3LEL | pdb_00003lel

Structural Insight into the Sequence-Dependence of Nucleosome Positioning

PDB DOI: https://doi.org/10.2210/pdb3LEL/pdb
NAKB: 3LEL

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

Deposited: 2010-01-15 Released: 2010-05-19
Deposition Author(s): Wu, B., Vasudevan, D., Davey, C.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.300 (Depositor), 0.297 (DCC)
R-Value Work:
0.229 (Depositor), 0.224 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural insight into the sequence dependence of nucleosome positioning

Wu, B., Mohideen, K., Vasudevan, D., Davey, C.A.

(2010) Structure 18: 528-536

PubMed: 20399189 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2010.01.015
Primary Citation Related Structures:
3LEL

PubMed Abstract:
Nucleosome positioning displays sequence dependency and contributes to genomic regulation in a site-specific manner. We solved the structures of nucleosome core particle composed of strong positioning TTTAA elements flanking the nucleosome center. The positioning strength of the super flexible TA dinucleotide is consistent with its observed central location within minor groove inward regions, where it can contribute maximally to energetically challenging minor groove bending, kinking and compression. The marked preference for TTTAA and positioning power of the site 1.5 double helix turns from the nucleosome center relates to a unique histone protein motif at this location, which enforces a sustained, extremely narrow minor groove via a hydrophobic "sugar clamp." Our analysis sheds light on the basis of nucleosome positioning and indicates that the histone octamer has evolved not to fully minimize sequence discrimination in DNA binding.

Organizational Affiliation

Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.

