3CPF | pdb_00003cpf

Crystal structure of human eukaryotic translation initiation factor EIF5A

• PDB DOI: https://doi.org/10.2210/pdb3CPF/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-31 Released: 2008-04-15 
• Deposition Author(s): Nedyalkova, L., Tong, Y., Tempel, W., Hong, B., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.300 (Depositor), 0.324 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.282 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human eIF5A1: insight into functional similarity of human eIF5A1 and eIF5A2.

Tong, Y., Park, I., Hong, B.S., Nedyalkova, L., Tempel, W., Park, H.W.

(2009) Proteins 75: 1040-1045

• PubMed: 19280598 
• DOI: https://doi.org/10.1002/prot.22378
• Primary Citation Related Structures: 
  3CPF

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Organizational Affiliation: 
• Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7 Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.34 kDa 
• Atom Count: 1,904 
• Modeled Residue Count: 258 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 5A-1	A, B	138	Homo sapiens	Mutation(s): 0  Gene Names: EIF5A
UniProt & NIH Common Fund Data Resources
Find proteins for P63241 (Homo sapiens) Explore P63241  Go to UniProtKB:  P63241
PHAROS:  P63241 GTEx:  ENSG00000132507

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.300 (Depositor), 0.324 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.282 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.119	α = 90
b = 76.119	β = 90
c = 107.752	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-15 
Deposition Author(s): Nedyalkova, L., Tong, Y., Tempel, W., Hong, B., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-04-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary