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3cpf

Crystal structure of human eukaryotic translation initiation factor EIF5A

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 15–151 Fragment：Residues 15-151 UNX UNKNOWN LIGAND × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；22% PEG 3350, 0.2M Ammonium sulfate, 0.1M Sodium cacodylate. Cryoprotected with 20% PEG 3350 and 20% Ethylene glycol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.50 Å R-free 0.300
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 15–151 Fragment：Residues 15-151 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；22% PEG 3350, 0.2M Ammonium sulfate, 0.1M Sodium cacodylate. Cryoprotected with 20% PEG 3350 and 20% Ethylene glycol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.50 Å R-free 0.300

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.

Other PDB Difference from Current Entry 3CPF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5DLQ Crystal structure of RanGTP-Exportin 4-eIF5A complex Deposited 2015-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 45–184（140 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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
5DLQ Crystal structure of RanGTP-Exportin 4-eIF5A complex Deposited 2015-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 45–184（140 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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
8Y0W dormant ribosome with eIF5A, eEF2 and SERBP1 Deposited 2024-01-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 81-meric
Chain 5 1–154（154 aa）
Not recorded MG MAGNESIUM ION × 226 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50mM HEPES, pH7.5, 100mM KOAc, 5mM Mg(OAc)2, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å

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 —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–138； UniProt 15–151 Author chain B； PDBConstruct 2–138； UniProt 15–151

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

暂无 SAXS 图

P(r) Distance Distribution P(r) Distribution

暂无 P(r) 图
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3cpf
Deposition date deposition_date2008-03-31
Structure title titleCrystal structure of human eukaryotic translation initiation factor EIF5A
Keywords keywordsStructural Genomics Consortium, leukemia, apoptosis, SGC, Hypusine, Initiation factor, Nucleus, Protein biosynthesis, CELL CYCLE; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

该条目暂无 SAXS 数据。

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

该条目暂无 P(r) 分析数据。

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3cpfa1
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.5 — Translation proteins SH3-like domain
Family Family familyb.34.5.0 — automated matches
Domain ID domain_idd3cpfa2
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.0 — automated matches
Domain ID domain_idd3cpfb1
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.5 — Translation proteins SH3-like domain
Family Family familyb.34.5.0 — automated matches
Domain ID domain_idd3cpfb2
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id3cpfA01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily30 —
Domain ID domain_id3cpfA02
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_id3cpfB01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily30 —
Domain ID domain_id3cpfB02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
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8. Citations (1)

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9. Files and Curves (0)