8off

Structure of BARD1 ARD-BRCTs in complex with H2AKc15ub nucleosomes (Map1)

Method: ELECTRON MICROSCOPY

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

Histone H3.1

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	DNA (142-MER) × 2 Histone H2B type 1-C/E/F/G/I × 2 （P62807） Histone H2A type 1 × 2 （P0C0S8） Histone H4 × 2 （P62805） BRCA1 associated RING domain 1 × 2 （M3WD26） Ubiquitin × 1 （P0CG48）	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	2
Chains and sequence ranges	Author chain Ca； PDBConstruct 1–135； UniProt 1–135 Author chain Cb； PDBConstruct 1–135； UniProt 1–135

Histone H2B type 1-C/E/F/G/I

Homo sapiens

UniProt P62807

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	DNA (142-MER) × 2 Histone H3.1 × 2 （P68431） Histone H2A type 1 × 2 （P0C0S8） Histone H4 × 2 （P62805） BRCA1 associated RING domain 1 × 2 （M3WD26） Ubiquitin × 1 （P0CG48）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B1C_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain Ba； PDBConstruct 1–126； UniProt 1–126 Author chain Bb； PDBConstruct 1–126； UniProt 1–126

Histone H2A type 1

Homo sapiens

UniProt P0C0S8

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	DNA (142-MER) × 2 Histone H3.1 × 2 （P68431） Histone H2B type 1-C/E/F/G/I × 2 （P62807） Histone H4 × 2 （P62805） BRCA1 associated RING domain 1 × 2 （M3WD26） Ubiquitin × 1 （P0CG48）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain Aa； PDBConstruct 1–130； UniProt 1–130 Author chain Ab； PDBConstruct 1–130； UniProt 1–130

Histone H4

Homo sapiens

UniProt P62805

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	DNA (142-MER) × 2 Histone H3.1 × 2 （P68431） Histone H2B type 1-C/E/F/G/I × 2 （P62807） Histone H2A type 1 × 2 （P0C0S8） BRCA1 associated RING domain 1 × 2 （M3WD26） Ubiquitin × 1 （P0CG48）	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 Da； PDBConstruct 1–103； UniProt 1–103 Author chain Db； PDBConstruct 1–103； UniProt 1–103

BRCA1 associated RING domain 1

Felis catus

UniProt M3WD26

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	DNA (142-MER) × 2 Histone H3.1 × 2 （P68431） Histone H2B type 1-C/E/F/G/I × 2 （P62807） Histone H2A type 1 × 2 （P0C0S8） Histone H4 × 2 （P62805） Ubiquitin × 1 （P0CG48）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	M3WD26_FELCA
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain Ea； PDBConstruct 1–773； UniProt 1–773 Author chain Eb； PDBConstruct 1–773； UniProt 1–773

Ubiquitin

Homo sapiens

UniProt P0CG48

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	DNA (142-MER) × 2 Histone H3.1 × 2 （P68431） Histone H2B type 1-C/E/F/G/I × 2 （P62807） Histone H2A type 1 × 2 （P0C0S8） Histone H4 × 2 （P62805） BRCA1 associated RING domain 1 × 2 （M3WD26）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain Fa； PDBConstruct 1–76； UniProt 1–76

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	8off
Deposition date deposition_date	2023-03-15
Structure title title	Structure of BARD1 ARD-BRCTs in complex with H2AKc15ub nucleosomes (Map1)
Keywords keywords	BRCA1-BARD1, chromatin recognition, nucleosomes, ubiquitin, DNA BINDING PROTEIN; DNA BINDING 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.

8off__assembly_1__model_1

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

Download this curve (.dat)

8off__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8off__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.16 Å
Rg (electron density)	40.69 Å
Total Rg	41.32 Å
Atom count	14422
Residues	1435
Excluded volume	237540 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8off__assembly_1__model_1`	13-meric （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 (7)

Entity 1 Entity 1 polymer

Description description	DNA (142-MER)
Molecular weight formula_weight	108097.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J,I
Atom count atom_count	14424

AATACGCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCGCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCAATGTGTTCCATATGGAACACATTGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGCGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGCGGCCGCGTATT

Source Source

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

Entity 2 Entity 2 polymer

Description description	Histone H3.1
Molecular weight formula_weight	15366.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Ca,Cb

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER

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 H2B type 1-C/E/F/G/I
Molecular weight formula_weight	13937.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Ba,Bb

MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

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	Histone H2A type 1
Molecular weight formula_weight	14121.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Aa,Ab

MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESHHKAKGK

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 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	Da,Db

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

Entity 6 Entity 6 polymer

Description description	BRCA1 associated RING domain 1
Molecular weight formula_weight	85897.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Ea,Eb

MPGNRQLRVRSGNEPRPAPAMEPEGRGAWAHSRAAFDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDVKINRQLDSMIQLCSKLRNLLHDNKLSDLKEDTSRQNVFNDAENKKNSIKMWFSPRSKKVRYVVTKVSVQTQPQVIDDGNAQQASVYKFVSTSPPTSVPERAKKASTRSRKKQKKKTLAEINQEWNFEAEKEDGEPDSKEEFKEKLVSFCSQPSVIASPQTNGGIDLLASDSVTESECSRSLTEVSLPLAEQIESPETGSRNEDATPEKNACVDHLTSKQPLPSGHNGRPGRRSRRSSPVSKRCRSSIPGTSGQQMLLSENKPLPGCSSPPPSKRKVGDTLRRKNSNISDESMSLSPGTPPSTLNSPSYRRMMFSPSAVKLSPGSLTAVKRNHRGETLLHIASIKGDLPSVEYLLQNGSDPNVKDHAGWTPLHEACNHGHLKVVELLLQHKALVNSTGYQNDSPLHDAAKNGHMDIVKLLLSYGASRNAVNIFGLRPVDYADGENMKSLLLLPEQNESSSTRHCSVTNTGQRRDGPLVLIGSGLSSEQQKMLSELAVILKAKKCAEFDSTVTHVIVPGDTVQSTLKCMLGILNGCWILKFEWVKACLQRKACEQEEKYEIPEGPQRSRLNKEQLLPKLFDGCYFYFGGAFKHHPKDNLVKLVTAAGGQVLSRKPKPDSDVTQTINTVAYHAKADSDQRFCTQYIIYEDLSNHRPERVRQGKVWMAPSSWFIDCVMSFELLPLDS

Source Source

Source organism organism	Felis catus
Common name common_name	domestic cat
NCBI taxonomy ID ncbi_taxonomy_id	9685
Host organism host_organism	Trichoplusia ni

Entity 7 Entity 7 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8576.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Fa

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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	3.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	359954

Structure of BARD1 ARD-BRCTs in complex with H2AKc15ub nucleosomes (Map1)

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

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 H2B type 1-C/E/F/G/I

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

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

BRCA1 associated RING domain 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

Ubiquitin

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

8off__assembly_1__model_1

8off__assembly_1__model_1 | I(q)

8off__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 (7)

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