SAXSdb — 8g8e

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	LIN28B DNA (32-MER) × 1 LIN28B DNA (32-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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	8g8e
Deposition date deposition_date	2023-02-17
Structure title title	Human Oct4 bound to nucleosome with human LIN28B sequence
Keywords keywords	Oct4, Nucleosome, LIN28B DNA, iPSC, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8g8e__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8g8e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8g8e__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	28.20 Å
Rg (electron density)	27.34 Å
Total Rg	27.82 Å
Atom count	2464
Residues	204
Excluded volume	39915 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8g8e__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	LIN28B DNA (32-MER)
Molecular weight formula_weight	56519.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J
Atom count atom_count	2464

GCATAAGTTAAGTGGTATTAACATATCCTCAGTGGTGAGTATTAACATGGAACTTACTCCAACAATACAGATGCTGAATAAATGTAGTCTAAGTGAAGAAAGAAGGAAAGGTGGGAGCTGCCATCACTCAGAATTGTCCAGCAGGGATTGTGCAAGCTTGTGAATAAAGACACATACTTCAT

Entity 2 Entity 2 polymer

Description description	LIN28B DNA (32-MER)
Molecular weight formula_weight	55827.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

ATGAAGTATGTGTCTTTATTCACAAGCTTGCACAATCCCTGCTGGACAATTCTGAGTGATGGCAGCTCCCACCTTTCCTTCTTTCTTCACTTAGACTACATTTATTCAGCATCTGTATTGTTGGAGTAAGTTCCATGTTAATACTCACCACTGAGGATATGTTAATACCACTTAACTTATGC

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

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

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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	3.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	65000

Human Oct4 bound to nucleosome with human LIN28B sequence

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8g8e__assembly_1__model_1

8g8e__assembly_1__model_1 | I(q)

8g8e__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. 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

Source Source

7. Citations (1)

Human Oct4 bound to nucleosome with human LIN28B sequence

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8g8e__assembly_1__model_1

8g8e__assembly_1__model_1 | I(q)

8g8e__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. 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

Source Source

7. Citations (1)