6L9Z

338 bp di-nucleosome assembled with linker histone H1.X


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Engineering nucleosomes for generating diverse chromatin assemblies.

Adhireksan, Z.Sharma, D.Lee, P.L.Bao, Q.Padavattan, S.Shum, W.K.Davey, G.E.Davey, C.A.

(2021) Nucleic Acids Res 49: e52-e52

  • DOI: https://doi.org/10.1093/nar/gkab070
  • Primary Citation of Related Structures:  
    6L9Z, 6LA2, 6LAB, 6LER, 7COW

  • PubMed Abstract: 

    Structural characterization of chromatin is challenging due to conformational and compositional heterogeneity in vivo and dynamic properties that limit achievable resolution in vitro. Although the maximum resolution for solving structures of large macromolecular assemblies by electron microscopy has recently undergone profound increases, X-ray crystallographic approaches may still offer advantages for certain systems. One such system is compact chromatin, wherein the crystalline state recapitulates the crowded molecular environment within the nucleus. Here we show that nucleosomal constructs with cohesive-ended DNA can be designed that assemble into different types of circular configurations or continuous fibers extending throughout crystals. We demonstrate the utility of the method for characterizing nucleosome compaction and linker histone binding at near-atomic resolution but also advance its application for tackling further problems in chromatin structural biology and for generating novel types of DNA nanostructures. We provide a library of cohesive-ended DNA fragment expression constructs and a strategy for engineering DNA-based nanomaterials with a seemingly vast potential variety of architectures and histone chemistries.


  • Organizational Affiliation

    NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
A, E, K, O
136Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
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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
103Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
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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
130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFA
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens)
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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
126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFR
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens)
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PHAROS:  P06899
GTEx:  ENSG00000124635 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H1x213Homo sapiensMutation(s): 0 
Gene Names: H1FX
UniProt & NIH Common Fund Data Resources
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Explore Q92522 
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PHAROS:  Q92522
GTEx:  ENSG00000184897 
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UniProt GroupQ92522
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (338-MER)338other sequences
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (338-MER)338other sequences
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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 
AB [auth I]
AC [auth J]
BA [auth G]
BB [auth I]
BC [auth J]
AB [auth I],
AC [auth J],
BA [auth G],
BB [auth I],
BC [auth J],
CA [auth G],
CB [auth I],
CC [auth J],
DA [auth G],
DB [auth I],
DC [auth J],
EB [auth I],
EC [auth J],
FA [auth I],
FB [auth I],
FC [auth J],
GA [auth I],
GB [auth I],
GC [auth J],
HA [auth I],
HC [auth J],
IA [auth I],
IC [auth J],
JA [auth I],
JC [auth J],
KA [auth I],
LA [auth I],
MA [auth I],
NA [auth I],
NB [auth J],
NC [auth M],
OA [auth I],
OB [auth J],
OC [auth M],
PA [auth I],
PB [auth J],
QA [auth I],
QB [auth J],
RA [auth I],
RB [auth J],
RC [auth N],
SA [auth I],
SB [auth J],
SC [auth N],
TA [auth I],
TB [auth J],
U [auth C],
UA [auth I],
UB [auth J],
UC [auth Q],
V [auth C],
VA [auth I],
VB [auth J],
VC [auth Q],
W [auth C],
WA [auth I],
WB [auth J],
XA [auth I],
XB [auth J],
XC [auth R],
YA [auth I],
YB [auth J],
Z [auth D],
ZA [auth I],
ZB [auth J]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
HB [auth I]
IB [auth I]
JB [auth I]
KB [auth I]
KC [auth J]
HB [auth I],
IB [auth I],
JB [auth I],
KB [auth I],
KC [auth J],
LB [auth I],
LC [auth J],
MB [auth I],
QC [auth M],
Y [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth E]
EA [auth G]
MC [auth K]
PC [auth M]
T [auth A]
AA [auth E],
EA [auth G],
MC [auth K],
PC [auth M],
T [auth A],
TC [auth O],
WC [auth Q],
X [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.5α = 90
b = 101.41β = 97.48
c = 215.67γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (Singapore)Singapore--

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-08-18
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Refinement description