Macromolecule Content

Total Structure Weight: 401.12 kDa
Atom Count: 24,335
Modeled Residue Count: 2,128
Deposited Residue Count: 2,552
Unique protein chains: 4
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E, K, O	136	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233 Go to UniProtKB: P84233
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84233
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F, L, P	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G, M, Q	128	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis) Explore Q6AZJ8 Go to UniProtKB: Q6AZJ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6AZJ8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	D, H, N, R	125	Xenopus laevis	Mutation(s): 0
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: 5
147-MER DNA	I, S	147	N/A
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 6
147-MER DNA	J, T	147	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 ZA [auth T] SDF format, chain Z [auth I] SDF format, chain YA [auth T] SDF format, chain Y [auth I] SDF format, chain XA [auth T] SDF format, chain X [auth I] SDF format, chain WA [auth T] SDF format, chain W [auth I] SDF format, chain VA [auth T] SDF format, chain V [auth I] SDF format, chain UA [auth T] SDF format, chain U [auth G] SDF format, chain TA [auth T] SDF format, chain SA [auth S] SDF format, chain RA [auth S] SDF format, chain QA [auth S] SDF format, chain PA [auth S] SDF format, chain OA [auth S] SDF format, chain NA [auth S] SDF format, chain MA [auth S] SDF format, chain LA [auth S] SDF format, chain KA [auth O] SDF format, chain JA [auth N] SDF format, chain IA [auth J] SDF format, chain HA [auth J] SDF format, chain GA [auth J] SDF format, chain FA [auth J] SDF format, chain EA [auth J] SDF format, chain DA [auth J] SDF format, chain CA [auth J] SDF format, chain BB [auth T] SDF format, chain BA [auth J] SDF format, chain AB [auth T] SDF format, chain AA [auth I] MOL2 format, chain ZA [auth T] MOL2 format, chain Z [auth I] MOL2 format, chain YA [auth T] MOL2 format, chain Y [auth I] MOL2 format, chain XA [auth T] MOL2 format, chain X [auth I] MOL2 format, chain WA [auth T] MOL2 format, chain W [auth I] MOL2 format, chain VA [auth T] MOL2 format, chain V [auth I] MOL2 format, chain UA [auth T] MOL2 format, chain U [auth G] MOL2 format, chain TA [auth T] MOL2 format, chain SA [auth S] MOL2 format, chain RA [auth S] MOL2 format, chain QA [auth S] MOL2 format, chain PA [auth S] MOL2 format, chain OA [auth S] MOL2 format, chain NA [auth S] MOL2 format, chain MA [auth S] MOL2 format, chain LA [auth S] MOL2 format, chain KA [auth O] MOL2 format, chain JA [auth N] MOL2 format, chain IA [auth J] MOL2 format, chain HA [auth J] MOL2 format, chain GA [auth J] MOL2 format, chain FA [auth J] MOL2 format, chain EA [auth J] MOL2 format, chain DA [auth J] MOL2 format, chain CA [auth J] MOL2 format, chain BB [auth T] MOL2 format, chain BA [auth J] MOL2 format, chain AB [auth T] MOL2 format, chain AA [auth I] mmCIF format, chain ZA [auth T] mmCIF format, chain Z [auth I] mmCIF format, chain YA [auth T] mmCIF format, chain Y [auth I] mmCIF format, chain XA [auth T] mmCIF format, chain X [auth I] mmCIF format, chain WA [auth T] mmCIF format, chain W [auth I] mmCIF format, chain VA [auth T] mmCIF format, chain V [auth I] mmCIF format, chain UA [auth T] mmCIF format, chain U [auth G] mmCIF format, chain TA [auth T] mmCIF format, chain SA [auth S] mmCIF format, chain RA [auth S] mmCIF format, chain QA [auth S] mmCIF format, chain PA [auth S] mmCIF format, chain OA [auth S] mmCIF format, chain NA [auth S] mmCIF format, chain MA [auth S] mmCIF format, chain LA [auth S] mmCIF format, chain KA [auth O] mmCIF format, chain JA [auth N] mmCIF format, chain IA [auth J] mmCIF format, chain HA [auth J] mmCIF format, chain GA [auth J] mmCIF format, chain FA [auth J] mmCIF format, chain EA [auth J] mmCIF format, chain DA [auth J] mmCIF format, chain CA [auth J] mmCIF format, chain BB [auth T] mmCIF format, chain BA [auth J] mmCIF format, chain AB [auth T] mmCIF format, chain AA [auth I]	AA [auth I] AB [auth T] BA [auth J] BB [auth T] CA [auth J] AA [auth I], AB [auth T], BA [auth J], BB [auth T], CA [auth J], DA [auth J], EA [auth J], FA [auth J], GA [auth J], HA [auth J], IA [auth J], JA [auth N], KA [auth O], LA [auth S], MA [auth S], NA [auth S], OA [auth S], PA [auth S], QA [auth S], RA [auth S], SA [auth S], TA [auth T], U [auth G], UA [auth T], V [auth I], VA [auth T], W [auth I], WA [auth T], X [auth I], XA [auth T], Y [auth I], YA [auth T], Z [auth I], ZA [auth T]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain AB [auth T] Focus chain BA [auth J] Focus chain BB [auth T] Focus chain CA [auth J] Focus chain DA [auth J] Focus chain EA [auth J] Focus chain FA [auth J] Focus chain GA [auth J] Focus chain HA [auth J] Focus chain IA [auth J] Focus chain JA [auth N] Focus chain KA [auth O] Focus chain LA [auth S] Focus chain MA [auth S] Focus chain NA [auth S] Focus chain OA [auth S] Focus chain PA [auth S] Focus chain QA [auth S] Focus chain RA [auth S] Focus chain SA [auth S] Focus chain TA [auth T] Focus chain U [auth G] Focus chain UA [auth T] Focus chain V [auth I] Focus chain VA [auth T] Focus chain W [auth I] Focus chain WA [auth T] Focus chain X [auth I] Focus chain XA [auth T] Focus chain Y [auth I] Focus chain YA [auth T] Focus chain Z [auth I] Focus chain ZA [auth T] Interactions & Density Focus chain AA [auth I] Focus chain AB [auth T] Focus chain BA [auth J] Focus chain BB [auth T] Focus chain CA [auth J] Focus chain DA [auth J] Focus chain EA [auth J] Focus chain FA [auth J] Focus chain GA [auth J] Focus chain HA [auth J] Focus chain IA [auth J] Focus chain JA [auth N] Focus chain KA [auth O] Focus chain LA [auth S] Focus chain MA [auth S] Focus chain NA [auth S] Focus chain OA [auth S] Focus chain PA [auth S] Focus chain QA [auth S] Focus chain RA [auth S] Focus chain SA [auth S] Focus chain TA [auth T] Focus chain U [auth G] Focus chain UA [auth T] Focus chain V [auth I] Focus chain VA [auth T] Focus chain W [auth I] Focus chain WA [auth T] Focus chain X [auth I] Focus chain XA [auth T] Focus chain Y [auth I] Focus chain YA [auth T] Focus chain Z [auth I] Focus chain ZA [auth T]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.300 (Depositor), 0.297 (DCC)
R-Value Work: 0.229 (Depositor), 0.224 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.747	α = 90
b = 178.508	β = 102.78
c = 110.412	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-05-19

Deposition Author(s):

Wu, B.

Vasudevan, D.

Davey, C.A.

Revision History (Full details and data files)

Version 1.0: 2010-05-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description