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(-) Description

Title :  RECOMBINANT HUMAN GAMMA-FIBRINOGEN CARBOXYL TERMINAL FRAGMENT (RESIDUES 143-411) COMPLEXED TO THE PEPTIDE GLY-PRO-ARG-PRO AT PH 6.0
 
Authors :  K. P. Pratt, H. C. F. Cote, D. W. Chung, R. E. Stenkamp, E. W. Davie
Date :  03 Jun 97  (Deposition) - 15 Oct 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fibrinogen, Blood Coagulation, Fibrin Polymerization, Complex (Blood Coagulation/Peptide) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. P. Pratt, H. C. Cote, D. W. Chung, R. E. Stenkamp, E. W. Davie
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. Usa V. 94 7176 1997
PubMed-ID: 9207064  |  Reference-DOI: 10.1073/PNAS.94.14.7176
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FIBRINOGEN
    ChainsA
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPIC9K
    Expression System Taxid4922
    FragmentGAMMA CHAIN, CARBOXYL TERMINAL FRAGMENT RESIDUES 143 - 411
    GeneHUMAN FIBRINOGEN GAMMA CHAIN CDNA ENCODING VAL 143 - VAL 411
    OrganBLOOD
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    TissueBLOOD PLASMA
 
Molecule 2 - GLY-PRO-ARG-PRO
    ChainsB
    EngineeredYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:318 , ASP A:320 , PHE A:322 , GLY A:324 , HOH A:413 , HOH A:414BINDING SITE FOR RESIDUE CA A 412

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:153 -A:182
2A:326 -A:339

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:338 -Cys A:339

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (20, 20)

Asymmetric/Biological Unit (20, 20)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_014170G191RFIBG_HUMANPolymorphism6063AG165R
02UniProtVAR_002409R301CFIBG_HUMANPolymorphism121913087AR275C
03UniProtVAR_002410R301HFIBG_HUMANDisease (DYSFIBRIN)121913088AR275H
04UniProtVAR_072726T303PFIBG_HUMANDisease (CAFBN)  ---AT277P
05UniProtVAR_002411G318VFIBG_HUMANDisease (DYSFIBRIN)121913089AG292V
06UniProtVAR_072727D327HFIBG_HUMANDisease (CAFBN)  ---AD301H
07UniProtVAR_002413N334IFIBG_HUMANPolymorphism121913090AN308I
08UniProtVAR_002412N334KFIBG_HUMANUnclassified  ---AN308K
09UniProtVAR_015853G335DFIBG_HUMANUnclassified  ---AG309D
10UniProtVAR_002414M336TFIBG_HUMANPolymorphism121913091AM310T
11UniProtVAR_072728N345DFIBG_HUMANDisease (CAFBN)  ---AN319D
12UniProtVAR_002416Q355RFIBG_HUMANPolymorphism121913092AQ329R
13UniProtVAR_002418D356VFIBG_HUMANDisease (DYSFIBRIN)121913094AD330V
14UniProtVAR_002417D356YFIBG_HUMANPolymorphism121913093AD330Y
15UniProtVAR_002419N363KFIBG_HUMANUnclassified  ---AN337K
16UniProtVAR_002421S384CFIBG_HUMANUnclassified  ---AS358C
17UniProtVAR_002422R401GFIBG_HUMANPolymorphism75848804AR375G
18UniProtVAR_072729R401WFIBG_HUMANDisease (CAFBN)75848804AR375W
19UniProtVAR_072621S404PFIBG_HUMANDisease (DYSFIBRIN)587777720AS378P
20UniProtVAR_014171M410VFIBG_HUMANPolymorphism6061AM384V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIBRINOGEN_C_2PS51406 Fibrinogen C-terminal domain profile.FIBG_HUMAN170-416  1A:144-390
2FIBRINOGEN_C_1PS00514 Fibrinogen C-terminal domain signature.FIBG_HUMAN360-372  1A:334-346

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1fENST000003360981fENSE00001820766chr4:155533800-155533684117FIBG_HUMAN1-26260--
1.2aENST000003360982aENSE00001781463chr4:155533587-15553354345FIBG_HUMAN27-41150--
1.2dENST000003360982dENSE00001624767chr4:155533353-155533170184FIBG_HUMAN42-103620--
1.2gENST000003360982gENSE00001652916chr4:155533050-15553295794FIBG_HUMAN103-134320--
1.3aENST000003360983aENSE00001127239chr4:155531349-155531219131FIBG_HUMAN134-178451A:143-15210
1.3fENST000003360983fENSE00002146570chr4:155530915-155530782134FIBG_HUMAN178-222451A:152-19645
1.4bENST000003360984bENSE00001127220chr4:155529802-155529618185FIBG_HUMAN223-284621A:197-25862
1.5ENST000003360985ENSE00001127212chr4:155528134-155527857278FIBG_HUMAN284-377941A:258-35194
1.6cENST000003360986cENSE00001344514chr4:155526218-155525728491FIBG_HUMAN377-453771A:351-39242

