5dlq

Crystal structure of RanGTP-Exportin 4-eIF5A complex

Method: X-RAY DIFFRACTION Dmax: 155.5 Å Quality: GOOD

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

Exportin-4

Mus musculus

UniProt Q9ESJ0

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 1–1151 Mutation:H1085Y GTP-binding nuclear protein Ran × 1 (P62826) Eukaryotic translation initiation factor 5A-1 × 1 (P63241) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.26;293 K;Peg 400, MES X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.26;293 K;Peg 400, MES, DTT Resolution 3.20 Å R-free 0.270
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–1151 Mutation:H1085Y GTP-binding nuclear protein Ran × 1 (P62826) Eukaryotic translation initiation factor 5A-1 × 1 (P63241) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.26;293 K;Peg 400, MES X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.26;293 K;Peg 400, MES, DTT Resolution 3.20 Å R-free 0.270

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name XPO4_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–1113; UniProt 1–1151 Author chain B; PDBConstruct 1–1113; UniProt 1–1151

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 C; UniProt 5–180 Mutation:Q69L Exportin-4 × 1 (Q9ESJ0) Eukaryotic translation initiation factor 5A-1 × 1 (P63241) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.26;293 K;Peg 400, MES X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.26;293 K;Peg 400, MES, DTT Resolution 3.20 Å R-free 0.270
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 5–180 Mutation:Q69L Exportin-4 × 1 (Q9ESJ0) Eukaryotic translation initiation factor 5A-1 × 1 (P63241) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.26;293 K;Peg 400, MES X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.26;293 K;Peg 400, MES, DTT Resolution 3.20 Å R-free 0.270

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 C; PDBConstruct 1–176; UniProt 5–180 Author chain D; PDBConstruct 1–176; UniProt 5–180

Eukaryotic translation initiation factor 5A-1

Homo sapiens

UniProt P63241

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 F; UniProt 45–184 Non-standard monomer:Yes (specific site not provided by mmCIF) Exportin-4 × 1 (Q9ESJ0) 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 6.26;293 K;Peg 400, MES X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.26;293 K;Peg 400, MES, DTT Resolution 3.20 Å R-free 0.270
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 45–184 Non-standard monomer:Yes (specific site not provided by mmCIF) Exportin-4 × 1 (Q9ESJ0) 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 6.26;293 K;Peg 400, MES X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.26;293 K;Peg 400, MES, DTT Resolution 3.20 Å R-free 0.270

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 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IF5A1_HUMAN
Isoform P63241-2
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 2–141; UniProt 45–184 Author chain F; PDBConstruct 2–141; UniProt 45–184

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 5dlq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5dlq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5dlq
Deposition date deposition_date2015-09-07
Structure title titleCrystal structure of RanGTP-Exportin 4-eIF5A complex
Keywords keywords;Active transport, Nuclear transport, Nuclear export Importin-Beta family, Exportin, HEAT repeat, GTPase, Nucleotide binding, eIF5A, Translation factor, Hypusine, Unusual amino acid, 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_guinier46.39
Radius of gyration Rg (electron density) rg_electron45.71
Forward intensity I(0) i01219750000.00
Molecular weight molecular_weight294330.0 kDa
Excluded volume excluded_volume370500 ų
Envelope volume envelope_volume536940 ų
Hydration-shell volume shell_volume96044 ų
Envelope diameter envelope_diameter169.2
Shell Rg shell_rg52.67
Envelope Rg envelope_rg44.03
Shape Rg shape_rg45.70
Total Rg total_rg46.06
Total atoms total_atoms20688
Residues n_residues2653
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 dmax155.5
Rg (real space) rg_real46.16
Rg uncertainty (real space) rg_real_error1.23
I(0) (real space) i0_real1.2200e+09
I(0) uncertainty (real space) i0_real_error2.2830e+07
Rg (reciprocal space) rg_reciprocal46.39
I(0) (reciprocal space) i0_reciprocal1220000000.0000
Solution quality estimate total_estimate0.8701
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary59.4
Skewness Skewness skewness0.208
Kurtosis Kurtosis kurtosis-0.274
Angular range angular_range— – 0.1700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha161500000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.794; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.955

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id5dlqA01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
Domain ID domain_id5dlqB01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
Domain ID domain_id5dlqC00
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_id5dlqD00
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_id5dlqE01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily30
Domain ID domain_id5dlqE02
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_id5dlqF01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily30
Domain ID domain_id5dlqF02
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)