PDBsum entry 1fib

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Blood coagulation factor PDB id
Protein chain
249 a.a. *
Waters ×177
* Residue conservation analysis
PDB id:
Name: Blood coagulation factor
Title: Recombinant human gamma-fibrinogen carboxyl terminal fragment (residues 143-411) bound to calcium at ph 6.0
Structure: Gamma-fibrinogen carboxyl terminal fragment. Chain: a. Fragment: carboxyl terminus, residues 143 - 411. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Organ: blood. Gene: human fibrinogen gamma chain c. Expressed in: pichia pastoris. Expression_system_taxid: 4922. Encoding val 143 - val 411
2.10Å     R-factor:   0.159     R-free:   0.227
Authors: V.C.Yee,D.C.Teller
Key ref:
V.C.Yee et al. (1997). Crystal structure of a 30 kDa C-terminal fragment from the gamma chain of human fibrinogen. Structure, 5, 125-138. PubMed id: 9016719 DOI: 10.1016/S0969-2126(97)00171-8
02-Apr-96     Release date:   01-Apr-97    
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Protein chain
Pfam   ArchSchema ?
P02679  (FIBG_HUMAN) -  Fibrinogen gamma chain
453 a.a.
249 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1016/S0969-2126(97)00171-8 Structure 5:125-138 (1997)
PubMed id: 9016719  
Crystal structure of a 30 kDa C-terminal fragment from the gamma chain of human fibrinogen.
V.C.Yee, K.P.Pratt, H.C.Côté, I.L.Trong, D.W.Chung, E.W.Davie, R.E.Stenkamp, D.C.Teller.
BACKGROUND: Blood coagulation occurs by a cascade of zymogen activation resulting from minor proteolysis. The final stage of coagulation involves thrombin generation and limited proteolysis of fibrinogen to give spontaneously polymerizing fibrin. The resulting fibrin network is covalently crosslinked by factor XIIIa to yield a stable blood clot. Fibrinogen is a 340 kDa glycoprotein composed of six polypeptide chains, (alphabetagamma)2, held together by 29 disulfide bonds. The globular C terminus of the gamma chain contains a fibrin-polymerization surface, the principal factor XIIIa crosslinking site, the platelet receptor recognition site, and a calcium-binding site. Structural information on this domain should thus prove helpful in understanding clot formation. RESULTS: The X-ray crystallographic structure of the 30 kDa globular C terminus of the gamma chain of human fibrinogen has been determined in one crystal form using multiple isomorphous replacement methods. The refined coordinates were used to solve the structure in two more crystal forms by molecular replacement; the crystal structures have been refined against diffraction data to either 2.5 A or 2.1 A resolution. Three domains were identified in the structure, including a C-terminal fibrin-polymerization domain (P), which contains a single calcium-binding site and a deep binding pocket that provides the polymerization surface. The overall structure has a pronounced dipole moment, and the C-terminal residues appear highly flexible. CONCLUSIONS: The polymerization domain in the gamma chain is the most variable among a family of fibrinogen-related proteins and contains many acidic residues. These residues contribute to the molecular dipole moment in the structure, which may allow electrostatic steering to guide the alignment of fibrin monomers during the polymerization process. The flexibility of the C-terminal residues, which contain one of the factor XIIIa crosslinking sites and the platelet receptor recognition site, may be important in the function of this domain.
  Selected figure(s)  
Figure 6.
Figure 6. Schematic representation of the longitudinal (L) versus transverse (T) end-to-end γ–γ crosslinking between adjacent fibrin molecules.
  The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 125-138) copyright 1997.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20640913 R.Kotlín, Z.Reicheltová, J.Suttnar, P.Salaj, I.Hrachovinová, T.Riedel, M.Malý, M.Oravec, J.Kvasnicka, and J.E.Dyr (2010).
Two novel fibrinogen variants in the C-terminus of the Bβ-chain: fibrinogen Rokycany and fibrinogen Znojmo.
  J Thromb Thrombolysis, 30, 311-318.  
19922791 T.M.Hansen, H.Singh, T.A.Tahir, and N.P.Brindle (2010).
Effects of angiopoietins-1 and -2 on the receptor tyrosine kinase Tie2 are differentially regulated at the endothelial cell surface.
  Cell Signal, 22, 527-532.  
19892701 T.Thomsen, J.B.Moeller, A.Schlosser, G.L.Sorensen, S.K.Moestrup, N.Palaniyar, R.Wallis, J.Mollenhauer, and U.Holmskov (2010).
The recognition unit of FIBCD1 organizes into a noncovalently linked tetrameric structure and uses a hydrophobic funnel (S1) for acetyl group recognition.
