SAXSdb — 3eu7

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

Partner and localizer of BRCA2

Homo sapiens

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 835–1186	Fragment：C-terminal WD40 Domain, residues 835-1186 Non-standard monomer：Yes (specific site not provided by mmCIF)	19meric peptide from Breast cancer type 2 susceptibility protein × 1 （P51587） GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M Na-Cacodylate pH 6.5, 0.2M magnesium acetate, 10% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.253

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 3EU7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2W18 Crystal structure of the C-terminal WD40 domain of human PALB2 Deposited 2008-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 835–1186（352 aa） Fragment：WD40 DOMAIN, RESIDUES 835-1186	Not recorded	GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；100 MM MES PH 6.0, 50 MM KH2PO4, 12-20% (W/V) PEG 8000	Resolution 1.90 Å R-free 0.246
7S4A MRG15 complex with PALB2 peptide Deposited 2021-09-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 597–630（34 aa） Fragment：UNP residues 597-630	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；Ammonium sulfate, Tris HCl	Resolution 2.69 Å R-free 0.297
7S4A MRG15 complex with PALB2 peptide Deposited 2021-09-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 597–630（34 aa） Fragment：UNP residues 597-630	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；Ammonium sulfate, Tris HCl	Resolution 2.69 Å R-free 0.297
8YAP Structure of human PALB2 coiled-coil domain Deposited 2024-02-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 6–41（36 aa） Fragment：coiled-coil domain Chain B 6–41（36 aa） Fragment：coiled-coil domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 8；298 K；Ionic strength (raw mmCIF value) 300；Pressure 1 NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] Palb2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PALB2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–356； UniProt 835–1186

19meric peptide from Breast cancer type 2 susceptibility protein

OrganismNot specified

UniProt P51587

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain X； UniProt 21–39	Fragment：Interaction with PALB2, residues 21-39	Partner and localizer of BRCA2 × 1 （Q86YC2） GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M Na-Cacodylate pH 6.5, 0.2M magnesium acetate, 10% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.253

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 3EU7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1N0W Crystal structure of a RAD51-BRCA2 BRC repeat complex Deposited 2002-10-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1517–1551（35 aa） Fragment：BRC repeat type 4	Not recorded	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；ETHYLENE GLYCOL, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.206
7BDX Armadillo domain of HSF2BP in complex with BRCA2 peptide Deposited 2020-12-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 2291–2343（53 aa） Chain F 2291–2343（53 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；PEG 3350 : 16% (w/v) Mes ph 6.0 100 mM MgCl2 100 mM	Resolution 2.60 Å R-free 0.241
7LDG Crystal structure of the MEILB2-BRCA2 complex Deposited 2021-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 2271–2335（65 aa） Fragment：MEILB2-binding domain (aa2271-2335) Chain D 2271–2335（65 aa） Fragment：MEILB2-binding domain (aa2271-2335)	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；289 K；0.1 M sodium acetate (pH 4.6), 2 M lithium acetate	Resolution 2.56 Å R-free 0.231
8BR9 Stapled peptide SP24 in complex with humanised RadA mutant HumRadA22 Deposited 2022-11-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1226–1263（38 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 RF6 4,6-diethylpyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M Na 3 Cit 4.2 pH (Buffer) 20 %w/v PEG 1K (Precipitant) 0.2 M Li 2 SO4 (Salt)	Resolution 1.63 Å R-free 0.282
8C3J Stapled peptide SP2 in complex with humanised RadA mutant HumRadA22 Deposited 2022-12-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1226–1244（19 aa） Chain C 2050–2064（15 aa）	Not recorded	TKI 2-[(4,6-diethyl-1,3,5-triazin-2-yl)-methyl-amino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein in 20 mM CHES pH 9.5, 100 mM NaCl. Condition: 8 % w/v PEG 8000 (precipitant) 0.08 M Potassium phosphate pH 5.6 (buffer) 200:200 uL drop	Resolution 3.02 Å R-free 0.281
8C3J Stapled peptide SP2 in complex with humanised RadA mutant HumRadA22 Deposited 2022-12-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 1226–1244（19 aa） Chain J 2050–2064（15 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein in 20 mM CHES pH 9.5, 100 mM NaCl. Condition: 8 % w/v PEG 8000 (precipitant) 0.08 M Potassium phosphate pH 5.6 (buffer) 200:200 uL drop	Resolution 3.02 Å R-free 0.281
8C3N Stapled peptide SP30 in complex with humanised RadA mutant HumRadA22 Deposited 2022-12-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1215–1243（29 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 RF6 4,6-diethylpyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein: 0.5 mM SP30:HumRadA22 in 20 mM CHES pH 9.5, 100 mM NaCl, 20 mM ADP/MgCl 2 Condition: 14% w/v PEG 4000 (precipitant), 6% v/v MPD (precipitant), 0.1M Na K Phos pH 6.2 (buffer)	Resolution 1.21 Å R-free 0.218
8PBC RAD51 filament on ssDNA bound by the BRCA2 c-terminus Deposited 2023-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 22-meric	Chain L 3260–3308（49 aa） Chain M 3260–3308（49 aa） Chain N 3260–3308（49 aa） Chain O 3260–3308（49 aa） Chain P 3260–3308（49 aa） Chain Q 3260–3308（49 aa） Chain R 3260–3308（49 aa） Chain S 3260–3308（49 aa） Chain T 3260–3308（49 aa） Chain U 3260–3308（49 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 11 CA CALCIUM ION × 22	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.61 Å
8PBD RAD51 filament on dsDNA bound by the BRCA2 c-terminus Deposited 2023-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric	Chain K 3260–3308（49 aa） Chain L 3260–3308（49 aa） Chain M 3260–3308（49 aa） Chain N 3260–3308（49 aa） Chain O 3260–3308（49 aa） Chain P 3260–3308（49 aa） Chain Q 3260–3308（49 aa） Chain R 3260–3308（49 aa） Chain S 3260–3308（49 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 10 CA CALCIUM ION × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å
8QQE Crystal structure of the complex between DMC1 and the PhePP domain of BRCA2 Deposited 2023-10-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain C 2398–2417（20 aa） Chain D 2398–2417（20 aa）	Not recorded	MG MAGNESIUM ION × 4 CL CHLORIDE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；0.1M MES at pH 6, 2.4 M sodium formate	Resolution 3.46 Å R-free 0.261
8R2G Crystal structure of a BRCA2-DMC1 complex Deposited 2023-11-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain I 2400–2413（14 aa） Chain J 2400–2413（14 aa） Chain K 2400–2413（14 aa） Chain L 2400–2413（14 aa） Chain M 2400–2413（14 aa） Chain N 2400–2413（14 aa） Chain O 2400–2413（14 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM HEPES-NaOH pH 7.4, 50 mM MgCl2, 500 mM NaCl, 8 % PEG 3350, 20 % glycerol	Resolution 3.45 Å R-free 0.306
8UVW Crystal structure of RAD51-BRCA2 Cter complex Deposited 2023-11-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1517–1547（31 aa） Chain D 3270–3305（36 aa）	Mutation：C319S Mutation：S208E,A209D,C3287A,C3304A,C391S	ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% v/v 1,4-Dioxane 0.05 M MOPS pH 7.0 0.005 M Magnesium chloride hexahydrate 0.001 M Spermine	Resolution 2.73 Å R-free 0.282

