5T5K

Structure of histone-based chromatin in Archaea

PDB DOI: https://doi.org/10.2210/pdb5T5K/pdb
NAKB: 5T5K

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Methanothermus fervidus, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-08-31 Released: 2017-08-23
Deposition Author(s): Bhattacharyya, S., Mattiroli, F., Dyer, P.N., Sandman, K., Reeve, J.N., Luger, K.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free: 0.262
R-Value Work: 0.214
R-Value Observed: 0.216

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of histone-based chromatin in Archaea.

Mattiroli, F., Bhattacharyya, S., Dyer, P.N., White, A.E., Sandman, K., Burkhart, B.W., Byrne, K.R., Lee, T., Ahn, N.G., Santangelo, T.J., Reeve, J.N., Luger, K.

(2017) Science 357: 609-612

PubMed: 28798133 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.aaj1849
Primary Citation of Related Structures:
5T5K

PubMed Abstract:
Small basic proteins present in most Archaea share a common ancestor with the eukaryotic core histones. We report the crystal structure of an archaeal histone-DNA complex. DNA wraps around an extended polymer, formed by archaeal histone homodimers, in a quasi-continuous superhelix with the same geometry as DNA in the eukaryotic nucleosome. Substitutions of a conserved glycine at the interface of adjacent protein layers destabilize archaeal chromatin, reduce growth rate, and impair transcription regulation, confirming the biological importance of the polymeric structure. Our data establish that the histone-based mechanism of DNA compaction predates the nucleosome, illuminating the origin of the nucleosome.

Organizational Affiliation

Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA.

Macromolecule Content

Total Structure Weight: 102.03 kDa
Atom Count: 6,831
Modelled Residue Count: 584
Deposited Residue Count: 594
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein HMf-2	A, B, C, D, E A, B, C, D, E, F	69	Methanothermus fervidus	Mutation(s): 0 Gene Names: hmfB
UniProt
Find proteins for P19267 (Methanothermus fervidus) Explore P19267 Go to UniProtKB: P19267
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19267
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (90-MER)	G [auth I]	90	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (90-MER)	H [auth J]	90	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth D] SDF format, chain K [auth F] MOL2 format, chain I [auth B] MOL2 format, chain J [auth D] MOL2 format, chain K [auth F] mmCIF format, chain I [auth B] mmCIF format, chain J [auth D] mmCIF format, chain K [auth F]	I [auth B], J [auth D], K [auth F]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Focus chain J [auth D] Focus chain K [auth F] Interactions & Density Focus chain I [auth B] Focus chain J [auth D] Focus chain K [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free: 0.262
R-Value Work: 0.214
R-Value Observed: 0.216
Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.454	α = 90
b = 99.454	β = 90
c = 171.73	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2017-08-23

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM 067777
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM53185

Revision History (Full details and data files)

Version 1.0: 2017-08-23
Type: Initial release
Version 1.1: 2019-12-25
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description