SAXSdb — 8g87

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1. Protein Identity and Related Structures Protein Identity & Related Structures

POU domain, class 5, transcription factor 1

Homo sapiens

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–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain X； UniProt 1–360	Not recorded	nMatn1 DNA (top strand) × 1 nMatn1 DNA (bottom strand) × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 8.10 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 8G87	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6T90 OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2019-10-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric	Chain K 1–360（360 aa）	Not recorded	PTD PENTANEDIAL × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.05 Å
6YOV OCT4-SOX2-bound nucleosome - SHL+6 Deposited 2020-04-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric	Chain K 1–360（360 aa）	Not recorded	PTD PENTANEDIAL × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.42 Å
7U0G structure of LIN28b nucleosome bound 3 OCT4 Deposited 2022-02-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain K 138–290（153 aa） Chain L 138–290（153 aa） Chain M 138–290（153 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
7U0I Structure of LIN28b nucleosome bound 2 OCT4 Deposited 2022-02-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric	Chain L 138–292（155 aa） Chain M 138–292（155 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8G88 Human Oct4 bound to nucleosome with human nMatn1 sequence Deposited 2023-02-17	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain X 1–360（360 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.30 Å
8G8B Nucleosome with human nMatn1 sequence in complex with Human Oct4 Deposited 2023-02-17	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain X 1–360（360 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
8G8E Human Oct4 bound to nucleosome with human LIN28B sequence Deposited 2023-02-17	Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain X 1–360（360 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8G8G Interaction of H3 tail in LIN28B nucleosome with Oct4 Deposited 2023-02-17	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain X 1–360（360 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8OTS OCT4 and MYC-MAX co-bound to a nucleosome Deposited 2023-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric	Chain K 1–273（273 aa）	Not recorded	PTD PENTANEDIAL × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8SPS High resolution structure of ESRRB nucleosome bound OCT4 at site a and site b Deposited 2023-05-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric	Chain L 138–290（153 aa） Chain M 138–290（153 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8SPU Structure of ESRRB nucleosome bound OCT4 at site c Deposited 2023-05-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric	Chain L 138–290（153 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9RL4 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2025-06-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric	Chain V 1–360（360 aa）	Not recorded	PTD PENTANEDIAL × 16 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9RMC Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1 Deposited 2025-06-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric	Chain V 1–360（360 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
9RN1 Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 bound to ATPase lobe 2 Deposited 2025-06-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric	Chain V 1–360（360 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.90 Å
9RN2 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2 Deposited 2025-06-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric	Chain V 1–360（360 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å

15 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PO5F1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain X； PDBConstruct 36–395； UniProt 1–360

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8g87
Deposition date deposition_date	2023-02-17
Structure title title	Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of Oct4 bound region)
Keywords keywords	Oct4, Nucleosome, Pioneer factor, nMatn1 DNA, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.33 Å
Radius of gyration Rg (electron density) rg_electron	20.07 Å
Forward intensity I(0) i0	18327500.00
Molecular weight molecular_weight	25903.0 kDa
Excluded volume excluded_volume	29612 Å³
Envelope volume envelope_volume	39686 Å³
Hydration-shell volume shell_volume	17138 Å³
Envelope diameter envelope_diameter	65.4 Å
Shell Rg shell_rg	25.48 Å
Envelope Rg envelope_rg	20.15 Å
Shape Rg shape_rg	20.06 Å
Total Rg total_rg	20.76 Å
Total atoms total_atoms	1777
Residues n_residues	166
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	65.0 Å
Rg (real space) rg_real	20.32 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	1.8330e+07
I(0) uncertainty (real space) i0_real_error	2.0660e+05
Rg (reciprocal space) rg_reciprocal	20.32 Å
I(0) (reciprocal space) i0_reciprocal	18330000.0000
Solution quality estimate total_estimate	0.9053
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.1 Å
Skewness Skewness skewness	0.282
Kurtosis Kurtosis kurtosis	-0.478
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2779000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.996

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	nMatn1 DNA (top strand)
Molecular weight formula_weight	56933.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I
Atom count atom_count	1777

ACATGCACACATGCTAATATATGCACACAATGCACACAGGTTAATATATACACATACACACACATGCACACACACGTGCACACATATATGCACATGCATGCACACACGTATATGCACACACATGCACATGCATGCGCACATAGTCACACACATGCACACATTAGCATATGCATACACATACATGCA

Entity 2 Entity 2 polymer

Description description	nMatn1 DNA (bottom strand)
Molecular weight formula_weight	57889.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

TGCATGTATGTGTATGCATATGCTAATGTGTGCATGTGTGTGACTATGTGCGCATGCATGTGCATGTGTGTGCATATACGTGTGTGCATGCATGTGCATATATGTGTGCACGTGTGTGTGCATGTGTGTGTATGTGTATATATTAACCTGTGTGCATTGTGTGCATATATTAGCATGTGTGCATGT

Entity 3 Entity 3 polymer

Description description	POU domain, class 5, transcription factor 1
Molecular weight formula_weight	42299.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRDPNSMAGHLASDFAFSPPPGGGGDGPGGPEPGWVDPRTWLSFQGPPGGPGIGPGVGPGSEVWGIPPCPPPYEFCGGMAYCGPQVGVGLVPQGGLETSQPEGEAGVGVESNSDGASPEPCTVTPGAVKLEKEKLEQNPEESQDIKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSFKNMCKLRPLLQKWVEEADNNENLQEICKAETLVQARKRKRTSIENRVRGNLENLFLQCPKPTLQQISHIAQQLGLEKDVVRVWFCNRRQKGKRSSSDYAQREDFEAAGSPFSGGPVSFPLAPGPHFGTPGYGSPHFTALYSSVPFPEGEAFPPVSVTTLGSPMHSN

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	8.10 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	18000

fit	/app/data/saxs_computation/g8/8g87/8g87.fit
pddf	/app/data/pr_computation/g8/8g87/8g87.pr.out
profile	/app/data/saxs_computation/g8/8g87/8g87.dat

Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of Oct4 bound region)

1. Protein Identity and Related Structures Protein Identity & Related Structures

POU domain, class 5, transcription factor 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)