1AOI

COMPLEX BETWEEN NUCLEOSOME CORE PARTICLE (H3,H4,H2A,H2B) AND 146 BP LONG DNA FRAGMENT

PDB DOI: https://doi.org/10.2210/pdb1AOI/pdb
NAKB: 1AOI

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Xenopus laevis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1997-07-03 Released: 1998-09-30
Deposition Author(s): Luger, K., Maeder, A.W., Richmond, R.K., Sargent, D.F., Richmond, T.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.302
R-Value Work: 0.224

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the nucleosome core particle at 2.8 A resolution.

Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F., Richmond, T.J.

(1997) Nature 389: 251-260

PubMed: 9305837 Search on PubMed
DOI: https://doi.org/10.1038/38444
Primary Citation of Related Structures:
1AOI

PubMed Abstract:
The X-ray crystal structure of the nucleosome core particle of chromatin shows in atomic detail how the histone protein octamer is assembled and how 146 base pairs of DNA are organized into a superhelix around it. Both histone/histone and histone/DNA interactions depend on the histone fold domains and additional, well ordered structure elements extending from this motif. Histone amino-terminal tails pass over and between the gyres of the DNA superhelix to contact neighbouring particles. The lack of uniformity between multiple histone/DNA-binding sites causes the DNA to deviate from ideal superhelix geometry.

Organizational Affiliation

Institut für Molekularbiologie und Biophysik, Zürich, Switzerland.

Macromolecule Content

Total Structure Weight: 184.55 kDa
Atom Count: 12,385
Modelled Residue Count: 1,097
Deposited Residue Count: 1,128
Unique protein chains: 4
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H3	C [auth A], G [auth E]	116	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P02302 (Xenopus laevis) Explore P02302 Go to UniProtKB: P02302
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02302
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H4	D [auth B], H [auth F]	87	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799 Go to UniProtKB: P62799
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62799
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H2A	E [auth C], I [auth G]	116	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897 Go to UniProtKB: P06897
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06897
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H2B	F [auth D], J [auth H]	99	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281 Go to UniProtKB: P02281
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02281
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
PALINDROMIC 146 BP DNA REPEAT 8/9 FROM HUMAN X-CHROMOSOME ALPHA SATELLITE DNA	A [auth I], B [auth J]	146	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain K [auth I] SDF format, chain L [auth I] SDF format, chain M [auth I] SDF format, chain N [auth J] SDF format, chain O [auth J] SDF format, chain P [auth J] MOL2 format, chain K [auth I] MOL2 format, chain L [auth I] MOL2 format, chain M [auth I] MOL2 format, chain N [auth J] MOL2 format, chain O [auth J] MOL2 format, chain P [auth J] mmCIF format, chain K [auth I] mmCIF format, chain L [auth I] mmCIF format, chain M [auth I] mmCIF format, chain N [auth J] mmCIF format, chain O [auth J] mmCIF format, chain P [auth J]	K [auth I] L [auth I] M [auth I] N [auth J] O [auth J] K [auth I], L [auth I], M [auth I], N [auth J], O [auth J], P [auth J]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain K [auth I] Focus chain L [auth I] Focus chain M [auth I] Focus chain N [auth J] Focus chain O [auth J] Focus chain P [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.302
R-Value Work: 0.224
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.04	α = 90
b = 181.78	β = 90
c = 110.12	γ = 90

Software Package:

Software Name	Purpose
LOCAL	model building
X-PLOR	refinement
IN-HOUSE	data reduction
IN-HOUSE	data scaling
IN-HOUSE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1998-09-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1998-09-30
Type: Initial release
Version 1.1: 2008-05-22
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references, Derived calculations