6a3e

MVM NES mutant Nm15 in complex with CRM1-Ran-RanBP1

Method: X-RAY DIFFRACTION Dmax: 109.7 Å Quality: EXCELLENT

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–216 Mutation:Y197A Ran-specific GTPase-activating protein 1 × 1 (P41920) Exportin-1 × 1 (P30822) MVM NES mutant Nm15 × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;18% PEG3350, 200mM Ammonium Nitrate, 100mM Bis-Tris pH6.6 Resolution 2.70 Å R-free 0.241

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 20–235; 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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 62–201 Not recorded GTP-binding nuclear protein Ran × 1 (P62826) Exportin-1 × 1 (P30822) MVM NES mutant Nm15 × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;18% PEG3350, 200mM Ammonium Nitrate, 100mM Bis-Tris pH6.6 Resolution 2.70 Å R-free 0.241

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 4–143; UniProt 62–201

Exportin-1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 1–1058 Mutation:D537G, T539C, V540E, K541Q, Y1022C, 377-413 deletion, 441-461 deletion GTP-binding nuclear protein Ran × 1 (P62826) Ran-specific GTPase-activating protein 1 × 1 (P41920) MVM NES mutant Nm15 × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;18% PEG3350, 200mM Ammonium Nitrate, 100mM Bis-Tris pH6.6 Resolution 2.70 Å R-free 0.241

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 4–1003; UniProt 1–1058

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 6a3e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6a3e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6a3e
Deposition date deposition_date2018-06-15
Structure title titleMVM NES mutant Nm15 in complex with CRM1-Ran-RanBP1
Keywords keywordstransport protein, nuclear export, complex, mutant, inhibitor; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier36.57
Radius of gyration Rg (electron density) rg_electron35.71
Forward intensity I(0) i0347885000.00
Molecular weight molecular_weight155510.0 kDa
Excluded volume excluded_volume196570 ų
Envelope volume envelope_volume259420 ų
Hydration-shell volume shell_volume58396 ų
Envelope diameter envelope_diameter122.9
Shell Rg shell_rg44.07
Envelope Rg envelope_rg35.01
Shape Rg shape_rg35.71
Total Rg total_rg36.27
Total atoms total_atoms10946
Residues n_residues1353
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 dmax109.7
Rg (real space) rg_real36.31
Rg uncertainty (real space) rg_real_error0.58
I(0) (real space) i0_real3.4790e+08
I(0) uncertainty (real space) i0_real_error4.6210e+06
Rg (reciprocal space) rg_reciprocal36.47
I(0) (reciprocal space) i0_reciprocal347900000.0000
Solution quality estimate total_estimate0.9071
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary48.5
Skewness Skewness skewness0.032
Kurtosis Kurtosis kurtosis-0.600
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha43590000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.937

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6a3ea_
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_idd6a3eb_
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_id6a3eA00
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_id6a3eB00
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)