4hax

Crystal structure of CRM1 inhibitor Ratjadone A in complex with CRM1(K579A)-Ran-RanBP1

Method: X-RAY DIFFRACTION Dmax: 111.1 Å Quality: EXCELLENT

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

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 1–376 Chain C; UniProt 414–1058 Fragment:SEE REMARK 999 Mutation:T539C,K579A,Y1022C GTP-binding nuclear protein Ran × 1 (P62826) Ran-specific GTPase-activating protein 1 × 1 (P41920) RJA Ratjadone A, bound form × 1 GOL GLYCEROL × 3 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 3 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.6;293 K;18% PEG3350, 200 mM ammonium nitrate, 100 mM Bis-Tris, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.28 Å R-free 0.216

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 1
Chains and sequence ranges Author chain C; PDBConstruct 3–378; UniProt 1–376 Author chain C; PDBConstruct 379–1023; UniProt 414–1058

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–216 Not recorded Exportin-1 × 1 (P30822) Ran-specific GTPase-activating protein 1 × 1 (P41920) RJA Ratjadone A, bound form × 1 GOL GLYCEROL × 3 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 3 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.6;293 K;18% PEG3350, 200 mM ammonium nitrate, 100 mM Bis-Tris, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.28 Å R-free 0.216

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 2
Chains and sequence ranges Author chain A; PDBConstruct 1–216; UniProt 1–216

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 62–201 Fragment:RanDB1 (UNP residues 62-201) Exportin-1 × 1 (P30822) GTP-binding nuclear protein Ran × 1 (P62826) RJA Ratjadone A, bound form × 1 GOL GLYCEROL × 3 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 3 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.6;293 K;18% PEG3350, 200 mM ammonium nitrate, 100 mM Bis-Tris, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.28 Å R-free 0.216

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 3
Chains and sequence ranges Author chain B; PDBConstruct 1–140; UniProt 62–201

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 4hax

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4hax
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4hax
Deposition date deposition_date2012-09-27
Structure title titleCrystal structure of CRM1 inhibitor Ratjadone A in complex with CRM1(K579A)-Ran-RanBP1
Keywords keywordsHEAT repeat, nuclear export, Ran-RanBP1, Ratjadone A, PROTEIN TRANSPORT-ANTIBIOTIC complex; PROTEIN TRANSPORT/ANTIBIOTIC
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier36.17
Radius of gyration Rg (electron density) rg_electron35.39
Forward intensity I(0) i0349142000.00
Molecular weight molecular_weight156280.0 kDa
Excluded volume excluded_volume197740 ų
Envelope volume envelope_volume256530 ų
Hydration-shell volume shell_volume58151 ų
Envelope diameter envelope_diameter125.1
Shell Rg shell_rg43.87
Envelope Rg envelope_rg34.81
Shape Rg shape_rg35.39
Total Rg total_rg35.98
Total atoms total_atoms10995
Residues n_residues1347
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 dmax111.1
Rg (real space) rg_real35.92
Rg uncertainty (real space) rg_real_error0.61
I(0) (real space) i0_real3.4910e+08
I(0) uncertainty (real space) i0_real_error5.7380e+06
Rg (reciprocal space) rg_reciprocal36.08
I(0) (reciprocal space) i0_reciprocal349200000.0000
Solution quality estimate total_estimate0.9053
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary48.0
Skewness Skewness skewness0.046
Kurtosis Kurtosis kurtosis-0.594
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha51170000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.974

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (10)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4haxa_
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
Domain ID domain_idd4haxb_
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_id4haxA00
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_id4haxB00
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)