6q84

Crystal structure of RanGTP-Pdr6-eIF5A export complex

Method: X-RAY DIFFRACTION Dmax: 189.8 Å Quality: GOOD

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

Importin beta-like protein KAP122

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P32767

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 2–1081 Not recorded GTP-binding nuclear protein Ran × 1 (P62826) Eukaryotic translation initiation factor 5A-1 × 1 (P23301) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.3;291 K;100 mM Sodium acetate pH 5.3 and 30% PEG 300 Resolution 3.70 Å R-free 0.247
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 2–1081 Not recorded GTP-binding nuclear protein Ran × 1 (P62826) Eukaryotic translation initiation factor 5A-1 × 1 (P23301) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.3;291 K;100 mM Sodium acetate pH 5.3 and 30% PEG 300 Resolution 3.70 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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KA122_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–1080; UniProt 2–1081 Author chain D; PDBConstruct 1–1080; UniProt 2–1081

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 B; UniProt 5–180 Mutation:Q69L Importin beta-like protein KAP122 × 1 (P32767) Eukaryotic translation initiation factor 5A-1 × 1 (P23301) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.3;291 K;100 mM Sodium acetate pH 5.3 and 30% PEG 300 Resolution 3.70 Å R-free 0.247
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 5–180 Mutation:Q69L Importin beta-like protein KAP122 × 1 (P32767) Eukaryotic translation initiation factor 5A-1 × 1 (P23301) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.3;291 K;100 mM Sodium acetate pH 5.3 and 30% PEG 300 Resolution 3.70 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.

137 other PDB entries and 202 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 B; PDBConstruct 1–176; UniProt 5–180 Author chain E; PDBConstruct 1–176; UniProt 5–180

Eukaryotic translation initiation factor 5A-1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P23301

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 16–157 Not recorded Importin beta-like protein KAP122 × 1 (P32767) GTP-binding nuclear protein Ran × 1 (P62826) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.3;291 K;100 mM Sodium acetate pH 5.3 and 30% PEG 300 Resolution 3.70 Å R-free 0.247
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 16–157 Not recorded Importin beta-like protein KAP122 × 1 (P32767) GTP-binding nuclear protein Ran × 1 (P62826) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.3;291 K;100 mM Sodium acetate pH 5.3 and 30% PEG 300 Resolution 3.70 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.

17 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IF5A1_YEAST
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–142; UniProt 16–157 Author chain F; PDBConstruct 1–142; UniProt 16–157

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 6q84

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6q84
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id6q84
Deposition date deposition_date2018-12-14
Structure title titleCrystal structure of RanGTP-Pdr6-eIF5A export complex
Keywords keywordsImportin-Beta family, biportin, nuclear export, translation factor, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier53.40
Radius of gyration Rg (electron density) rg_electron53.75
Forward intensity I(0) i01221670000.00
Molecular weight molecular_weight301430.0 kDa
Excluded volume excluded_volume381230 ų
Envelope volume envelope_volume552050 ų
Hydration-shell volume shell_volume88467 ų
Envelope diameter envelope_diameter190.0
Shell Rg shell_rg54.05
Envelope Rg envelope_rg52.67
Shape Rg shape_rg53.78
Total Rg total_rg53.65
Total atoms total_atoms21207
Residues n_residues2641
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 dmax189.8
Rg (real space) rg_real53.66
Rg uncertainty (real space) rg_real_error2.16
I(0) (real space) i0_real1.2220e+09
I(0) uncertainty (real space) i0_real_error2.5660e+07
Rg (reciprocal space) rg_reciprocal53.17
I(0) (reciprocal space) i0_reciprocal1221000000.0000
Solution quality estimate total_estimate0.8283
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary52.3
Skewness Skewness skewness0.503
Kurtosis Kurtosis kurtosis-0.343
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha159300000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.673; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.765

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id6q84B00
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_id6q84C01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily30
Domain ID domain_id6q84C02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id6q84E00
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_id6q84F01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily30
Domain ID domain_id6q84F02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins

8. Citations (1)

9. Files and Curves (10)