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(-) Description

Title :  THE FIRST EGF-LIKE DOMAIN FROM HUMAN BLOOD COAGULATION FVII, NMR, MINIMIZED AVERAGE STRUCTURE
 
Authors :  Y. -H. Kao, G. F. Lee, Y. Wang, M. A. Starovasnik, R. F. Kelley, M. W. Spellman, L. Lerner
Date :  19 Feb 99  (Deposition) - 16 Jun 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Factor Vii, Blood Coagulation, Egf-Like Domain, Blood Clotting (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. H. Kao, G. F. Lee, Y. Wang, M. A. Starovasnik, R. F. Kelley, M. W. Spellman, L. Lerner
The Effect Of O-Fucosylation On The First Egf-Like Domain From Human Blood Coagulation Factor Vii.
Biochemistry V. 38 7097 1999
PubMed-ID: 10353820  |  Reference-DOI: 10.1021/BI990234Z
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (BLOOD COAGULATION FACTOR VII)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentFIRST EGF-LIKE DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCALCIUM BOUND FORM

 Structural Features

(-) Chains, Units

  
NMR Structure 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1F7M)

(-) Sites  (0, 0)

(no "Site" information available for 1F7M)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:50 -A:61
2A:55 -A:70
3A:72 -A:81

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F7M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (13, 13)

NMR Structure (13, 13)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_065376N117DFA7_HUMANDisease (FA7D)121964932AN57D
02UniProtVAR_015136S120PFA7_HUMANDisease (FA7D)  ---AS60P
03UniProtVAR_014407C121FFA7_HUMANDisease (FA7D)  ---AC61F
04UniProtVAR_014408L125PFA7_HUMANDisease (FA7D)  ---AL65P
05UniProtVAR_014409Y128CFA7_HUMANDisease (FA7D)  ---AY68C
06UniProtVAR_065377G138DFA7_HUMANDisease (FA7D)  ---AG78D
07UniProtVAR_006497R139KFA7_HUMANDisease (FA7D)  ---AR79K
08UniProtVAR_006498R139QFA7_HUMANDisease (FA7D)150525536AR79Q
09UniProtVAR_006499R139WFA7_HUMANDisease (FA7D)776796178AR79W
10UniProtVAR_065378G156SFA7_HUMANDisease (FA7D)563972504AG88S
11UniProtVAR_006501G157CFA7_HUMANDisease (FA7D)  ---AS89C
12UniProtVAR_006500G157SFA7_HUMANDisease (FA7D)763458490AS89S
13UniProtVAR_014411G157VFA7_HUMANDisease (FA7D)771335282AS89V

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

(-) PROSITE Motifs  (4, 4)

NMR Structure (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_3PS50026 EGF-like domain profile.FA7_HUMAN106-142  1A:46-82
2EGF_CAPS01187 Calcium-binding EGF-like domain signature.FA7_HUMAN106-130  1A:46-70
3ASX_HYDROXYLPS00010 Aspartic acid and asparagine hydroxylation site.FA7_HUMAN121-132  1A:61-72
4EGF_1PS00022 EGF-like domain signature 1.FA7_HUMAN130-141  1A:70-81

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003755811bENSE00001891092chr13:113760121-11376021999FA7_HUMAN1-22220--
1.2ENST000003755812ENSE00000862519chr13:113761159-11376122466FA7_HUMAN22-44230--
1.3cENST000003755813cENSE00001135032chr13:113765004-113765164161FA7_HUMAN44-97540--
1.4aENST000003755814aENSE00000862522chr13:113768066-11376809025FA7_HUMAN98-10691A:45-462
1.4cENST000003755814cENSE00001135014chr13:113768161-113768274114FA7_HUMAN106-144391A:46-8439
1.7ENST000003755817ENSE00001786842chr13:113769974-113770114141FA7_HUMAN144-191481A:84-90 (gaps)15
1.8cENST000003755818cENSE00001134999chr13:113771080-113771189110FA7_HUMAN191-227370--
1.9ENST000003755819ENSE00000687189chr13:113771787-113771910124FA7_HUMAN228-269420--
1.10bENST0000037558110bENSE00001467515chr13:113772727-1137749952269FA7_HUMAN269-4661980--

