7mns

Crystal Structure of the ZnF4 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP

Method: X-RAY DIFFRACTION Dmax: 66.7 Å Quality: GOOD

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

GTP-binding nuclear protein Ran

Homo sapiens

UniProt P62826

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 1–216 Mutation:F35S E3 SUMO-protein ligase RanBP2 × 1 (P49792) GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;294 K;18 % (w/v) PEG 3,350; 0.1M Bis-Tris Resolution 2.10 Å R-free 0.203

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.

137 other PDB entries and 203 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAN_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 21–236; UniProt 1–216

E3 SUMO-protein ligase RanBP2

Homo sapiens

UniProt P49792

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 B; UniProt 1535–1571 Not recorded GTP-binding nuclear protein Ran × 1 (P62826) GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;294 K;18 % (w/v) PEG 3,350; 0.1M Bis-Tris Resolution 2.10 Å R-free 0.203

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.

31 other PDB entries and 68 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RBP2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 7–43; UniProt 1535–1571

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 7mns

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7mns
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7mns
Deposition date deposition_date2021-05-01
Structure title titleCrystal Structure of the ZnF4 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP
Keywords keywordsNUCLEAR PORE COMPLEX COMPONENT, NUCLEOCYTOPLASMIC TRANSPORT, TRANSPORT PROTEIN, ZINC FINGER; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier18.97
Radius of gyration Rg (electron density) rg_electron17.71
Forward intensity I(0) i013889200.00
Molecular weight molecular_weight27667.0 kDa
Excluded volume excluded_volume34534 ų
Envelope volume envelope_volume39504 ų
Hydration-shell volume shell_volume18534 ų
Envelope diameter envelope_diameter62.2
Shell Rg shell_rg24.25
Envelope Rg envelope_rg18.09
Shape Rg shape_rg17.68
Total Rg total_rg18.80
Total atoms total_atoms3850
Residues n_residues240
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax66.7
Rg (real space) rg_real18.88
Rg uncertainty (real space) rg_real_error0.45
I(0) (real space) i0_real1.3890e+07
I(0) uncertainty (real space) i0_real_error1.8490e+05
Rg (reciprocal space) rg_reciprocal18.90
I(0) (reciprocal space) i0_reciprocal13890000.0000
Solution quality estimate total_estimate0.7768
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.1
Skewness Skewness skewness0.223
Kurtosis Kurtosis kurtosis-0.254
Angular range angular_range— – 0.4200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2853000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.701; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)