Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 152.49 kDa 
• Atom Count: 11144 
• 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, synthetic construct
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• 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: 2.60 Å
• R-Value Free: 0.260 
• R-Value Work: 0.220 
• R-Value Observed: 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
• Primary Citation of Related Structures:  
  3BVH


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen alpha chain	A, D	62	Homo sapiens	Mutation(s): 0  Gene Names: FGA
Find proteins for P02671 (Homo sapiens) Explore P02671  Go to UniProtKB:  P02671
NIH Common Fund Data Resources
PHAROS:  P02671 GTEx:  ENSG00000171560

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen beta chain	B, E	298	Homo sapiens	Mutation(s): 0  Gene Names: FGB
Find proteins for P02675 (Homo sapiens) Explore P02675  Go to UniProtKB:  P02675
NIH Common Fund Data Resources
PHAROS:  P02675 GTEx:  ENSG00000171564

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen gamma chain	C, F	293	Homo sapiens	Mutation(s): 1  Gene Names: FGG, PRO2061
Find proteins for P02679 (Homo sapiens) Explore P02679  Go to UniProtKB:  P02679
NIH Common Fund Data Resources
PHAROS:  P02679 GTEx:  ENSG00000171557

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
4-mer peptide GPRP	G, H, I, J	4	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	K, L	3		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B, C, E, F	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.260 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.844	α = 90
b = 94.913	β = 90
c = 225.754	γ = 90

Software Package:

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

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
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2018-12-26
  Changes: Data collection, Derived calculations, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary