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1k5g

Crystal structure of Ran-GDP-AlFx-RanBP1-RanGAP complex

Method: X-RAY DIFFRACTION
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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 Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Ran-specific GTPase-activating protein × 1 （P43487） Ran GTPase activating protein 1 × 1 （P41391） MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Ran-specific GTPase-activating protein × 1 （P43487） Ran GTPase activating protein 1 × 1 （P41391） MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Ran-specific GTPase-activating protein × 1 （P43487） Ran GTPase activating protein 1 × 1 （P41391） MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Ran-specific GTPase-activating protein × 1 （P43487） Ran GTPase activating protein 1 × 1 （P41391） MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2mmc 2mmg 2n1b 3gj0 3gj0 5ciq 5ciq 5cit 5cit 5ciw 5ciw 5cj2

19 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1i2m 1i2m 1i2m 1ibr 1ibr 1k5d 1k5d 1k5d 1k5d 1k5g 1k5g 1k5g

185 assemblies; showing the first 12

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 Author chain D； PDBConstruct 1–216； UniProt 1–216 Author chain G； PDBConstruct 1–216； UniProt 1–216 Author chain J； PDBConstruct 1–216； UniProt 1–216

Ran-specific GTPase-activating protein

Homo sapiens

UniProt P43487

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 GTP-binding nuclear protein RAN × 1 （P62826） Ran GTPase activating protein 1 × 1 （P41391） MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 GTP-binding nuclear protein RAN × 1 （P62826） Ran GTPase activating protein 1 × 1 （P41391） MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 GTP-binding nuclear protein RAN × 1 （P62826） Ran GTPase activating protein 1 × 1 （P41391） MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 GTP-binding nuclear protein RAN × 1 （P62826） Ran GTPase activating protein 1 × 1 （P41391） MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1k5d 1k5d 1k5d 1k5d 1k5g 1k5g 1k5g 1k5g 9n85 9yb5

10 assemblies

View Construct and Data Evidence
UniProt name RANG_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–201； UniProt 1–201 Author chain E； PDBConstruct 1–201； UniProt 1–201 Author chain H； PDBConstruct 1–201； UniProt 1–201 Author chain K； PDBConstruct 1–201； UniProt 1–201

Ran GTPase activating protein 1

Schizosaccharomyces pombe

UniProt P41391

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 GTP-binding nuclear protein RAN × 1 （P62826） Ran-specific GTPase-activating protein × 1 （P43487） MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 GTP-binding nuclear protein RAN × 1 （P62826） Ran-specific GTPase-activating protein × 1 （P43487） MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 GTP-binding nuclear protein RAN × 1 （P62826） Ran-specific GTPase-activating protein × 1 （P43487） MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 GTP-binding nuclear protein RAN × 1 （P62826） Ran-specific GTPase-activating protein × 1 （P43487） MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1yrg 1yrg 2ca6 2ca6

4 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1k5d 1k5d 1k5d 1k5d 1k5g 1k5g 1k5g 1k5g

8 assemblies

View Construct and Data Evidence
UniProt name RNA1_SCHPO
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–386； UniProt 1–386 Author chain F； PDBConstruct 1–386； UniProt 1–386 Author chain I； PDBConstruct 1–386； UniProt 1–386 Author chain L； PDBConstruct 1–386； UniProt 1–386

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id1k5g
Deposition date deposition_date2001-10-10
Structure title titleCrystal structure of Ran-GDP-AlFx-RanBP1-RanGAP complex
Keywords keywords;RAN, RANBP1, RANGAP, GAP, SIGNAL TRANSDUCTION, NUCLEAR TRANSPORT, GTP HYDROLYSIS, ACTIVATION STATE, COMPLEX (GTP-BINDING-GTPASE ACTIVATION), SIGNALING PROTEIN-SIGNALING ACTIVATOR COMPLEX ;; SIGNALING PROTEIN/SIGNALING ACTIVATOR
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1k5g__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1k5g__assembly_1__model_1 | I(q)

10-2 10-1 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1k5g__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）29.83 Å
Rg (electron density)29.16 Å
Total Rg29.82 Å
Atom count5599
Residues696
Excluded volume99856 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1k5g__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1k5g__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1k5g__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1k5g__assembly_4__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1k5ga_
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_idd1k5gb_
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.3 — Ran-binding domain
Domain ID domain_idd1k5gc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamilyc.10.1 — RNI-like
Family Family familyc.10.1.2 — Rna1p (RanGAP1), N-terminal domain
Domain ID domain_idd1k5gd_
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_idd1k5ge_
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.3 — Ran-binding domain
Domain ID domain_idd1k5gf_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamilyc.10.1 — RNI-like
Family Family familyc.10.1.2 — Rna1p (RanGAP1), N-terminal domain
Domain ID domain_idd1k5gg_
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_idd1k5gh_
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.3 — Ran-binding domain
Domain ID domain_idd1k5gi_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamilyc.10.1 — RNI-like
Family Family familyc.10.1.2 — Rna1p (RanGAP1), N-terminal domain
Domain ID domain_idd1k5gj_
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_idd1k5gk_
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.3 — Ran-binding domain
Domain ID domain_idd1k5gl_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamilyc.10.1 — RNI-like
Family Family familyc.10.1.2 — Rna1p (RanGAP1), N-terminal domain

CATH v4.4 (12 domains)

Domain ID domain_id1k5gA00
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_id1k5gB00
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)
Domain ID domain_id1k5gC00
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id1k5gD00
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_id1k5gE00
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)
Domain ID domain_id1k5gF00
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id1k5gG00
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_id1k5gH00
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)
Domain ID domain_id1k5gI00
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id1k5gJ00
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_id1k5gK00
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)
Domain ID domain_id1k5gL00
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
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7. Citations (6)