8itv

KL2.1 in complex with CRM1-Ran-RanBP1

Method: X-RAY DIFFRACTION Dmax: 109.4 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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–216 Mutation:Q69L, L182A YRB1 isoform 1 × 1 (A0A6A5PZB5) CRM1 isoform 1 × 1 (A0A6A5PZI8) MG MAGNESIUM ION × 1 NO3 NITRATE ION × 14 DMS DIMETHYL SULFOXIDE × 9 GOL GLYCEROL × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 1 Q73 (3~{S},5~{R},6~{E},8~{Z},10~{R},12~{E},14~{E},16~{S})-3,16-bis(azanyl)-8,10,12-trimethyl-16-[(2~{S},4~{R},5~{S},6~{S})-5-methyl-4-oxidanyl-6-[(~{E})-prop-1-enyl]oxan-2-yl]-5-oxidanyl-hexadeca-6,8,12,14-tetraenoic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;0.12 M Monosaccharides (20 mM D-Glucose; 20 mM D-Mannose; 20 mM D-Galactose; 20 mM L-Fucose; 20 mM D-Xylose; 20 mM N-Acetyl-D-Glucosamine), 0.1 M buffer system 1 pH 6.5 (sodium HEPES and MOPS), and 50 % Precipitant Mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000) Resolution 2.30 Å R-free 0.224

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 1–216; UniProt 1–216

YRB1 isoform 1

Saccharomyces cerevisiae

UniProt A0A6A5PZB5

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 Not recorded GTP-binding nuclear protein Ran × 1 (P62826) CRM1 isoform 1 × 1 (A0A6A5PZI8) MG MAGNESIUM ION × 1 NO3 NITRATE ION × 14 DMS DIMETHYL SULFOXIDE × 9 GOL GLYCEROL × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 1 Q73 (3~{S},5~{R},6~{E},8~{Z},10~{R},12~{E},14~{E},16~{S})-3,16-bis(azanyl)-8,10,12-trimethyl-16-[(2~{S},4~{R},5~{S},6~{S})-5-methyl-4-oxidanyl-6-[(~{E})-prop-1-enyl]oxan-2-yl]-5-oxidanyl-hexadeca-6,8,12,14-tetraenoic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;0.12 M Monosaccharides (20 mM D-Glucose; 20 mM D-Mannose; 20 mM D-Galactose; 20 mM L-Fucose; 20 mM D-Xylose; 20 mM N-Acetyl-D-Glucosamine), 0.1 M buffer system 1 pH 6.5 (sodium HEPES and MOPS), and 50 % Precipitant Mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000) Resolution 2.30 Å R-free 0.224

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.

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A6A5PZB5_YEASX
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–140; UniProt 62–201

CRM1 isoform 1

Saccharomyces cerevisiae

UniProt A0A6A5PZI8

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 1–1058 Mutation:S27E , Q49E, A51V, del377-413, del441-461, D537G, T539C, V540E, K541Q, S553R, Q561E, A741T, Y1022C GTP-binding nuclear protein Ran × 1 (P62826) YRB1 isoform 1 × 1 (A0A6A5PZB5) MG MAGNESIUM ION × 1 NO3 NITRATE ION × 14 DMS DIMETHYL SULFOXIDE × 9 GOL GLYCEROL × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 1 Q73 (3~{S},5~{R},6~{E},8~{Z},10~{R},12~{E},14~{E},16~{S})-3,16-bis(azanyl)-8,10,12-trimethyl-16-[(2~{S},4~{R},5~{S},6~{S})-5-methyl-4-oxidanyl-6-[(~{E})-prop-1-enyl]oxan-2-yl]-5-oxidanyl-hexadeca-6,8,12,14-tetraenoic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;0.12 M Monosaccharides (20 mM D-Glucose; 20 mM D-Mannose; 20 mM D-Galactose; 20 mM L-Fucose; 20 mM D-Xylose; 20 mM N-Acetyl-D-Glucosamine), 0.1 M buffer system 1 pH 6.5 (sodium HEPES and MOPS), and 50 % Precipitant Mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000) Resolution 2.30 Å R-free 0.224

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.

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A6A5PZI8_YEASX
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 8itv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8itv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8itv
Deposition date deposition_date2023-03-23
最后修订 last_revision2024-03-27
Structure title titleKL2.1 in complex with CRM1-Ran-RanBP1
Keywords keywordsnuclear export inhibitor, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier36.18
Radius of gyration Rg (electron density) rg_electron35.43
Forward intensity I(0) i0351558000.00
Molecular weight molecular_weight155050.0 kDa
Excluded volume excluded_volume195500 ų
Envelope volume envelope_volume254660 ų
Hydration-shell volume shell_volume57855 ų
Envelope diameter envelope_diameter111.8
Shell Rg shell_rg43.79
Envelope Rg envelope_rg34.62
Shape Rg shape_rg35.43
Total Rg total_rg36.01
Total atoms total_atoms10892
Residues n_residues1324
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 dmax109.4
Rg (real space) rg_real35.92
Rg uncertainty (real space) rg_real_error0.55
I(0) (real space) i0_real3.5160e+08
I(0) uncertainty (real space) i0_real_error4.6830e+06
Rg (reciprocal space) rg_reciprocal36.08
I(0) (reciprocal space) i0_reciprocal351600000.0000
Solution quality estimate total_estimate0.9076
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.2
Skewness Skewness skewness0.033
Kurtosis Kurtosis kurtosis-0.618
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha46410000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.959

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (12)

8. Citations (1)

9. Files and Curves (10)