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2w18

Crystal structure of the C-terminal WD40 domain of human PALB2

Method: X-RAY DIFFRACTION Dmax: 61.1 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PARTNER AND LOCALIZER OF BRCA2

HOMO SAPIENS

UniProt Q86YC2

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 835–1186 Fragment：WD40 DOMAIN, RESIDUES 835-1186 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

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 2W18 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 A 835–1186（352 aa） Fragment：C-terminal WD40 Domain, residues 835-1186
Non-standard monomer：Yes (specific site not provided by mmCIF) 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
7S4A MRG15 complex with PALB2 peptide Deposited 2021-09-08 Different construct 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 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 oligomeric state 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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2w18

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2w18
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2w18
Deposition date deposition_date2008-10-15
Structure title titleCrystal structure of the C-terminal WD40 domain of human PALB2
Keywords keywords;FANCONI ANEMIA, HOMOLOGOUS RECOMINATION, POLYMORPHISM, PHOSPHOPROTEIN, BETA-PROPELLER, WD40, FANC-N, NUCLEUS, WD REPEAT, COILED COIL, NUCLEAR PROTEIN ;; NUCLEAR PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.21 Å
Radius of gyration Rg (electron density) rg_electron19.10 Å
Forward intensity I(0) i017478100.00
Molecular weight molecular_weight33432.0 kDa
Excluded volume excluded_volume42495 ų
Envelope volume envelope_volume48389 ų
Hydration-shell volume shell_volume20734 ų
Envelope diameter envelope_diameter62.4 Å
Shell Rg shell_rg25.74 Å
Envelope Rg envelope_rg19.09 Å
Shape Rg shape_rg19.09 Å
Total Rg total_rg20.03 Å
Total atoms total_atoms2350
Residues n_residues306
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax61.1 Å
Rg (real space) rg_real20.07 Å
Rg uncertainty (real space) rg_real_error0.31 Å
I(0) (real space) i0_real1.7480e+07
I(0) uncertainty (real space) i0_real_error1.9480e+05
Rg (reciprocal space) rg_reciprocal20.09 Å
I(0) (reciprocal space) i0_reciprocal17480000.0000
Solution quality estimate total_estimate0.9072
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.2 Å
Skewness Skewness skewness0.066
Kurtosis Kurtosis kurtosis-0.543
Angular range angular_range— – 0.3950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4603000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.991
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2w18A00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
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8. Citations (1)

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9. Files and Curves (10)