SAXSdb — 6gvw

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

BRCA1-A complex subunit Abraxas 1

Mus musculus

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 heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 1–407 Chain F； UniProt 1–407	Not recorded	Lys-63-specific deubiquitinase BRCC36 × 2 （P46737） BRISC and BRCA1-A complex member 2 × 2 （Q8K3W0） BRISC and BRCA1-A complex member 1 × 2 （Q3UI43） BRCA1-A complex subunit RAP80 × 2 （Q5U5Q9） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；292 K；100 mM MES-KOH pH 5.6, 200 mM MgCl2, 8% (w/v) PEG6000	Resolution 3.75 Å R-free 0.259

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	ABRX1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–411； UniProt 1–407 Author chain F； PDBConstruct 5–411； UniProt 1–407

Lys-63-specific deubiquitinase BRCC36

Mus musculus

UniProt P46737

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 heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain B； UniProt 1–291 Chain G； UniProt 1–291	Not recorded	BRCA1-A complex subunit Abraxas 1 × 2 （Q8BPZ8） BRISC and BRCA1-A complex member 2 × 2 （Q8K3W0） BRISC and BRCA1-A complex member 1 × 2 （Q3UI43） BRCA1-A complex subunit RAP80 × 2 （Q5U5Q9） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；292 K；100 mM MES-KOH pH 5.6, 200 mM MgCl2, 8% (w/v) PEG6000	Resolution 3.75 Å R-free 0.259

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	BRCC3_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–295； UniProt 1–291 Author chain G； PDBConstruct 5–295； UniProt 1–291

BRISC and BRCA1-A complex member 2

Mus musculus

UniProt Q8K3W0

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 heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain C； UniProt 1–383 Chain H； UniProt 1–383	Not recorded	BRCA1-A complex subunit Abraxas 1 × 2 （Q8BPZ8） Lys-63-specific deubiquitinase BRCC36 × 2 （P46737） BRISC and BRCA1-A complex member 1 × 2 （Q3UI43） BRCA1-A complex subunit RAP80 × 2 （Q5U5Q9） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；292 K；100 mM MES-KOH pH 5.6, 200 mM MgCl2, 8% (w/v) PEG6000	Resolution 3.75 Å R-free 0.259

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	BABA2_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 5–387； UniProt 1–383 Author chain H； PDBConstruct 5–387； UniProt 1–383

BRISC and BRCA1-A complex member 1

Mus musculus

UniProt Q3UI43

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 heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain D； UniProt 1–333 Chain I； UniProt 1–333	Not recorded	BRCA1-A complex subunit Abraxas 1 × 2 （Q8BPZ8） Lys-63-specific deubiquitinase BRCC36 × 2 （P46737） BRISC and BRCA1-A complex member 2 × 2 （Q8K3W0） BRCA1-A complex subunit RAP80 × 2 （Q5U5Q9） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；292 K；100 mM MES-KOH pH 5.6, 200 mM MgCl2, 8% (w/v) PEG6000	Resolution 3.75 Å R-free 0.259

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	BABA1_MOUSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 5–337； UniProt 1–333 Author chain I； PDBConstruct 5–337； UniProt 1–333

BRCA1-A complex subunit RAP80

Mus musculus

UniProt Q5U5Q9

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 heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain E； UniProt 275–334 Chain J； UniProt 275–334	Not recorded	BRCA1-A complex subunit Abraxas 1 × 2 （Q8BPZ8） Lys-63-specific deubiquitinase BRCC36 × 2 （P46737） BRISC and BRCA1-A complex member 2 × 2 （Q8K3W0） BRISC and BRCA1-A complex member 1 × 2 （Q3UI43） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；292 K；100 mM MES-KOH pH 5.6, 200 mM MgCl2, 8% (w/v) PEG6000	Resolution 3.75 Å R-free 0.259

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 6GVW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3A1Q Crystal structure of the mouse RAP80 UIMs in complex with Lys63-linked di-ubiquitin Deposited 2009-04-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 80–120（41 aa） Fragment：UNP residues 80-120	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100mM Tris-HCl(pH8.5), 32% PEG4000, 200mM sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.268
3A1Q Crystal structure of the mouse RAP80 UIMs in complex with Lys63-linked di-ubiquitin Deposited 2009-04-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 80–120（41 aa） Fragment：UNP residues 80-120	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100mM Tris-HCl(pH8.5), 32% PEG4000, 200mM sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.268

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UIMC1_MOUSE
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 5–64； UniProt 275–334 Author chain J； PDBConstruct 5–64； UniProt 275–334

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	6gvw
Deposition date deposition_date	2018-06-21
Structure title title	Crystal structure of the BRCA1-A complex
Keywords keywords	Deubiquitinase complex, DUB, Lysine-63 linkage specific, BRCC36-containing, BRCA1A binding, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	66.50 Å
Radius of gyration Rg (electron density) rg_electron	67.45 Å
Forward intensity I(0) i0	1146370000.00
Molecular weight molecular_weight	286410.0 kDa
Excluded volume excluded_volume	359030 Å³
Envelope volume envelope_volume	628760 Å³
Hydration-shell volume shell_volume	83009 Å³
Envelope diameter envelope_diameter	222.5 Å
Shell Rg shell_rg	63.47 Å
Envelope Rg envelope_rg	63.67 Å
Shape Rg shape_rg	67.48 Å
Total Rg total_rg	67.23 Å
Total atoms total_atoms	40104
Residues n_residues	2517
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	201.1 Å
Rg (real space) rg_real	67.22 Å
Rg uncertainty (real space) rg_real_error	1.87 Å
I(0) (real space) i0_real	1.1460e+09
I(0) uncertainty (real space) i0_real_error	2.2030e+07
Rg (reciprocal space) rg_reciprocal	65.76 Å
I(0) (reciprocal space) i0_reciprocal	1143000000.0000
Solution quality estimate total_estimate	0.8075
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	67.0 Å
Skewness Skewness skewness	0.344
Kurtosis Kurtosis kurtosis	-0.788
Angular range angular_range	— – 0.1200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	31270000.0000
Real-space data points n_real_points	25
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.835; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	BRCA1-A complex subunit Abraxas 1
Molecular weight formula_weight	46431.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F
Atom count atom_count	40106

