3m1i

Crystal structure of yeast CRM1 (Xpo1p) in complex with yeast RanBP1 (Yrb1p) and yeast RanGTP (Gsp1pGTP)

Method: X-RAY DIFFRACTION Dmax: 109.0 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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–219 Mutation:Q71L Ran-specific GTPase-activating protein 1 × 1 (P41920) Exportin-1 × 1 (P30822) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.6;293 K;0.1M Bis-Tris, 0.2M ammonium nitrate, 18% PEG3350, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.00 Å R-free 0.220

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 1–219; UniProt 1–219

Ran-specific GTPase-activating protein 1

Saccharomyces cerevisiae

UniProt P41920

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 11–201 Mutation:A deletion mutant (residues 1-10 deleted) GTP-binding nuclear protein GSP1/CNR1 × 1 (P32835) Exportin-1 × 1 (P30822) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.6;293 K;0.1M Bis-Tris, 0.2M ammonium nitrate, 18% PEG3350, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.00 Å R-free 0.220

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.

65 other PDB entries and 65 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name YRB1_YEAST
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–191; UniProt 11–201

Exportin-1

Saccharomyces cerevisiae

UniProt P30822

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 1–1084 Mutation:A deletion mutant (residues 377-413 deleted) GTP-binding nuclear protein GSP1/CNR1 × 1 (P32835) Ran-specific GTPase-activating protein 1 × 1 (P41920) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.6;293 K;0.1M Bis-Tris, 0.2M ammonium nitrate, 18% PEG3350, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.00 Å R-free 0.220

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.

69 other PDB entries and 73 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name XPO1_YEAST
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 3–1049; UniProt 1–1084

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 3m1i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3m1i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3m1i
Deposition date deposition_date2010-03-05
Structure title titleCrystal structure of yeast CRM1 (Xpo1p) in complex with yeast RanBP1 (Yrb1p) and yeast RanGTP (Gsp1pGTP)
Keywords keywordsHEAT REPEAT, EXPORTIN, GTP-binding, Nucleotide-binding, Nucleus, Protein transport, Transport, GTPase activation; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier36.05
Radius of gyration Rg (electron density) rg_electron35.22
Forward intensity I(0) i0341480000.00
Molecular weight molecular_weight154270.0 kDa
Excluded volume excluded_volume195050 ų
Envelope volume envelope_volume251370 ų
Hydration-shell volume shell_volume57390 ų
Envelope diameter envelope_diameter108.7
Shell Rg shell_rg43.70
Envelope Rg envelope_rg34.46
Shape Rg shape_rg35.22
Total Rg total_rg35.80
Total atoms total_atoms10865
Residues n_residues1354
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 dmax109.0
Rg (real space) rg_real35.80
Rg uncertainty (real space) rg_real_error0.58
I(0) (real space) i0_real3.4150e+08
I(0) uncertainty (real space) i0_real_error5.6300e+06
Rg (reciprocal space) rg_reciprocal35.96
I(0) (reciprocal space) i0_reciprocal341500000.0000
Solution quality estimate total_estimate0.9067
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.1
Skewness Skewness skewness0.034
Kurtosis Kurtosis kurtosis-0.613
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha45690000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.952

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3m1ib_
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id3m1iA00
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_id3m1iB00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

8. Citations (1)

9. Files and Curves (10)