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:250
 aligned with FIBG_HUMAN | P02679 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:250
                                   178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418
           FIBG_HUMAN   169 VQIHDITGKDCQDIANKGAKQSGLYFIKPLKANQQFLVYCEIDGSGNGWTVFQKRLDGSVDFKKNWIQYKEGFGHLSPTGTTEFWLGNEKIHLISTQSAIPYALRVELEDWNGRTSTADYAMFKVGPEADKYRLTYAYFAGGDAGDAFDGFDFGDDPSDKFFTSHNGMQFSTWDNDNDKFEGNCAEQDGSGWWMNKCHAGHLNGVYYQGGTYSKASTPNGYDNGIIWATWKTRWYSMKKTTMKIIPFNRL 418
               SCOP domains d2fiba_ A: Fibrinogen C-terminal domains                                                                                                                                                                                                                   SCOP domains
               CATH domains -2fibA01 A:144-286,A:381-391 Gamma Fibrinogen, chain A, domain 1                                                                                2fibA02 A:287-380 Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2                       2fibA01    - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhh......eeeee........eeeeeee.....eeeeeeee..........hhhhhh................hhhhhhhh.hhh..eeeeeeee.....eeeeeee......hhh.......eeee.....hhh.........hhhhh....................hhhhh.........................hhh......................eeeeeeeehhh. Sec.struct. author
             SAPs(SNPs) (1) ----------------------R-------------------------------------------------------------------------------------------------------------C-P--------------V--------H------IDT--------D---------RV------K--------------------C----------------G--P-----V-------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------H--------------------------------K---------------------Y--------------------------------------------W----------------- SAPs(SNPs) (2)
                PROSITE (1) -FIBRINOGEN_C_2  PDB: A:144-390 UniProt: 170-416                                                                                                                                                                                                        -- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FIBRINOGEN_C_---------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3a --------------------------------------------Exon 1.4b  PDB: A:197-258 UniProt: 223-284                    --------------------------------------------------------------------------------------------Exon 1.6c  PDB: A:351-392 UniProt: 377-453 Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.3f  PDB: A:152-196 UniProt: 178-222   -------------------------------------------------------------Exon 1.5  PDB: A:258-351 UniProt: 284-377                                                     ----------------------------------------- Transcript 1 (2)
                 2fib A 143 VQIHDITGKDCQDIANKGAKQSGLYFIKPLKANQQFLVYCEIDGSGNGWTVFQKRLDGSVDFKKNWIQYKEGFGHLSPTGTTEFWLGNEKIHLISTQSAIPYALRVELEDWNGRTSTADYAMFKVGPEADKYRLTYAYFAGGDAGDAFDGFDFGDDPSDKFFTSHNGMQFSTWDNDNDKFEGNCAEQDGSGWWMNKCHAGHLNGVYYQGGTYSKASTPNGYDNGIIWATWKTRWYSMKKTTMKIIPFNRL 392
                                   152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392

Chain B from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 2fib B   2 GPRP   5

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FIB)

(-) Gene Ontology  (42, 42)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FIBG_HUMAN | P02679)
molecular function
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0072378    blood coagulation, fibrin clot formation    A protein activation cascade that contributes to blood coagulation and consists of the cascade of enzymatic reactions initiated by physical damage to the wall of a blood vessel, leading to the formation of a formation of a fibrin clot at the site of the injury. The process also includes numerous positive and negative regulatory events.
    GO:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0043623    cellular protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:2000352    negative regulation of endothelial cell apoptotic process    Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell apoptotic process.
    GO:1902042    negative regulation of extrinsic apoptotic signaling pathway via death domain receptors    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
    GO:0031639    plasminogen activation    The process in which inactive plasminogen is processed to active plasmin. This process includes cleavage at an internal Arg-Val site to form an N-terminal A-chain and C-terminal B-chain held together by a disulfide bond, and can include further proteolytic cleavage events to remove the preactivation peptide.
    GO:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0070527    platelet aggregation    The adhesion of one platelet to one or more other platelets via adhesion molecules.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0045921    positive regulation of exocytosis    Any process that activates or increases the frequency, rate or extent of exocytosis.
    GO:0034116    positive regulation of heterotypic cell-cell adhesion    Any process that activates or increases the frequency, rate, or extent of heterotypic cell-cell adhesion.
    GO:0090277    positive regulation of peptide hormone secretion    Any process that increases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules.
    GO:0050714    positive regulation of protein secretion    Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
    GO:1900026    positive regulation of substrate adhesion-dependent cell spreading    Any process that activates or increases the frequency, rate or extent of substrate adhesion-dependent cell spreading.
    GO:0045907    positive regulation of vasoconstriction    Any process that activates or increases the frequency, rate or extent of vasoconstriction.
    GO:0051258    protein polymerization    The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein.
    GO:0009306    protein secretion    The controlled release of proteins from a cell.
    GO:0051592    response to calcium ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005577    fibrinogen complex    A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0031091    platelet alpha granule    A secretory organelle found in blood platelets, which is unique in that it exhibits further compartmentalization and acquires its protein content via two distinct mechanisms: (1) biosynthesis predominantly at the megakaryocyte (MK) level (with some vestigial platelet synthesis) (e.g. platelet factor 4) and (2) endocytosis and pinocytosis at both the MK and circulating platelet levels (e.g. fibrinogen (Fg) and IgG).
    GO:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        FIBG_HUMAN | P026791dug 1fib 1fic 1fid 1fza 1fzb 1fzc 1fze 1fzf 1fzg 1lt9 1ltj 1n86 1n8e 1re3 1re4 1rf0 1rf1 2a45 2ffd 2h43 2hlo 2hod 2hpc 2hwl 2oyh 2oyi 2q9i 2vdo 2vdp 2vdq 2vdr 2vr3 2xnx 2xny 2y7l 2z4e 3bvh 3e1i 3fib 3ghg 3h32 3hus 4b60

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2FIB)