Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 6-mer -A4B2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 6-mer -A4B2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 652018.31 
• Atom Count: 31833 
• Residue Count: 5768 
• Unique protein chains: 5

3GHG

Crystal Structure of Human Fibrinogen

• DOI: 10.2210/pdb3GHG/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens


• Deposited: 2009-03-03 Released: 2009-05-19 
• Deposition Author(s): Doolittle, R.F., Kollman, J.M., Sawaya, M.R., Pandi, L., Riley, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.309 
• R-Value Work: 0.252 

Literature

Crystal structure of human fibrinogen.

Kollman, J.M., Pandi, L., Sawaya, M.R., Riley, M., Doolittle, R.F.

(2009) Biochemistry 48: 3877-3886

• PubMed: 19296670 
• DOI: 10.1021/bi802205g


• PubMed Abstract: 
  

A crystal structure of human fibrinogen has been determined at approximately 3.3 A resolution. The protein was purified from human blood plasma, first by a cold ethanol precipitation procedure and then by stepwise chromatography on DEAE-cellulose. A product was obtained that was homogeneous on SDS-polyacrylamide gels. Nonetheless, when individual crystals used for X-ray diffraction were examined by SDS gel electrophoresis after data collection, two species of alpha chain were present, indicating that some proteolysis had occurred during the course of operations. Amino-terminal sequencing on post-X-ray crystals showed mostly intact native alpha- and gamma-chain sequences (the native beta chain is blocked). The overall structure differs from that of a native fibrinogen from chicken blood and those reported for a partially proteolyzed bovine fibrinogen in the nature of twist in the coiled-coil regions, likely due to weak forces imparted by unique crystal packing. As such, the structure adds to the inventory of possible conformations that may occur in solution. Other features include a novel interface with an antiparallel arrangement of beta chains and a unique tangential association of coiled coils from neighboring molecules. The carbohydrate groups attached to beta chains are unusually prominent, the full sweep of 11 sugar residues being positioned. As was the case for native chicken fibrinogen, no resolvable electron density could be associated with alphaC domains.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry and Division of Biology, University of California at San Diego, La Jolla, California 92093-0314, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Fibrinogen alpha chain	A, D, G, J	562	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, H, K	461	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, I, L	411	Homo sapiens	Mutation(s): 0  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
A knob	M, N, Q, R	4	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
B knob	O, P, S, T	4	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	B, C, E, F, H, I, K, L	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MAN	B, E, H, K	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
GAL	B, E, K	BETA-D-GALACTOSE C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
BMA	B, E, H, K	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NDG	B, E, H, K	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG	B, E, H, K, L	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SIA	B, E, K	O-SIALIC ACID C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.309 
• R-Value Work: 0.252 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 135.238	α = 90.00
b = 94.866	β = 94.81
c = 300.812	γ = 90.00

Software Package:

Software Name	Purpose
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHASES	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-03-03 
• Released Date: 2009-05-19 
• Deposition Author(s): Doolittle, R.F., Kollman, J.M., Sawaya, M.R., Pandi, L., Riley, M.

Revision History 

• Version 1.0: 2009-05-19
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Refinement description, Version format compliance