1M18 | pdb_00001m18

LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA

PDB DOI: https://doi.org/10.2210/pdb1M18/pdb
NAKB: 1M18

Classification: STRUCTURAL PROTEIN/DNA
Organism(s): Xenopus laevis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2002-06-18 Released: 2003-02-18
Deposition Author(s): Suto, R.K., Edayathumangalam, R.S., White, C.L., Melander, C., Gottesfeld, J.M., Dervan, P.B., Luger, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.257 (Depositor)
R-Value Work:
0.222 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands

Suto, R.K., Edayathumangalam, R.S., White, C.L., Melander, C., Gottesfeld, J.M., Dervan, P.B., Luger, K.

(2003) J Mol Biology 326: 371-380

PubMed: 12559907 Search on PubMed
DOI: https://doi.org/10.1016/s0022-2836(02)01407-9
Primary Citation Related Structures:
1M18, 1M19, 1M1A

PubMed Abstract:
We determined the crystal structures of three nucleosome core particles in complex with site-specific DNA-binding ligands, the pyrrole-imidazole polyamides. While the structure of the histone octamer and its interaction with the DNA remain unaffected by ligand binding, nucleosomal DNA undergoes significant structural changes at the ligand-binding sites and in adjacent regions to accommodate the ligands. Our findings suggest that twist diffusion occurs over long distances through tightly bound nucleosomal DNA. This may be relevant to the mechanism of ATP-dependent and spontaneous nucleosome translocation, and to the effect of bound factors on nucleosome dynamics.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA.

Macromolecule Content

Total Structure Weight: 201.95 kDa
Atom Count: 12,676
Modeled Residue Count: 1,052
Deposited Residue Count: 1,274
Unique protein chains: 4
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	C [auth A], G [auth E]	135	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P02302 (Xenopus laevis) Explore P02302 Go to UniProtKB: P02302
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02302
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	D [auth B], H [auth F]	102	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799 Go to UniProtKB: P62799
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62799
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A.1	E [auth C], I [auth G]	129	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897 Go to UniProtKB: P06897
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06897
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B.1	F [auth D], J [auth H]	125	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281 Go to UniProtKB: P02281
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02281
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
Palindromic 146 Base Pair DNA Fragment	A [auth I], B [auth J]	146	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1SZ Query on 1SZ Download:Ideal Coordinates CCD File SDF format, chain V [auth J] SDF format, chain O [auth I] MOL2 format, chain V [auth J] MOL2 format, chain O [auth I] mmCIF format, chain V [auth J] mmCIF format, chain O [auth I]	O [auth I], V [auth J]	N-[5-[[4-[[5-[[5-[[5-[[5-[[3-[3-(dimethylamino)propylamino]-3-oxidanylidene-propyl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]amino]-4-oxidanylidene-butyl]carbamoyl]-1-methyl-pyrrol-3-yl]-1-methyl-4-[[1-methyl-4-[(1-methylimidazol-2-yl)carbonylamino]pyrrol-2-yl]carbonylamino]imidazole-2-carboxamide C₅₈ H₇₁ N₂₁ O₁₀ TUWUDTOJENRSJG-UHFFFAOYSA-N		Interactions Focus chain O [auth I] Focus chain V [auth J]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain U [auth J] SDF format, chain T [auth J] SDF format, chain S [auth J] SDF format, chain R [auth J] SDF format, chain Q [auth J] SDF format, chain P [auth J] SDF format, chain N [auth I] SDF format, chain M [auth I] SDF format, chain L [auth I] SDF format, chain K [auth I] MOL2 format, chain W [auth D] MOL2 format, chain U [auth J] MOL2 format, chain T [auth J] MOL2 format, chain S [auth J] MOL2 format, chain R [auth J] MOL2 format, chain Q [auth J] MOL2 format, chain P [auth J] MOL2 format, chain N [auth I] MOL2 format, chain M [auth I] MOL2 format, chain L [auth I] MOL2 format, chain K [auth I] mmCIF format, chain W [auth D] mmCIF format, chain U [auth J] mmCIF format, chain T [auth J] mmCIF format, chain S [auth J] mmCIF format, chain R [auth J] mmCIF format, chain Q [auth J] mmCIF format, chain P [auth J] mmCIF format, chain N [auth I] mmCIF format, chain M [auth I] mmCIF format, chain L [auth I] mmCIF format, chain K [auth I]	K [auth I] L [auth I] M [auth I] N [auth I] P [auth J] K [auth I], L [auth I], M [auth I], N [auth I], P [auth J], Q [auth J], R [auth J], S [auth J], T [auth J], U [auth J], W [auth D]	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 I] Focus chain P [auth J] Focus chain Q [auth J] Focus chain R [auth J] Focus chain S [auth J] Focus chain T [auth J] Focus chain U [auth J] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.257 (Depositor)
R-Value Work: 0.222 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.839	α = 90
b = 109.628	β = 90
c = 183.172	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-02-18

Deposition Author(s):

Suto, R.K.

Edayathumangalam, R.S.

Revision History (Full details and data files)

Version 1.0: 2003-02-18
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2013-07-17
Changes: Database references, Non-polymer description
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations, Refinement description