Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer -A2B 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer -A2B 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 152562.92 
• Atom Count: 10698 
• Residue Count: 1322 
• Unique protein chains: 4

3BVH

Crystal Structure of Recombinant gammaD364A Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide

• DOI: 10.2210/pdb3BVH/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): 1 


• Deposited: 2008-01-07 Released: 2008-09-02 
• Deposition Author(s): Bowley, S.R., Merenbloom, B.K., Betts, L., Okumura, N., Heroux, A., Gorkun, O.V., Lord, S.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.260 
• R-Value Work: 0.220 

Literature

Polymerization-defective fibrinogen variant gammaD364A binds knob "A" peptide mimic.

Bowley, S.R., Merenbloom, B.K., Okumura, N., Betts, L., Heroux, A., Gorkun, O.V., Lord, S.T.

(2008) Biochemistry 47: 8607-8613

• PubMed: 18642883 
• DOI: 10.1021/bi8000769


• PubMed Abstract: 
  

Fibrin polymerization is supported in part by interactions called "A:a". Crystallographic studies revealed gamma364Asp is part of hole "a" that interacts with knob "A" peptide mimic, GPRP. Biochemical studies have shown gamma364Asp is critical to polymerization, as polymerization of variants gammaD364A, gammaD364H, and gammaD364V is exceptionally impaired. To understand the molecular basis for the aberrant function, we solved the crystal structure of fragment D from gammaD364A. Surprisingly, the structure (rfD-gammaD364A+GP) showed near normal "A:a" interactions with GPRP bound to hole "a" and no change in the overall structure of gammaD364A. Of note, inspection of the structure showed negative electrostatic potential inside hole "a" was diminished by this substitution. We examined GPRP binding to the gamma364Asp variants in solution by plasmin protection assay. We found no protection of either gammaD364H or gammaD364V but partial protection of gammaD364A, indicating the peptide does not bind to either gammaD364H or gammaD364V and binds more weakly than normal to gammaD364A. We also examined protection by calcium and found all variants were indistinguishable from normal, suggesting the global structures of the variants are not markedly different from normal. Our data imply that gamma364Asp per se is not required for knob "A" binding to hole "a"; rather, this residue's negative charge has a critical role in the electrostatic interactions that facilitate the important first step in fibrin polymerization.

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Organizational Affiliation: 

Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Fibrinogen alpha chain	A, D	62	Homo sapiens	Mutation(s): 0  Gene Names: FGA
Find proteins for P02671 (Homo sapiens) Go to Gene View: FGA Go to UniProtKB:  P02671

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Fibrinogen beta chain	B, E	298	Homo sapiens	Mutation(s): 0  Gene Names: FGB
Find proteins for P02675 (Homo sapiens) Go to Gene View: FGB Go to UniProtKB:  P02675

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Fibrinogen gamma chain	C, F	293	Homo sapiens	Mutation(s): 1  Gene Names: FGG
Find proteins for P02679 (Homo sapiens) Go to Gene View: FGG Go to UniProtKB:  P02679

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
4-mer peptide GPRP	G, I, H, J	4	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	B, C, E, F	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
FUC	B, E	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
NAG	B, E	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.260 
• R-Value Work: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 89.844	α = 90.00
b = 94.913	β = 90.00
c = 225.754	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
CNS	phasing
SCALEPACK	data scaling
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-01-07 
• Released Date: 2008-09-02 
• Deposition Author(s): Bowley, S.R., Merenbloom, B.K., Betts, L., Okumura, N., Heroux, A., Gorkun, O.V., Lord, S.T.

Revision History 

• Version 1.0: 2008-09-02
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Non-polymer description, Version format compliance
• Version 1.2: 2018-12-26
  Type: Data collection, Derived calculations, Source and taxonomy