1CJF | pdb_00001cjf

PROFILIN BINDS PROLINE-RICH LIGANDS IN TWO DISTINCT AMIDE BACKBONE ORIENTATIONS

• PDB DOI: https://doi.org/10.2210/pdb1CJF/pdb

• Classification: STRUCTURAL REGULATION PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1999-04-13 Released: 1999-07-07 
• Deposition Author(s): Mahoney, N.M., Fedorov, A.A., Fedorov, E., Rozwarski, D.A., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.293 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.179 (DCC) 

Starting Model: experimental

Literature

Profilin binds proline-rich ligands in two distinct amide backbone orientations.

Mahoney, N.M., Rozwarski, D.A., Fedorov, E., Fedorov, A.A., Almo, S.C.

(1999) Nat Struct Biol 6: 666-671

• PubMed: 10404225 
• DOI: https://doi.org/10.1038/10722
• Primary Citation Related Structures: 
  1CF0, 1CJF


• PubMed Abstract: 
  

  The actin regulatory protein profilin is targeted to specific cellular regions through interactions with highly proline-rich motifs embedded within its binding partners. New X-ray crystallographic results demonstrate that profilin, like SH3 domains, can bind proline-rich ligands in two distinct amide backbone orientations. By further analogy with SH3 domains, these data suggest that non-proline residues in profilin ligands may dictate the polarity and register of binding, and the detailed organization of the assemblies involving profilin. This degeneracy may be a general feature of modules that bind proline-rich ligands, including WW and EVH1 domains, and has implications for the assembly and activity of macromolecular complexes involved in signaling and the regulation of the actin cytoskeleton.

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Organizational Affiliation: 
• Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.27 kDa 
• Atom Count: 2,343 
• Modeled Residue Count: 306 
• Deposited Residue Count: 308 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (HUMAN PLATELET PROFILIN)	A, C [auth B]	139	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P07737 (Homo sapiens) Explore P07737  Go to UniProtKB:  P07737
PHAROS:  P07737 GTEx:  ENSG00000108518

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PROLINE PEPTIDE)	B [auth C], D	15	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HOM	E [auth C], F [auth D]	7-HYDROXY-4-METHYL-3-(2-HYDROXY-ETHYL)COUMARIN C12 H12 O4 VCGFYFKJZGIZMX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.293 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.179 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.4	α = 90
b = 51.8	β = 131.1
c = 77.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
XSCALE	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-07-07 
Deposition Author(s): Mahoney, N.M., Fedorov, A.A., Fedorov, E., Rozwarski, D.A., Almo, S.C.

Revision History  

• Version 1.0: 1999-07-07
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description