  J Biol Chem, 285, 1229-1238.  
20036106 Y.Takada, Y.Ono, J.Saegusa, J.Sagusa, C.Mitsiades, N.Mitsiades, J.Tsai, Y.He, E.Maningding, A.Coleman, D.Ramirez-Maverakis, R.Rodrigues, R.Rodriquez, Y.Takada, and E.Maverakis (2010).
A T cell-binding fragment of fibrinogen can prevent autoimmunity.
  J Autoimmun, 34, 453-459.  
19036059 L.Medved, and J.W.Weisel (2009).
Recommendations for nomenclature on fibrinogen and fibrin.
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19122172 M.Guo, D.Daines, J.Tang, Q.Shen, R.M.Perrin, Y.Takada, S.Y.Yuan, and M.H.Wu (2009).
Fibrinogen-gamma C-terminal fragments induce endothelial barrier dysfunction and microvascular leak via integrin-mediated and RhoA-dependent mechanism.
  Arterioscler Thromb Vasc Biol, 29, 394-400.  
18421149 M.Tanio, S.Kondo, S.Sugio, and T.Kohno (2008).
Trimeric structure and conformational equilibrium of M-ficolin fibrinogen-like domain.
  J Synchrotron Radiat, 15, 243-245.  
18710925 T.A.Springer, J.Zhu, and T.Xiao (2008).
Structural basis for distinctive recognition of fibrinogen gammaC peptide by the platelet integrin alphaIIbbeta3.
  J Cell Biol, 182, 791-800.
PDB codes: 2vc2 2vdk 2vdl 2vdm 2vdn 2vdo 2vdp 2vdq 2vdr
17952642 M.Guthold, W.Liu, E.A.Sparks, L.M.Jawerth, L.Peng, M.Falvo, R.Superfine, R.R.Hantgan, and S.T.Lord (2007).
A comparison of the mechanical and structural properties of fibrin fibers with other protein fibers.
  Cell Biochem Biophys, 49, 165-181.  
17590019 R.A.Burton, G.Tsurupa, R.R.Hantgan, N.Tjandra, and L.Medved (2007).
NMR solution structure, stability, and interaction of the recombinant bovine fibrinogen alphaC-domain fragment.
  Biochemistry, 46, 8550-8560.
PDB code: 2jor
16940416 R.I.Litvinov, O.V.Gorkun, D.K.Galanakis, S.Yakovlev, L.Medved, H.Shuman, and J.W.Weisel (2007).
Polymerization of fibrin: Direct observation and quantification of individual B:b knob-hole interactions.
  Blood, 109, 130-138.  
17331136 R.Kotlín, M.Chytilová, J.Suttnar, P.Salaj, T.Riedel, J.Santrůcek, P.Klener, and J.E.Dyr (2007).
A novel fibrinogen variant--Praha I: hypofibrinogenemia associated with gamma Gly351Ser substitution.
  Eur J Haematol, 78, 410-416.  
17215869 V.Garlatti, N.Belloy, L.Martin, M.Lacroix, M.Matsushita, Y.Endo, T.Fujita, J.C.Fontecilla-Camps, G.J.Arlaud, N.M.Thielens, and C.Gaboriaud (2007).
Structural insights into the innate immune recognition specificities of L- and H-ficolins.
  EMBO J, 26, 623-633.
PDB codes: 2j0g 2j0h 2j0y 2j1g 2j2p 2j3f 2j3g 2j3o 2j3u 2j5z 2j60 2j61 2j64
16999847 R.Asselta, S.Duga, and M.L.Tenchini (2006).
The molecular basis of quantitative fibrinogen disorders.
  J Thromb Haemost, 4, 2115-2129.  
16575257 R.C.Marchi, Z.Carvajal, C.Boyer-Neumann, E.Anglés-Cano, and J.W.Weisel (2006).
Functional characterization of fibrinogen Bicêtre II: a gamma 308 Asn-->Lys mutation located near the fibrin D:D interaction sites.
  Blood Coagul Fibrinolysis, 17, 193-201.  
16877710 R.R.Hantgan, M.C.Stahle, J.H.Connor, D.A.Horita, M.Rocco, M.A.McLane, S.Yakovlev, and L.Medved (2006).
Integrin alphaIIbbeta3:ligand interactions are linked to binding-site remodeling.
  Protein Sci, 15, 1893-1906.  
16732286 W.A.Barton, D.Tzvetkova-Robev, E.P.Miranda, M.V.Kolev, K.R.Rajashankar, J.P.Himanen, and D.B.Nikolov (2006).
Crystal structures of the Tie2 receptor ectodomain and the angiopoietin-2-Tie2 complex.