(-) Sequences/Alignments

NMR Structure
   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:46
 aligned with FA7_HUMAN | P08709 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:54
                                   114       124       134       144       154    
            FA7_HUMAN   105 SDGDQCASSPCQNGGSCKDQLQSYICFCLPAFEGRNCETHKDDQLICVNENGGC 158
               SCOP domains d1f7ma_ A: Coagulation factor VIIa                     SCOP domains
               CATH domains 1f7mA00 A:45-90 Laminin                                CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ...............eeee....eeee....ee.....ee...--------... Sec.struct. author
             SAPs(SNPs) (1) ------------D--PF---P--C---------DK----------------SC- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------Q-----------------S- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------W-----------------V- SAPs(SNPs) (3)
                PROSITE (1) -EGF_CA  PDB: A:46-70     ---------------------------- PROSITE (1)
                PROSITE (2) -EGF_3  PDB: A:46-82 UniProt: 106-142 ---------------- PROSITE (2)
                PROSITE (3) ----------------ASX_HYDROXYL-------------------------- PROSITE (3)
                PROSITE (4) -------------------------EGF_1       ----------------- PROSITE (4)
           Transcript 1 (1) 1.-------------------------------------Exon 1.7        Transcript 1 (1)
           Transcript 1 (2) -Exon 1.4c  PDB: A:46-84                -------------- Transcript 1 (2)
                 1f7m A  45 SDGDQCASSPCQNGGSCKDQLQSYICFCLPAFEGRNCETHKDD--------GSA  90
                                    54        64        74        84  |      - |  
                                                                     87       88  

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F7M)

(-) Gene Ontology  (35, 35)

NMR Structure(hide GO term definitions)
Chain A   (FA7_HUMAN | P08709)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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: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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0031100    animal organ regeneration    The regrowth of a lost or destroyed animal organ.
    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:0007598    blood coagulation, extrinsic pathway    A protein activation cascade that contributes to blood coagulation and consists of the self-limited process linking exposure and activation of tissue factor to the activation of clotting factor X.
    GO:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0017187    peptidyl-glutamic acid carboxylation    The gamma-carboxylation of peptidyl-glutamic acid; catalyzed by the vitamin K dependent gamma-glutamyl carboxylase.
    GO:0030194    positive regulation of blood coagulation    Any process that activates or increases the frequency, rate or extent of blood coagulation.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0002690    positive regulation of leukocyte chemotaxis    Any process that activates or increases the frequency, rate, or extent of leukocyte chemotaxis.
    GO:0010641    positive regulation of platelet-derived growth factor receptor signaling pathway    Any process that increases the frequency, rate or extent of the platelet-derived growth factor receptor signaling pathway.
    GO:0050927    positive regulation of positive chemotaxis    Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical.
    GO:0051897    positive regulation of protein kinase B signaling    Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0043627    response to estrogen    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 stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics.
    GO:0060416    response to growth hormone    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 growth hormone stimulus. Growth hormone is a peptide hormone that binds to the growth hormone receptor and stimulates growth.
    GO:0009725    response to hormone    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 hormone stimulus.
    GO:0031667    response to nutrient levels    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 stimulus reflecting the presence, absence, or concentration of nutrients.
    GO:0014070    response to organic cyclic compound    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 an organic cyclic compound stimulus.
    GO:0032571    response to vitamin K    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 vitamin K stimulus.
    GO:0006465    signal peptide processing    The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.
cellular component
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    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: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:0031982    vesicle    Any small, fluid-filled, spherical organelle enclosed by membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FA7_HUMAN | P087091bf9 1cvw 1dan 1dva 1f7e 1fak 1ff7 1ffm 1j9c 1jbu 1kli 1klj 1nl8 1o5d 1qfk 1w0y 1w2k 1w7x 1w8b 1wqv 1wss 1wtg 1wun 1wv7 1ygc 1z6j 2a2q 2aei 2aer 2b7d 2b8o 2bz6 2c4f 2ec9 2f9b 2fir 2flb 2flr 2puq 2zp0 2zwl 2zzu 3ela 3th2 3th3 3th4 4ibl 4ish 4isi 4jyu 4jyv 4jzd 4jze 4jzf 4na9 4ng9 4nga 4x8s 4x8t 4x8u 4x8v 4ylq 4yt6 4yt7 4z6a 4zma 4zxx 4zxy 5i46 5l2y 5l2z 5l30 5pa8 5pa9 5paa 5pab 5pac 5pae 5paf 5pag 5pai 5paj 5pak 5pam 5pan 5pao 5paq 5par 5pas 5pat 5pau 5pav 5paw 5pax 5pay 5pb0 5pb1 5pb2 5pb3 5pb4 5pb5 5pb6 5tqe 5tqf 5tqg 5u6j

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