8grq

Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome

Method: ELECTRON MICROSCOPY

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

Histone H3

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 11 DNA 2	Histone H4 × 2 （A0A0P9AXL3） Histone H2A type 1-H × 2 （Q8CGP6） H2B × 2 DNA (147-MER) × 1 DNA (147-MER) × 1 Breast cancer type 1 susceptibility protein × 1 （P38398） BRCA1-associated RING domain protein 1 × 1 （Q99728） Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a × 1 ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A653DHJ5_CALMS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–98； UniProt 38–135 Author chain E； PDBConstruct 1–98； UniProt 38–135

Histone H4

Homo sapiens

UniProt A0A0P9AXL3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 11 DNA 2	Histone H3 × 2 （A0A653DHJ5） Histone H2A type 1-H × 2 （Q8CGP6） H2B × 2 DNA (147-MER) × 1 DNA (147-MER) × 1 Breast cancer type 1 susceptibility protein × 1 （P38398） BRCA1-associated RING domain protein 1 × 1 （Q99728） Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a × 1 ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0P9AXL3_DROAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–80； UniProt 5–84 Author chain F； PDBConstruct 1–80； UniProt 5–84

Histone H2A type 1-H

Homo sapiens

UniProt Q8CGP6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 11 DNA 2	Histone H3 × 2 （A0A653DHJ5） Histone H4 × 2 （A0A0P9AXL3） H2B × 2 DNA (147-MER) × 1 DNA (147-MER) × 1 Breast cancer type 1 susceptibility protein × 1 （P38398） BRCA1-associated RING domain protein 1 × 1 （Q99728） Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a × 1 ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1H_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–110； UniProt 11–120 Author chain G； PDBConstruct 1–110； UniProt 11–120

Breast cancer type 1 susceptibility protein

Homo sapiens

UniProt P38398

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 11 DNA 2	Histone H3 × 2 （A0A653DHJ5） Histone H4 × 2 （A0A0P9AXL3） Histone H2A type 1-H × 2 （Q8CGP6） H2B × 2 DNA (147-MER) × 1 DNA (147-MER) × 1 BRCA1-associated RING domain protein 1 × 1 （Q99728） Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a × 1 ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BRCA1_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain K； PDBConstruct 1–92； UniProt 6–97

BRCA1-associated RING domain protein 1

Homo sapiens

UniProt Q99728

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 11 DNA 2	Histone H3 × 2 （A0A653DHJ5） Histone H4 × 2 （A0A0P9AXL3） Histone H2A type 1-H × 2 （Q8CGP6） H2B × 2 DNA (147-MER) × 1 DNA (147-MER) × 1 Breast cancer type 1 susceptibility protein × 1 （P38398） Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a × 1 ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BARD1_HUMAN
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain M； PDBConstruct 1–92； UniProt 26–117

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	8grq
Deposition date deposition_date	2022-09-02
Structure title title	Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome
Keywords keywords	nucleosome, BRCA1/BARD1, BRCA1, BARD1, H2AK127, H2AK127-UbcH5c-Ub, NUCLEAR PROTEIN; NUCLEAR PROTEIN
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.

8grq__assembly_1__model_1

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

Download this curve (.dat)

8grq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8grq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.14 Å
Rg (electron density)	40.10 Å
Total Rg	40.66 Å
Atom count	14563
Residues	1378
Excluded volume	240550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8grq__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 (10)

Entity 1 Entity 1 polymer

Description description	Histone H3
Molecular weight formula_weight	11530.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	14563

KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLSAIHAKRVTIMPKDIQLARRIRGER

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

Entity 2 Entity 2 polymer

Description description	Histone H4
Molecular weight formula_weight	9123.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFG

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

Entity 3 Entity 3 polymer

Description description	Histone H2A type 1-H
Molecular weight formula_weight	12066.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

ARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK

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

Entity 4 Entity 4 polymer

Description description	H2B
Molecular weight formula_weight	20938.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSARSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	DNA (147-MER)
Molecular weight formula_weight	45604.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	DNA (147-MER)
Molecular weight formula_weight	45145.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGT

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	Breast cancer type 1 susceptibility protein
Molecular weight formula_weight	10626.7 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

LRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDT

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

Entity 8 Entity 8 polymer

Description description	BRCA1-associated RING domain protein 1
Molecular weight formula_weight	10348.1 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHD

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

Entity 9 Entity 9 polymer

Description description	Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a
Molecular weight formula_weight	16657.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MALKRINKELSDLARDPPAQSSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSISSLLSDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM

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

Entity 10 Entity 10 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id	8grqA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	8grqD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	8grqE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	8grqF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	8grqG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	8grqH01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	8grqN01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

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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	3.87 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	68006

Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome

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

Histone H3

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 1-H

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Breast cancer type 1 susceptibility protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

BRCA1-associated RING domain protein 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

8grq__assembly_1__model_1

8grq__assembly_1__model_1 | I(q)

8grq__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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

Polymer Polymer

Source Source

Entity 9 Entity 9 polymer

Polymer Polymer

Source Source

Entity 10 Entity 10 non-polymer