T]
AC [auth S],
BA [auth C],
CB [auth L],
DA [auth G],
DC [auth T],
EA [auth G],
EC [auth T],
FA [auth G],
FB [auth N],
FC [auth T],
GC [auth T],
HA [auth I],
HB [auth Q],
HC [auth T],
IA [auth I],
IB [auth Q],
IC [auth T],
JA [auth I],
JB [auth Q],
JC [auth T],
KA [auth I],
LA [auth I],
LB [auth R],
MA [auth I],
MB [auth S],
NA [auth I],
NB [auth S],
OA [auth I],
OB [auth S],
PB [auth S],
QB [auth S],
RA [auth J],
RB [auth S],
SA [auth J],
SB [auth S],
TA [auth J],
TB [auth S],
UA [auth J],
UB [auth S],
VA [auth J],
VB [auth S],
WA [auth J],
WB [auth S],
X [auth C],
XA [auth J],
XB [auth S],
Y [auth C],
YA [auth J],
YB [auth S],
ZA [auth J],
ZB [auth S]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth J]
BC [auth S]
CC [auth S]
EB [auth M]
AA [auth C],
AB [auth J],
BC [auth S],
CC [auth S],
EB [auth M],
KC [auth T],
PA [auth I],
QA [auth I]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BB [auth K]
CA [auth E]
DB [auth M]
GA [auth G]
GB [auth O]
BB [auth K],
CA [auth E],
DB [auth M],
GA [auth G],
GB [auth O],
KB [auth Q],
W [auth A],
Z [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.852α = 90
b = 102.111β = 96.34
c = 216.179γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata 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: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description