  Nat Struct Mol Biol, 13, 524-532.
PDB codes: 2gy5 2gy7
16102057 M.W.Mosesson (2005).
Fibrinogen and fibrin structure and functions.
  J Thromb Haemost, 3, 1894-1904.  
15893672 W.A.Barton, D.Tzvetkova, and D.B.Nikolov (2005).
Structure of the angiopoietin-2 receptor binding domain and identification of surfaces involved in Tie2 recognition.
  Structure, 13, 825-832.
PDB codes: 1z3s 1z3u
16150145 X.Wang, Q.Zhao, and B.M.Christensen (2005).
Identification and characterization of the fibrinogen-like domain of fibrinogen-related proteins in the mosquito, Anopheles gambiae, and the fruitfly, Drosophila melanogaster, genomes.
  BMC Genomics, 6, 114.  
15613026 A.Dear, C.E.Dempfle, S.O.Brennan, W.Kirschstein, and P.M.George (2004).
Fibrinogen Mannheim II: a novel gamma307 His-->Tyr substitution in the gammaD domain causes hypofibrinogenemia.
  J Thromb Haemost, 2, 2194-2199.  
15009453 J.W.Weisel (2004).
Cross-linked gamma-chains in fibrin fibrils bridge transversely between strands: no.
  J Thromb Haemost, 2, 394-399.  
15009452 M.W.Mosesson (2004).
Cross-linked gamma-chains in fibrin fibrils bridge 'transversely' between strands: yes.
  J Thromb Haemost, 2, 388-393.  
15099268 R.F.Doolittle (2004).
Determining the crystal structure of fibrinogen.
  J Thromb Haemost, 2, 683-689.  
14660572 T.Ohashi, and H.P.Erickson (2004).
The disulfide bonding pattern in ficolin multimers.
  J Biol Chem, 279, 6534-6539.  
12695754 F.Mathonnet, L.Guillon, H.Detruit, G.M.Mazmanian, M.Dreyfus, J.C.Alvarez, Y.Giudicelli, and Mazancourt (2003).
Fibrinogen Poissy II (gammaN361K): a novel dysfibrinogenemia associated with defective polymerization and peptide B release.
  Blood Coagul Fibrinolysis, 14, 293-298.  
12871291 R.F.Doolittle (2003).
X-ray crystallographic studies on fibrinogen and fibrin.
  J Thromb Haemost, 1, 1559-1565.  
12490209 R.F.Doolittle (2003).
Structural basis of the fibrinogen-fibrin transformation: contributions from X-ray crystallography.
  Blood Rev, 17, 33-41.  
11877390 G.Camenisch, M.T.Pisabarro, D.Sherman, J.Kowalski, M.Nagel, P.Hass, M.H.Xie, A.Gurney, S.Bodary, X.H.Liang, K.Clark, M.Beresini, N.Ferrara, and H.P.Gerber (2002).
ANGPTL3 stimulates endothelial cell adhesion and migration via integrin alpha vbeta 3 and induces blood vessel formation in vivo.
  J Biol Chem, 277, 17281-17290.  
12012345 M.A.Huntley, and G.B.Golding (2002).
Simple sequences are rare in the Protein Data Bank.
  Proteins, 48, 134-140.  
  12617173 S.J.Everse (2002).
New insights into fibrin (ogen) structure and function.
  Vox Sang, 83, 375-382.  
12162736 Z.Yang, G.Spraggon, L.Pandi, S.J.Everse, M.Riley, and R.F.Doolittle (2002).
Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide.
  Biochemistry, 41, 10218-10224.
PDB code: 1lwu
11593005 J.Madrazo, J.H.Brown, S.Litvinovich, R.Dominguez, S.Yakovlev, L.Medved, and C.Cohen (2001).
Crystal structure of the central region of bovine fibrinogen (E5 fragment) at 1.4-A resolution.
  Proc Natl Acad Sci U S A, 98, 11967-11972.
PDB codes: 1jy2 1jy3
11707569 N.Kairies, H.G.Beisel, P.Fuentes-Prior, R.Tsuda, T.Muta, S.Iwanaga, W.Bode, R.Huber, and S.Kawabata (2001).
The 2.0-A crystal structure of tachylectin 5A provides evidence for the common origin of the innate immunity and the blood coagulation systems.
  Proc Natl Acad Sci U S A, 98, 13519-13524.
PDB code: 1jc9
11468358 R.R.Hantgan, M.Rocco, C.Nagaswami, and J.W.Weisel (2001).
Binding of a fibrinogen mimetic stabilizes integrin alphaIIbbeta3's open conformation.
