Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 169.89 kDa 
• Atom Count: 10668 
• Modelled Residue Count: 1291 
• Deposited Residue Count: 1478 
• Unique protein chains: 4

3E1I

Crystal Structure of BbetaD432A Variant Fibrinogen Fragment D with the Peptide Ligand Gly-His-Arg-Pro-amide

• PDB DOI: 10.2210/pdb3E1I/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2008-08-04 Released: 2009-01-13 
• Deposition Author(s): Bowley, S.R., Lord, S.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.242 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

Literature

Fibrinogen variant BbetaD432A has normal polymerization but does not bind knob "B".

Bowley, S.R., Lord, S.T.

(2009) Blood 113: 4425-4430

• PubMed: 19075185 
• DOI: 10.1182/blood-2008-09-178178
• Primary Citation of Related Structures:  
  3E1I


• PubMed Abstract: 
  

Fibrinogen residue Bbeta432Asp is part of hole "b" that interacts with knob "B," whose sequence starts with Gly-His-Arg-Pro-amide (GHRP). Because previous studies showed BbetaD432A has normal polymerization, we hypothesized that Bbeta432Asp is not critical for knob "B" binding and that new knob-hole interactions would compensate for the loss of this Asp residue. To test this hypothesis, we solved the crystal structure of fragment D from BbetaD432A. Surprisingly, the structure (rfD-BbetaD432A+GH) showed the peptide GHRP was not bound to hole "b." We then re-evaluated the polymerization of this variant by examining clot turbidity, clot structure, and the rate of FXIIIa cross-linking. The turbidity and the rate of gamma-gamma dimer formation for BbetaD432A were indistinguishable compared with normal fibrinogen. Scanning electron microscopy showed no significant differences between the clots of BbetaD432A and normal, but the thrombin-derived clots had thicker fibers than clots obtained from batroxobin, suggesting that cleavage of FpB is more important than "B:b" interactions. We conclude that hole "b" and "B:b" knob-hole binding per se have no influence on fibrin polymerization.

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Organizational Affiliation: 

Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-7525, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen alpha chain	A, D	87	Homo sapiens	Mutation(s): 0  Gene Names: FGA
UniProt & NIH Common Fund Data Resources
Find proteins for P02671 (Homo sapiens) Explore P02671  Go to UniProtKB:  P02671
PHAROS:  P02671 GTEx:  ENSG00000171560

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen beta chain	B, E	328	Homo sapiens	Mutation(s): 1  Gene Names: FGB
UniProt & NIH Common Fund Data Resources
Find proteins for P02675 (Homo sapiens) Explore P02675  Go to UniProtKB:  P02675
PHAROS:  P02675 GTEx:  ENSG00000171564

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen gamma chain	C, F	319	Homo sapiens	Mutation(s): 0  Gene Names: FGG, PRO2061
UniProt & NIH Common Fund Data Resources
Find proteins for P02679 (Homo sapiens) Explore P02679  Go to UniProtKB:  P02679
PHAROS:  P02679 GTEx:  ENSG00000171557

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Gly-His-Arg-Pro-amide	G, H	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth B], N [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	J [auth B], K [auth B], L [auth C], M [auth C], O [auth E], P [auth E], Q [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.242 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.476	α = 90
b = 146.596	β = 90
c = 228.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-08-04 
• Released Date: 2009-01-13 
Deposition Author(s): Bowley, S.R., Lord, S.T.

Revision History  

• Version 1.0: 2009-01-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2013-09-18
  Changes: Derived calculations
• Version 1.3: 2019-07-24
  Changes: Data collection, Refinement description, Source and taxonomy, Structure summary
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.5: 2021-10-20
  Changes: Database references, Structure summary