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1hst

CRYSTAL STRUCTURE OF GLOBULAR DOMAIN OF HISTONE H5 AND ITS IMPLICATIONS FOR NUCLEOSOME BINDING

Method: X-RAY DIFFRACTION Dmax: 57.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

HISTONE H5

Gallus gallus

UniProt P02259

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 19–108 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.60 Å
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 19–108 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1HST Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4QLC Crystal structure of chromatosome at 3.5 angstrom resolution Deposited 2014-06-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain U 23–99（77 aa）
Not recorded CIT CITRIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.75；291 K；0.1 mM Citric acid, 0.1mM potassium chloride, and 10% MPD, pH 3.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.50 Å R-free 0.243
5WCU Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5 Deposited 2017-07-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain U 23–98（76 aa） Fragment：UNP residues 23-98
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；291 K；0.1 M NH4NO3, 10% MPD (v/v)
Resolution 5.53 Å R-free 0.238
5WCU Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5 Deposited 2017-07-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain V 23–98（76 aa） Fragment：UNP residues 23-98
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；291 K；0.1 M NH4NO3, 10% MPD (v/v)
Resolution 5.53 Å R-free 0.238
7C0J Crystal structure of chimeric mutant of GH5 in complex with Z-DNA Deposited 2020-05-01 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 25–64（40 aa）
Chain A 76–88（13 aa）
Chain A 92–93（2 aa）
Chain A 95–98（4 aa）
Chain B 25–64（40 aa）
Chain B 76–88（13 aa）
Chain B 92–93（2 aa）
Chain B 95–98（4 aa）
Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；MES pH 6.0, PEG 4000, ethylene glycol
Resolution 2.75 Å R-free 0.248
7XVM Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain U 2–190（189 aa）
Chain V 2–190（189 aa）
Not recorded CA CALCIUM ION × 18 CL CHLORIDE ION × 3 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 2.84 Å R-free 0.259
8XJV Structural basis for the linker histone H5-nucleosome binding and chromatin compaction Deposited 2023-12-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 108 PDB declaration: 110-meric
Chain Ah 1–190（190 aa）
Chain Ai 1–190（190 aa）
Chain Aj 1–190（190 aa）
Chain Ak 1–190（190 aa）
Chain Al 1–190（190 aa）
Chain Am 1–190（190 aa）
Chain An 1–190（190 aa）
Chain Ao 1–190（190 aa）
Chain Ap 1–190（190 aa）
Chain Aq 1–190（190 aa）
Chain Ar 1–190（190 aa）
Chain As 1–190（190 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.60 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H5_CHICK
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–90； UniProt 19–108 Author chain B； PDBConstruct 1–90； UniProt 19–108

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1hst

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1hst
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1hst
Deposition date deposition_date1993-03-30
Structure title titleCRYSTAL STRUCTURE OF GLOBULAR DOMAIN OF HISTONE H5 AND ITS IMPLICATIONS FOR NUCLEOSOME BINDING
Keywords keywordsCHROMOSOMAL PROTEIN; CHROMOSOMAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.55 Å
Radius of gyration Rg (electron density) rg_electron16.66 Å
Forward intensity I(0) i05041960.00
Molecular weight molecular_weight16037.0 kDa
Excluded volume excluded_volume20164 ų
Envelope volume envelope_volume24613 ų
Hydration-shell volume shell_volume12979 ų
Envelope diameter envelope_diameter61.1 Å
Shell Rg shell_rg21.64 Å
Envelope Rg envelope_rg16.92 Å
Shape Rg shape_rg16.61 Å
Total Rg total_rg17.71 Å
Total atoms total_atoms1128
Residues n_residues148
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax57.2 Å
Rg (real space) rg_real17.54 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real5.0420e+06
I(0) uncertainty (real space) i0_real_error6.5510e+04
Rg (reciprocal space) rg_reciprocal17.54 Å
I(0) (reciprocal space) i0_reciprocal5042000.0000
Solution quality estimate total_estimate0.8041
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.3 Å
Skewness Skewness skewness0.314
Kurtosis Kurtosis kurtosis-0.432
Angular range angular_range— – 0.4550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2008000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.828; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1hsta_
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.13 — Linker histone H1/H5
Domain ID domain_idd1hstb_
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.13 — Linker histone H1/H5

CATH v4.4 (2 domains)

Domain ID domain_id1hstA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id1hstB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
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8. Citations (2)

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9. Files and Curves (10)