  Protein Sci, 10, 1614-1626.  
10618375 J.H.Brown, N.Volkmann, G.Jun, A.H.Henschen-Edman, and C.Cohen (2000).
The crystal structure of modified bovine fibrinogen.
  Proc Natl Acad Sci U S A, 97, 85-90.
PDB code: 1deq
11087365 K.R.Siebenlist, D.A.Meh, and M.W.Mosesson (2000).
Position of gamma-chain carboxy-terminal regions in fibrinogen/fibrin cross-linking mixtures.
  Biochemistry, 39, 14171-14175.  
10911375 M.L.Linenberger, J.Kindelan, R.L.Bennett, A.P.Reiner, and H.C.Côté (2000).
Fibrinogen bellingham: a gamma-chain R275C substitution and a beta-promoter polymorphism in a thrombotic member of an asymptomatic family.
  Am J Hematol, 64, 242-250.  
10939439 N.Okumura, F.Terasawa, K.Fujita, M.Tozuka, H.Ota, and T.Katsuyama (2000).
Difference in electrophoretic mobility and plasmic digestion profile between four recombinant fibrinogens, gamma 308K, gamma 308I, gamma 308A, and wild type (gamma 308N).
  Electrophoresis, 21, 2309-2315.  
10618368 S.N.Murthy, J.H.Wilson, T.J.Lukas, Y.Veklich, J.W.Weisel, and L.Lorand (2000).
Transglutaminase-catalyzed crosslinking of the Aalpha and gamma constituent chains in fibrinogen.
  Proc Natl Acad Sci U S A, 97, 44-48.  
  10880389 S.O.Brennan, J.Wyatt, D.Medicina, F.Callea, and P.M.George (2000).
Fibrinogen brescia: hepatic endoplasmic reticulum storage and hypofibrinogenemia because of a gamma284 Gly-->Arg mutation.
  Am J Pathol, 157, 189-196.  
11123898 S.Yakovlev, E.Makogonenko, N.Kurochkina, W.Nieuwenhuizen, K.Ingham, and L.Medved (2000).
Conversion of fibrinogen to fibrin: mechanism of exposure of tPA- and plasminogen-binding sites.
  Biochemistry, 39, 15730-15741.  
11123897 S.Yakovlev, S.Litvinovich, D.Loukinov, and L.Medved (2000).
Role of the beta-strand insert in the central domain of the fibrinogen gamma-module.
  Biochemistry, 39, 15721-15729.  
10737772 Z.Yang, I.Mochalkin, L.Veerapandian, M.Riley, and R.F.Doolittle (2000).
Crystal structure of native chicken fibrinogen at 5.5-A resolution.
  Proc Natl Acad Sci U S A, 97, 3907-3912.
PDB code: 1ei3
11121023 Z.Yang, I.Mochalkin, and R.F.Doolittle (2000).
A model of fibrin formation based on crystal structures of fibrinogen and fibrin fragments complexed with synthetic peptides.
  Proc Natl Acad Sci U S A, 97, 14156-14161.  
10231539 K.Yokoyama, X.P.Zhang, L.Medved, and Y.Takada (1999).
Specific binding of integrin alpha v beta 3 to the fibrinogen gamma and alpha E chain C-terminal domains.
  Biochemistry, 38, 5872-5877.  
  10456895 L.Pei, M.Palma, M.Nilsson, B.Guss, and J.I.Flock (1999).
Functional studies of a fibrinogen binding protein from Staphylococcus epidermidis.
  Infect Immun, 67, 4525-4530.  
9873007 L.V.Medved, M.Migliorini, I.Mikhailenko, L.G.Barrientos, M.Llinás, and D.K.Strickland (1999).
Domain organization of the 39-kDa receptor-associated protein.
  J Biol Chem, 274, 717-727.  
10542261 M.Lausen, N.Lynch, A.Schlosser, I.Tornoe, S.G.Saekmose, B.Teisner, A.C.Willis, E.Crouch, W.Schwaeble, and U.Holmskov (1999).
Microfibril-associated protein 4 is present in lung washings and binds to the collagen region of lung surfactant protein D.
  J Biol Chem, 274, 32234-32240.  
10479736 M.S.Weiss, and R.Hilgenfeld (1999).
A method to detect nonproline cis peptide bonds in proteins.
  Biopolymers, 50, 536-544.  
10074346 S.J.Everse, G.Spraggon, L.Veerapandian, and R.F.Doolittle (1999).
Conformational changes in fragments D and double-D from human fibrin(ogen) upon binding the peptide ligand Gly-His-Arg-Pro-amide.
