8qyz

Crystal structure of hiNES2 in complex with Xpo1 and RanGTP

Method: X-RAY DIFFRACTION Dmax: 224.5 Å Quality: GOOD

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

GTP-binding nuclear protein GSP1/CNR1

Saccharomyces cerevisiae S288C

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 1–182 Mutation:1-182, Q71L Exportin-1 × 1 (P30822) hiNES2 × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;Tris, PEG 20K, magnesium acetate Resolution 3.00 Å R-free 0.247
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 1–182 Mutation:1-182, Q71L Exportin-1 × 1 (P30822) hiNES2 × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;Tris, PEG 20K, magnesium acetate Resolution 3.00 Å R-free 0.247
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 1–182 Mutation:1-182, Q71L Exportin-1 × 1 (P30822) hiNES2 × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;Tris, PEG 20K, magnesium acetate Resolution 3.00 Å R-free 0.247
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain G; UniProt 1–182 Mutation:1-182, Q71L Exportin-1 × 1 (P30822) hiNES2 × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;Tris, PEG 20K, magnesium acetate Resolution 3.00 Å R-free 0.247

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 12 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 1–182; UniProt 1–182 Author chain B; PDBConstruct 1–182; UniProt 1–182 Author chain E; PDBConstruct 1–182; UniProt 1–182 Author chain G; PDBConstruct 1–182; UniProt 1–182

Exportin-1

Saccharomyces cerevisiae 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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 1–1084 Mutation:del(377-413) GTP-binding nuclear protein GSP1/CNR1 × 1 (P32835) hiNES2 × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;Tris, PEG 20K, magnesium acetate Resolution 3.00 Å R-free 0.247
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 1–1084 Mutation:del(377-413) GTP-binding nuclear protein GSP1/CNR1 × 1 (P32835) hiNES2 × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;Tris, PEG 20K, magnesium acetate Resolution 3.00 Å R-free 0.247
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 1–1084 Mutation:del(377-413) GTP-binding nuclear protein GSP1/CNR1 × 1 (P32835) hiNES2 × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;Tris, PEG 20K, magnesium acetate Resolution 3.00 Å R-free 0.247
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain H; UniProt 1–1084 Mutation:del(377-413) GTP-binding nuclear protein GSP1/CNR1 × 1 (P32835) hiNES2 × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;Tris, PEG 20K, magnesium acetate Resolution 3.00 Å R-free 0.247

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 70 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name XPO1_YEAST
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 2–1048; UniProt 1–1084 Author chain D; PDBConstruct 2–1048; UniProt 1–1084 Author chain F; PDBConstruct 2–1048; UniProt 1–1084 Author chain H; PDBConstruct 2–1048; 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 8qyz

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8qyz
Deposition date deposition_date2023-10-26
最后修订 last_revision2024-11-06
Structure title titleCrystal structure of hiNES2 in complex with Xpo1 and RanGTP
Keywords keywordsNES, Exportin, RanGTP, 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_guinier66.61
Radius of gyration Rg (electron density) rg_electron66.52
Forward intensity I(0) i03960300000.00
Molecular weight molecular_weight554200.0 kDa
Excluded volume excluded_volume702030 ų
Envelope volume envelope_volume1037200 ų
Hydration-shell volume shell_volume127210 ų
Envelope diameter envelope_diameter211.4
Shell Rg shell_rg71.00
Envelope Rg envelope_rg63.92
Shape Rg shape_rg66.51
Total Rg total_rg66.61
Total atoms total_atoms39020
Residues n_residues4810
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 dmax224.5
Rg (real space) rg_real66.68
Rg uncertainty (real space) rg_real_error2.24
I(0) (real space) i0_real3.9600e+09
I(0) uncertainty (real space) i0_real_error9.0790e+07
Rg (reciprocal space) rg_reciprocal66.47
I(0) (reciprocal space) i0_reciprocal3958000000.0000
Solution quality estimate total_estimate0.8653
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary65.5
Skewness Skewness skewness0.252
Kurtosis Kurtosis kurtosis-0.730
Angular range angular_range— – 0.1200 −1
Current regularization parameter α current_alpha0.0003
Highest regularization parameter α highest_alpha330300000.0000
Real-space data points n_real_points25
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.631

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)