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4ioy

Structure of the Spt16 Middle Domain Reveals Functional Features of the Histone Chaperone FACT

Method: X-RAY DIFFRACTION Dmax: 73.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

FACT complex subunit SPT16

Saccharomyces cerevisiae

UniProt P32558

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 X； UniProt 675–958 Fragment：Middle Domain (UNP residues 675-958) PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；277.15 K；0.1 M sodium/potassium phosphate, pH 6.0, 0.2 M sodium chloride, 40% PEG400, 10 mM TCEP-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K Resolution 1.95 Å R-free 0.197

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 4IOY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3BIP Crystal structure of yeast Spt16 N-terminal Domain Deposited 2007-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–465（465 aa） Fragment：residues 1-465
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；298 K；25% Pentaerythritol Ethoxylate (15/4 EO/OH), 100mM Sodium Acetate, pH 4.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.94 Å R-free 0.244
3BIP Crystal structure of yeast Spt16 N-terminal Domain Deposited 2007-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–465（465 aa） Fragment：residues 1-465
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；298 K；25% Pentaerythritol Ethoxylate (15/4 EO/OH), 100mM Sodium Acetate, pH 4.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.94 Å R-free 0.244
3BIQ Crystal structure of yeast Spt16 N-terminal Domain Deposited 2007-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–465（465 aa） Fragment：residues 1-465
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；298 K；25% Pentaerythritol Ethoxylate (15/4 EO/OH), 100mM Sodium Acetate, pH 4.5, vapor diffusion, temperature 298K
Resolution 1.73 Å R-free 0.213
3BIT Crystal structure of yeast Spt16 N-terminal Domain Deposited 2007-11-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–451（451 aa） Fragment：residues 1-451
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 BME BETA-MERCAPTOETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；278 K；35% PEG 300, 200mM NaCl, 100mM Sodium Acetate, pH 4.5, vapor diffusion, temperature 278K
Resolution 1.90 Å R-free 0.224
3BIT Crystal structure of yeast Spt16 N-terminal Domain Deposited 2007-11-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–451（451 aa） Fragment：residues 1-451
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 BME BETA-MERCAPTOETHANOL × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；278 K；35% PEG 300, 200mM NaCl, 100mM Sodium Acetate, pH 4.5, vapor diffusion, temperature 278K
Resolution 1.90 Å R-free 0.224
7NKY RNA Polymerase II-Spt4/5-nucleosome-FACT structure Deposited 2021-02-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 27-meric
Chain Q 1–1035（1035 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8XGC Structure of yeast replisome associated with FACT and histone hexamer, Composite map Deposited 2023-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain L 1–1035（1035 aa）
Not recorded ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPT16_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain X； PDBConstruct 9–285； UniProt 675–958

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 4ioy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ioy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4ioy
Deposition date deposition_date2013-01-08
Structure title titleStructure of the Spt16 Middle Domain Reveals Functional Features of the Histone Chaperone FACT
Keywords keywordsSpt16, FACT, double pleckstrin homology domain, H3-H4 histones, TRANSCRIPTION; TRANSCRIPTION
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_guinier20.97 Å
Radius of gyration Rg (electron density) rg_electron19.83 Å
Forward intensity I(0) i013637600.00
Molecular weight molecular_weight28283.0 kDa
Excluded volume excluded_volume35716 ų
Envelope volume envelope_volume43037 ų
Hydration-shell volume shell_volume18657 ų
Envelope diameter envelope_diameter76.3 Å
Shell Rg shell_rg25.99 Å
Envelope Rg envelope_rg20.29 Å
Shape Rg shape_rg19.83 Å
Total Rg total_rg20.77 Å
Total atoms total_atoms1991
Residues n_residues243
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 dmax73.7 Å
Rg (real space) rg_real20.95 Å
Rg uncertainty (real space) rg_real_error0.65 Å
I(0) (real space) i0_real1.3640e+07
I(0) uncertainty (real space) i0_real_error1.9220e+05
Rg (reciprocal space) rg_reciprocal20.95 Å
I(0) (reciprocal space) i0_reciprocal13640000.0000
Solution quality estimate total_estimate0.7854
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.5 Å
Skewness Skewness skewness0.315
Kurtosis Kurtosis kurtosis-0.297
Angular range angular_range— – 0.3800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2173000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.748; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4ioyX01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily150 —
Domain ID domain_id4ioyX02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
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8. Citations (1)

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9. Files and Curves (10)