2x19

Crystal structure of Importin13 - RanGTP complex

Method: X-RAY DIFFRACTION Dmax: 101.9 Å Quality: EXCELLENT

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

GTP-BINDING NUCLEAR PROTEIN GSP1/CNR1

SACCHAROMYCES CEREVISIAE

UniProt P32835

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 8–179 Fragment:RESIDUES 8-179 Mutation:YES IMPORTIN-13 × 1 (O94829) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6;100MM BIS-TRIS PH 6 23% 9W/V) PEG 3350 100MM NA-THIIOCYANATE RT Resolution 2.80 Å R-free 0.268

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.

11 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GSP1_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–172; UniProt 8–179

IMPORTIN-13

HOMO SAPIENS

UniProt O94829

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 1–963 Non-standard monomer:Yes (specific site not provided by mmCIF) GTP-BINDING NUCLEAR PROTEIN GSP1/CNR1 × 1 (P32835) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6;100MM BIS-TRIS PH 6 23% 9W/V) PEG 3350 100MM NA-THIIOCYANATE RT Resolution 2.80 Å R-free 0.268

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.

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

View Construct and Data Evidence
UniProt name IPO13_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–963; UniProt 1–963

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 2x19

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2x19
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2x19
Deposition date deposition_date2009-12-23
Structure title titleCrystal structure of Importin13 - RanGTP complex
Keywords keywordsNUCLEAR TRANSPORT, PROTEIN TRANSPORT; NUCLEAR TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier33.50
Radius of gyration Rg (electron density) rg_electron32.72
Forward intensity I(0) i0217254000.00
Molecular weight molecular_weight120030.0 kDa
Excluded volume excluded_volume150710 ų
Envelope volume envelope_volume197430 ų
Hydration-shell volume shell_volume49099 ų
Envelope diameter envelope_diameter102.4
Shell Rg shell_rg40.95
Envelope Rg envelope_rg31.89
Shape Rg shape_rg32.72
Total Rg total_rg33.40
Total atoms total_atoms8382
Residues n_residues1057
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 dmax101.9
Rg (real space) rg_real33.31
Rg uncertainty (real space) rg_real_error0.70
I(0) (real space) i0_real2.1730e+08
I(0) uncertainty (real space) i0_real_error3.2180e+06
Rg (reciprocal space) rg_reciprocal33.43
I(0) (reciprocal space) i0_reciprocal217300000.0000
Solution quality estimate total_estimate0.9089
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary45.5
Skewness Skewness skewness0.057
Kurtosis Kurtosis kurtosis-0.594
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha42020000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.970

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2x19a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins

CATH v4.4 (2 domains)

Domain ID domain_id2x19A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id2x19B00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant

8. Citations (1)

9. Files and Curves (10)