11 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BRCA2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain X； PDBConstruct 1–19； UniProt 21–39

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	3eu7
Deposition date deposition_date	2008-10-09
Structure title title	Crystal Structure of a PALB2 / BRCA2 complex
Keywords keywords	;WD40 domain, Beta Propeller, Protein-Peptide Complex, Fanconi anemia, Nucleus, Phosphoprotein, WD repeat, Disease mutation, DNA damage, DNA repair, Transcription-antitumor Protein COMPLEX ;; Transcription/antitumor 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	20.88 Å
Radius of gyration Rg (electron density) rg_electron	19.74 Å
Forward intensity I(0) i0	19521600.00
Molecular weight molecular_weight	35302.0 kDa
Excluded volume excluded_volume	44825 Å³
Envelope volume envelope_volume	51403 Å³
Hydration-shell volume shell_volume	21442 Å³
Envelope diameter envelope_diameter	66.7 Å
Shell Rg shell_rg	26.56 Å
Envelope Rg envelope_rg	19.69 Å
Shape Rg shape_rg	19.73 Å
Total Rg total_rg	20.68 Å
Total atoms total_atoms	2481
Residues n_residues	326
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	64.8 Å
Rg (real space) rg_real	20.74 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	1.9520e+07
I(0) uncertainty (real space) i0_real_error	2.2170e+05
Rg (reciprocal space) rg_reciprocal	20.77 Å
I(0) (reciprocal space) i0_reciprocal	19520000.0000
Solution quality estimate total_estimate	0.8263
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.2 Å
Skewness Skewness skewness	0.105
Kurtosis Kurtosis kurtosis	-0.503
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4402000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Partner and localizer of BRCA2
Molecular weight formula_weight	39195.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2585

GPHMSVEQTETAELPASDSINPGNLQLVSELKNPSGSCSVDVSAMFWERAGCKEPCIITACEDVVSLWKALDAWQWEKLYTWHFAEVPVLQIVPVPDVYNLVCVALGNLEIREIRALFCSSDDESEKQVLLKSGNIKAVLGLTKRRLVSSSGTLSDQQVEVMTFAEDGGGKENQFLMPPEETILTFAEVQGMQEALLGTTIMNNIVIWNLKTGQLLKKMHIDDSYQASVCHKAYSEMGLLFIVLSHPCAKESESLRSPVFQLIVINPKTTLSVGVMLYCLPPGQAGRFLEGDVKDHCAAAILTSGTIAIWDLLLGQCTALLPPVSDQHWSFVKWSGTDSHLLAGQKDGNIFVYHYS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	19meric peptide from Breast cancer type 2 susceptibility protein
Molecular weight formula_weight	2107.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

KADLGPISLNWFEELSSEA

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	98

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3eu7A00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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8. Citations (1)

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Unit-cell length a length_a	82.815 Å
Unit-cell length b length_b	62.026 Å
Unit-cell length c length_c	77.975 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.23 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	37.495 Å
R factor r_factor	0.1999
R_work r_work	0.1971
R_free r_free	0.2526

fit	/app/data/saxs_computation/eu/3eu7/3eu7.fit
pddf	/app/data/pr_computation/eu/3eu7/3eu7.pr.out
profile	/app/data/saxs_computation/eu/3eu7/3eu7.dat

Crystal Structure of a PALB2 / BRCA2 complex

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

Partner and localizer of BRCA2

State in the Current Structure

Other States of the Same Protein in the Database

19meric peptide from Breast cancer type 2 susceptibility protein

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)