GGGRMEGESTLGVLSGFVLGALTFHHLNTDSDTEGFLLGEMKGEAKNSITDSQMDNVKVVYTIDIQKYIPCYRLFSFYNSLGEVNEHALKKVLSNVRKTVVGWYKFRRHSDQIMTFREQLLHRNLQTHLSSPELVFLLLTPSITTESCSTHCLEHALYKPQRGLFHRVPLVVTNLGMSDQLGYKTEPASCTSTVFSRAVRTHSSQFFNEDGSLKEVHKINEMYAAVQEELKSICQKVEQSEREVEKLLMDVNQLKEVRRTQQARATGAGEKNVQRNPQENILLCQALRTFFPESEVLHSCVISLKNRHISPSGCNVNHHVDVVDQLTLMVEYVYSPEASPVPTAQLRKRKALDTHDQGSVKRPRLLETESRPSVAASRSRHQDKASSSSLDIDIEMGSPEDDADYPRSPTF

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	House mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Lys-63-specific deubiquitinase BRCC36
Molecular weight formula_weight	33711.4 kDa
EC 编号 ec_number	3.4.19.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GGGRMAVQVVQAVQAVHLESDAFLVCLNHALSTEKEEVMGLCIGELNDDIRSDSKFTYTGTEMRTVQEKMDTIRIVHIHSVIILRRSDKRKDRVEISPEQLSAASTEAERLAELTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVLYTCFQSIQAQKSSEYERIEIPIHIVPHITIGKVCLESAVELPKILCQEEQDAYRRIHSLTHLDSVTKIHNGSVFTKNLCSQMSAVSGPLLQWLEDRLEQNQQHLQELQQEKEELMEELSSLE

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	House mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	BRISC and BRCA1-A complex member 2
Molecular weight formula_weight	43915.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GGGRMSPEIALNRISPMLSPFISSVVRNGKVGLDATNCLRITDLKSGCTSLTPGPNCDRFKLHIPYAGETLKWDIIFNAQYPELPPDFIFGEDAEFLPDPSALHNLASWNPSNPECLLLVVKELVQQYHQFQCGRLRESSRLMFEYQTLLEEPQYGENMEIYAGKKNNWTGEFSARFLLKLPVDFSNIPTYLLKDVNEDPGEDVALLSVSFEDTEATQVYPKLYLSPRIEHALGGSSALHIPAFPGGGCLIDYVPQVCHLLTNKVQYVIQGYHKRREYIAAFLSHFGTGVVEYDAEGFTKLTLLLMWKDFCFLVHIDLPLFFPRDQPTLTFQSVYHFTNSGQLYSQAQKNYPYSPRWDGNEMAKRAKAYFKTFVPQFQEAAFANGKL

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	House mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Trichoplusia ni

Entity 4 Entity 4 polymer

Description description	BRISC and BRCA1-A complex member 1
Molecular weight formula_weight	37155.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GGGRMEVAEANSPTEEEEEEEEEGEETISEPRPHTRSNPEGAEDRALGAQASVGSRSEGEGEAATADGGAASVPGAGPKPWQVPASASEVQIRTPRVNCPEKVIICLDLSEEMSVPKLESFNGSRTNALNVSQKMVEMFVRTKHKIDKSHEFALVVVNDDSAWLSGLTSDPRELCSCLYDLETASCSTFNLEGLFSLIQQKTELPVTENVQTIPPPYVVRTILVYSRPPCQPQFSLTEPMKKMFQCPYFFFDIVYIHNGTEEKEEDMSWKDMFAFMGSLDTKGASYKYEVALAGPALELHNCMAKLLAHPLQRPCQTHASYSLLEEDEEAGEEEATV

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	House mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Trichoplusia ni

Entity 5 Entity 5 polymer

Description description	BRCA1-A complex subunit RAP80
Molecular weight formula_weight	7327.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GGGRHYYWGIPFCPAGVDPNQYTNVILCQLEVYQKSLKMAQRQLVKKRGFGEPVLPRPPFLIQN

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	House mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Trichoplusia ni

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6gvwB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	6gvwG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

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8. Citations (1)

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Unit-cell length a length_a	97.096 Å
Unit-cell length b length_b	122.645 Å
Unit-cell length c length_c	431.325 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.750 Å
Low-resolution limit resolution_low	29.990 Å
R factor r_factor	0.2290
R_work r_work	0.2273
R_free r_free	0.2591

fit	/app/data/saxs_computation/gv/6gvw/6gvw.fit
pddf	/app/data/pr_computation/gv/6gvw/6gvw.pr.out
profile	/app/data/saxs_computation/gv/6gvw/6gvw.dat

Crystal structure of the BRCA1-A complex

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

BRCA1-A complex subunit Abraxas 1

State in the Current Structure

Other States of the Same Protein in the Database

Lys-63-specific deubiquitinase BRCC36

State in the Current Structure

Other States of the Same Protein in the Database

BRISC and BRCA1-A complex member 2

State in the Current Structure

Other States of the Same Protein in the Database

BRISC and BRCA1-A complex member 1

State in the Current Structure

Other States of the Same Protein in the Database

BRCA1-A complex subunit RAP80

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)