  Biochemistry, 38, 2941-2946.
PDB codes: 1fze 1fzf 1fzg
  10631982 S.Ware, J.P.Donahue, J.Hawiger, and W.F.Anderson (1999).
Structure of the fibrinogen gamma-chain integrin binding and factor XIIIa cross-linking sites obtained through carrier protein driven crystallization.
  Protein Sci, 8, 2663-2671.
PDB code: 1dug
9799488 C.A.Behnke, V.C.Yee, I.L.Trong, L.C.Pedersen, R.E.Stenkamp, S.S.Kim, G.R.Reeck, and D.C.Teller (1998).
Structural determinants of the bifunctional corn Hageman factor inhibitor: x-ray crystal structure at 1.95 A resolution.
  Biochemistry, 37, 15277-15288.
PDB codes: 1bea 1bfa
9746538 E.Di Stasio, C.Nagaswami, J.W.Weisel, and E.Di Cera (1998).
Cl- regulates the structure of the fibrin clot.
  Biophys J, 75, 1973-1979.  
9689040 G.Spraggon, D.Applegate, S.J.Everse, J.Z.Zhang, L.Veerapandian, C.Redman, R.F.Doolittle, and G.Grieninger (1998).
Crystal structure of a recombinant alphaEC domain from human fibrinogen-420.
  Proc Natl Acad Sci U S A, 95, 9099-9104.
PDB code: 1fzd
9582359 M.Palma, D.Wade, M.Flock, and J.I.Flock (1998).
Multiple binding sites in the interaction between an extracellular fibrinogen-binding protein from Staphylococcus aureus and fibrinogen.
  J Biol Chem, 273, 13177-13181.  
9724734 M.W.Mosesson, K.R.Siebenlist, D.A.Meh, J.S.Wall, and J.F.Hainfeld (1998).
The location of the carboxy-terminal region of gamma chains in fibrinogen and fibrin D domains.
  Proc Natl Acad Sci U S A, 95, 10511-10516.  
9914253 R.F.Doolittle, G.Spraggon, and S.J.Everse (1998).
Three-dimensional structural studies on fragments of fibrinogen and fibrin.
  Curr Opin Struct Biol, 8, 792-798.  
9628725 S.J.Everse, G.Spraggon, L.Veerapandian, M.Riley, and R.F.Doolittle (1998).
Crystal structure of fragment double-D from human fibrin with two different bound ligands.
  Biochemistry, 37, 8637-8642.
PDB code: 1fzc
9712878 T.P.Ugarova, D.A.Solovjov, L.Zhang, D.I.Loukinov, V.C.Yee, L.V.Medved, and E.F.Plow (1998).
Identification of a novel recognition sequence for integrin alphaM beta2 within the gamma-chain of fibrinogen.
  J Biol Chem, 273, 22519-22527.  
9559681 Y.Le, S.H.Lee, O.L.Kon, and J.Lu (1998).
Human L-ficolin: plasma levels, sugar specificity, and assignment of its lectin activity to the fibrinogen-like (FBG) domain.
  FEBS Lett, 425, 367-370.  
9465033 Y.Veklich, E.K.Ang, L.Lorand, and J.W.Weisel (1998).
The complementary aggregation sites of fibrin investigated through examination of polymers of fibrinogen with fragment E.
  Proc Natl Acad Sci U S A, 95, 1438-1442.  
9295325 H.C.Côté, K.P.Pratt, E.W.Davie, and D.W.Chung (1997).
The polymerization pocket "a" within the carboxyl-terminal region of the gamma chain of human fibrinogen is adjacent to but independent from the calcium-binding site.
  J Biol Chem, 272, 23792-23798.  
9207064 K.P.Pratt, H.C.Côté, D.W.Chung, R.E.Stenkamp, and E.W.Davie (1997).
The primary fibrin polymerization pocket: three-dimensional structure of a 30-kDa C-terminal gamma chain fragment complexed with the peptide Gly-Pro-Arg-Pro.
  Proc Natl Acad Sci U S A, 94, 7176-7181.
PDB codes: 2fib 3fib
9109680 L.Medved, S.Litvinovich, T.Ugarova, Y.Matsuka, and K.Ingham (1997).
Domain structure and functional activity of the recombinant human fibrinogen gamma-module (gamma148-411).
  Biochemistry, 36, 4685-4693.  
9368024 N.Okumura, O.V.Gorkun, and S.T.Lord (1997).
Severely impaired polymerization of recombinant fibrinogen gamma-364 Asp --> His, the substitution discovered in a heterozygous individual.
  J Biol Chem, 272, 29596-29601.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.