8spu

Structure of ESRRB nucleosome bound OCT4 at site c

Method: ELECTRON MICROSCOPY

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

Maltodextrin-binding protein,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	Insufficient information	Heteromer	Protein 11 DNA 2	DNA (168-MER) × 1 DNA (168-MER) × 1 Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 2-C × 2 （Q16777） Histone H2B type 2-E × 2 （Q16778） ScFv × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A376KDN7_ECOLX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain L； PDBConstruct 4–365； UniProt 26–387

Maltodextrin-binding protein,POU domain, class 5, transcription factor 1

Homo sapiens

UniProt Q01860

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 11 DNA 2	DNA (168-MER) × 1 DNA (168-MER) × 1 Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 2-C × 2 （Q16777） Histone H2B type 2-E × 2 （Q16778） ScFv × 2	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 L； PDBConstruct 390–542； UniProt 138–290

Histone H3.1

Homo sapiens

UniProt P68431

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 11 DNA 2	DNA (168-MER) × 1 DNA (168-MER) × 1 Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 × 1 （A0A376KDN7,Q01860） Histone H4 × 2 （P62805） Histone H2A type 2-C × 2 （Q16777） Histone H2B type 2-E × 2 （Q16778） ScFv × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H31_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 1–136； UniProt 1–136 Author chain E； PDBConstruct 1–136； UniProt 1–136

Histone H4

Homo sapiens

UniProt P62805

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 11 DNA 2	DNA (168-MER) × 1 DNA (168-MER) × 1 Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 × 1 （A0A376KDN7,Q01860） Histone H3.1 × 2 （P68431） Histone H2A type 2-C × 2 （Q16777） Histone H2B type 2-E × 2 （Q16778） ScFv × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain B； PDBConstruct 1–103； UniProt 1–103 Author chain F； PDBConstruct 1–103； UniProt 1–103

Histone H2A type 2-C

Homo sapiens

UniProt Q16777

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 11 DNA 2	DNA (168-MER) × 1 DNA (168-MER) × 1 Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 × 1 （A0A376KDN7,Q01860） Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2B type 2-E × 2 （Q16778） ScFv × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A2C_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain C； PDBConstruct 1–129； UniProt 1–129 Author chain G； PDBConstruct 1–129； UniProt 1–129

Histone H2B type 2-E

Homo sapiens

UniProt Q16778

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 11 DNA 2	DNA (168-MER) × 1 DNA (168-MER) × 1 Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 × 1 （A0A376KDN7,Q01860） Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 2-C × 2 （Q16777） ScFv × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B2E_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain D； PDBConstruct 1–126； UniProt 1–126 Author chain H； PDBConstruct 1–126； UniProt 1–126

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	8spu
Deposition date deposition_date	2023-05-03
Structure title title	Structure of ESRRB nucleosome bound OCT4 at site c
Keywords keywords	nucleosome, transcription factor, transcription, CHROMATIN BINDING PROTEIN-DNA complex, GENE REGULATION, TRANSCRIPTION-DNA complex; TRANSCRIPTION/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.

8spu__assembly_1__model_1

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

Download this curve (.dat)

8spu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8spu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.17 Å
Rg (electron density)	40.38 Å
Total Rg	40.91 Å
Atom count	16181
Residues	1583
Excluded volume	268760 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8spu__assembly_1__model_1`	tridecameric （13）	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 (8)

Entity 1 Entity 1 polymer

Description description	DNA (168-MER)
Molecular weight formula_weight	51224.5 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	16181

GCGTGCTGATTCCCTCCATTCGCTCTGCATAACTATCACTTTCTGGAACTCCATGGTCTCCTAGGTCGCCAGGCCTTTGCTTTGCAGCTTAGAACAGACTCTCTATGCTCCCTCCACCCTCTGTTTCTCCAGGTCCCACATGGGGAGGCGCTCCTTCTCCCTGCTGAT

Entity 2 Entity 2 polymer

Description description	DNA (168-MER)
Molecular weight formula_weight	52499.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

ATCAGCAGGGAGAAGGAGCGCCTCCCCATGTGGGACCTGGAGAAACAGAGGGTGGAGGGAGCATAGAGAGTCTGTTCTAAGCTGCAAAGCAAAGGCCTGGCGACCTAGGAGACCATGGAGTTCCAGAAAGTGATAGTTATGCAGAGCGAATGGAGGGAATCAGCACGC

Entity 3 Entity 3 polymer

Description description	Maltodextrin-binding protein,POU domain, class 5, transcription factor 1
Molecular weight formula_weight	61285.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MKEAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAGSENLYFQGSVDSAAASDIKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSFKNMCKLRPLLQKWVEEADNNENLQEICKAETLVQARKRKRTSIENRVRGNLENLFLQCPKPTLQQISHIAQQLGLEKDVVRVWFCNRRQKGKRSSSEFHHHHHH

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 'BL21-Gold(DE3)pLysS AG' ;

Entity 4 Entity 4 polymer

Description description	Histone H3.1
Molecular weight formula_weight	15437.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,A

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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 'BL21-Gold(DE3)pLysS AG' ;

Entity 5 Entity 5 polymer

Description description	Histone H4
Molecular weight formula_weight	11394.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,B

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

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 'BL21-Gold(DE3)pLysS AG' ;

Entity 6 Entity 6 polymer

Description description	Histone H2A type 2-C
Molecular weight formula_weight	14017.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,C

MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESHKAKSK

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 'BL21-Gold(DE3)pLysS AG' ;

Entity 7 Entity 7 polymer

Description description	Histone H2B type 2-E
Molecular weight formula_weight	13951.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,D

MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

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 'BL21-Gold(DE3)pLysS AG' ;

Entity 8 Entity 8 polymer

Description description	ScFv
Molecular weight formula_weight	29030.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N,K

MKSSHHHHHHENLYFQSNAMEVQLQQSGPELVEPGTSVKMPCKASGYTFTSYTIQWVKQTPRQGLEWIGYIYPYNAGTKYNEKFKGKATLTSDKSSSTVYMELSSLTSEDSAVYYCARKSSRLRSTLDYWGQGTSVTVSSGGGGSGGGGSGGGGSMDIKMTQSPSSMHASLGERVTITCKASQDIRSYLSWYQQKPWKSPKTLIYYATSLADGVPSRFSGSGSGQDFSLTINNLESDDTATYYCLQHGESPYTFGSGTKLEIKRA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	8spuK01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8spuN01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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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	2.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	110991

Structure of ESRRB nucleosome bound OCT4 at site c

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

Maltodextrin-binding protein,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

Maltodextrin-binding protein,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

Histone H3.1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H2A type 2-C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H2B type 2-E

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

8spu__assembly_1__model_1

8spu__assembly_1__model_1 | I(q)

8spu__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 polymer