1FZV | pdb_00001fzv

THE CRYSTAL STRUCTURE OF HUMAN PLACENTA GROWTH FACTOR-1 (PLGF-1), AN ANGIOGENIC PROTEIN AT 2.0A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1FZV/pdb

• Classification: HORMONE/GROWTH FACTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-10-04 Released: 2001-05-09 
• Deposition Author(s): Iyer, S., Leonidas, D.D., Swaminathan, G.J., Maglione, D., Battisti, M., Tucci, M., Persico, M.G., Acharya, K.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.247 (Depositor) 
• R-Value Work: 
  0.216 (Depositor) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

The crystal structure of human placenta growth factor-1 (PlGF-1), an angiogenic protein, at 2.0 A resolution.

Iyer, S., Leonidas, D.D., Swaminathan, G.J., Maglione, D., Battisti, M., Tucci, M., Persico, M.G., Acharya, K.R.

(2001) J Biological Chem 276: 12153-12161

• PubMed: 11069911 
• DOI: https://doi.org/10.1074/jbc.M008055200
• Primary Citation Related Structures: 
  1FZV


• PubMed Abstract: 
  

  The angiogenic molecule placenta growth factor (PlGF) is a member of the cysteine-knot family of growth factors. In this study, a mature isoform of the human PlGF protein, PlGF-1, was crystallized as a homodimer in the crystallographic asymmetric unit, and its crystal structure was elucidated at 2.0 A resolution. The overall structure of PlGF-1 is similar to that of vascular endothelial growth factor (VEGF) with which it shares 42% amino acid sequence identity. Based on structural and biochemical data, we have mapped several important residues on the PlGF-1 molecule that are involved in recognition of the fms-like tyrosine kinase receptor (Flt-1, also known as VEGFR-1). We propose a model for the association of PlGF-1 and Flt-1 domain 2 with precise shape complementarity, consider the relevance of this assembly for PlGF-1 signal transduction, and provide a structural basis for altered specificity of this molecule.

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Organizational Affiliation: 
• Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.98 kDa 
• Atom Count: 1,694 
• Modeled Residue Count: 200 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLACENTA GROWTH FACTOR	A, B	132	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P49763 (Homo sapiens) Explore P49763  Go to UniProtKB:  P49763
PHAROS:  P49763 GTEx:  ENSG00000119630

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A], D [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.247 (Depositor) 
• R-Value Work:  0.216 (Depositor) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.6	α = 90
b = 62.6	β = 90
c = 84.107	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-05-09 
Deposition Author(s): Iyer, S., Leonidas, D.D., Swaminathan, G.J., Maglione, D., Battisti, M., Tucci, M., Persico, M.G., Acharya, K.R.

Revision History  

• Version 1.0: 2001-05-09
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2022-12-21
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-16
  Changes: Data collection, Structure summary