SAXSdb — 7ldg

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

Heat shock factor 2-binding protein

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 83–334 Chain C； UniProt 83–334	Fragment：aa83-334 Non-standard monomer：Yes (specific site not provided by mmCIF)	Breast cancer type 2 susceptibility protein × 4 （P51587）	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

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 7LDG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 A 122–334（213 aa） Chain B 122–334（213 aa） Chain C 122–334（213 aa） Chain D 122–334（213 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 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
8A50 Crystal structure of HSF2BP-ALPHA1 tetramer Deposited 2022-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 19–50（32 aa） Chain B 19–50（32 aa）	Not recorded	PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M LiCl 0.1 M sodium acetate trihydrate pH 5 20% PEG6000	Resolution 1.48 Å R-free 0.217
8A51 Crystal structure of HSF2BP-BRME1 complex Deposited 2022-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 19–50（32 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 6 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M HEPES sodium salt, pH 7.5, 40% PEG200	Resolution 1.90 Å R-free 0.243

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

View Construct and Data Evidence

UniProt name	HSF2B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–253； UniProt 83–334 Author chain C； PDBConstruct 2–253； UniProt 83–334

Breast cancer type 2 susceptibility protein

Homo sapiens

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain B； UniProt 2271–2335 Chain D； UniProt 2271–2335	Fragment：MEILB2-binding domain (aa2271-2335) Non-standard monomer：Yes (specific site not provided by mmCIF)	Heat shock factor 2-binding protein × 4 （O75031）	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

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 7LDG	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 mutation/modification 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
3EU7 Crystal Structure of a PALB2 / BRCA2 complex Deposited 2008-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 21–39（19 aa） Fragment：Interaction with PALB2, residues 21-39	Not recorded	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
7BDX Armadillo domain of HSF2BP in complex with BRCA2 peptide Deposited 2020-12-22	Different construct 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
8BR9 Stapled peptide SP24 in complex with humanised RadA mutant HumRadA22 Deposited 2022-11-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 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 oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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 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 B； PDBConstruct 2–66； UniProt 2271–2335 Author chain D； PDBConstruct 2–66； UniProt 2271–2335

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	7ldg
Deposition date deposition_date	2021-01-13
Structure title title	Crystal structure of the MEILB2-BRCA2 complex
Keywords keywords	Complex, Recruiter, Protein-protein interaction, Armadillo-repeat, RECOMBINATION; RECOMBINATION
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	28.94 Å
Radius of gyration Rg (electron density) rg_electron	28.44 Å
Forward intensity I(0) i0	47186000.00
Molecular weight molecular_weight	54781.0 kDa
Excluded volume excluded_volume	69129 Å³
Envelope volume envelope_volume	92290 Å³
Hydration-shell volume shell_volume	28301 Å³
Envelope diameter envelope_diameter	99.9 Å
Shell Rg shell_rg	34.12 Å
Envelope Rg envelope_rg	29.12 Å
Shape Rg shape_rg	28.49 Å
Total Rg total_rg	28.89 Å
Total atoms total_atoms	3806
Residues n_residues	479
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	95.6 Å
Rg (real space) rg_real	29.05 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	4.7190e+07
I(0) uncertainty (real space) i0_real_error	7.0870e+05
Rg (reciprocal space) rg_reciprocal	29.01 Å
I(0) (reciprocal space) i0_reciprocal	47180000.0000
Solution quality estimate total_estimate	0.8655
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.1 Å
Skewness Skewness skewness	0.399
Kurtosis Kurtosis kurtosis	-0.475
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14110000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.830; Smooth: 0.843

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Heat shock factor 2-binding protein
Molecular weight formula_weight	28304.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	3812

SARLETVQADNIREKKEKLALRQQLNEAKQQLLQQAEYCTEMGAAACTLLWGVSSSEEVVKAILGGDKALKFFSITGQTMESFVKSLDGDVQELDSDESQFVFALAGIVTNVAAIACGREFLVNSSRVLLDTILQLLGDLKPGQCTKLKVLMLMSLYNVSINLKGLKYISESPGFIPLLWWLLSDPDAEVCLHVLRLVQSVVLEPEVFSKSASEFRSSLPLQRILAMSKSRNPRLQTAAQELLEDLRTLEHNV

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Breast cancer type 2 susceptibility protein
Molecular weight formula_weight	7738.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MKRRGEPLILVGEPSIKRNLLNEFDRIIENQEKSLKASKSTPDGTIKDRRLFMHHVSLEPITCVPF

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	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	6

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7ldgA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	7ldgC01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

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8. Citations (1)

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Unit-cell length a length_a	179.889 Å
Unit-cell length b length_b	179.889 Å
Unit-cell length c length_c	179.186 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	trigonal

Resolution resolution	2.560 Å
Low-resolution limit resolution_low	31.100 Å
R factor r_factor	—
R_work r_work	0.2106
R_free r_free	0.2307

fit	/app/data/saxs_computation/ld/7ldg/7ldg.fit
pddf	/app/data/pr_computation/ld/7ldg/7ldg.pr.out
profile	/app/data/saxs_computation/ld/7ldg/7ldg.dat

Crystal structure of the MEILB2-BRCA2 complex

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

Heat shock factor 2-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 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)