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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C2 DOMAIN OF HUMAN FACTOR VIII AT 1.5 A RESOLUTION AT 1.5 A
 
Authors :  K. P. Pratt, B. W. Shen, B. L. Stoddard
Date :  19 Oct 99  (Deposition) - 01 Dec 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  M
Keywords :  Beta Sandwich, Blood Clotting (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. P. Pratt, B. W. Shen, K. Takeshima, E. W. Davie, K. Fujikawa, B. L. Stoddard
Structure Of The C2 Domain Of Human Factor Viii At 1. 5 A Resolution.
Nature V. 402 439 1999
PubMed-ID: 10586887  |  Reference-DOI: 10.1038/46601

(-) Compounds

Molecule 1 - COAGULATION FACTOR VIII PRECURSOR
    ChainsM
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonBAKER'S YEAST
    Expression System Taxid4932
    FragmentC2-DOMAIN
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    TissueBLOOD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit M

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1CYS1Mod. Amino AcidCYSTEINE
2GOL1Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH M:31 , HOH M:40 , HOH M:118 , HIS M:2211 , GLN M:2213 , GLN M:2246 , PHE M:2290 , ARG M:2320BINDING SITE FOR RESIDUE SO4 M 2332
2AC2SOFTWAREHOH M:140 , VAL M:2223 , ASN M:2224 , ASN M:2277 , LYS M:2279BINDING SITE FOR RESIDUE SO4 M 2333
3AC3SOFTWAREHOH M:111 , ASN M:2172 , SER M:2175 , THR M:2241 , GLN M:2270 , TRP M:2271 , THR M:2272 , VAL M:2294 , CYS M:2296BINDING SITE FOR RESIDUE CYS M 2330
4AC4SOFTWAREHOH M:73 , HOH M:80 , HOH M:412 , MET M:2176 , ALA M:2201 , TRP M:2203 , ARG M:2220 , SER M:2250 , GLY M:2278BINDING SITE FOR RESIDUE GOL M 2331

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1M:2174 -M:2326

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp M:2298 -Pro M:2299

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (49, 49)

Asymmetric/Biological Unit (49, 49)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_028689S2192IFA8_HUMANDisease (HEMA)782098979MS2173I
02UniProtVAR_017341C2193GFA8_HUMANDisease (HEMA)  ---MC2174G
03UniProtVAR_028690P2196RFA8_HUMANDisease (HEMA)  ---MP2177R
04UniProtVAR_028691G2198VFA8_HUMANDisease (HEMA)  ---MG2179V
05UniProtVAR_028692E2200DFA8_HUMANDisease (HEMA)  ---ME2181D
06UniProtVAR_001197I2204TFA8_HUMANDisease (HEMA)  ---MI2185T
07UniProtVAR_001198I2209NFA8_HUMANDisease (HEMA)  ---MI2190N
08UniProtVAR_001199A2211PFA8_HUMANDisease (HEMA)137852468MA2192P
09UniProtVAR_028693A2220PFA8_HUMANDisease (HEMA)782548763MA2201P
10UniProtVAR_028695P2224LFA8_HUMANDisease (HEMA)  ---MP2205L
11UniProtVAR_001201R2228GFA8_HUMANDisease (HEMA)137852355MR2209G
12UniProtVAR_001202R2228LFA8_HUMANDisease (HEMA)137852358MR2209L
13UniProtVAR_028696R2228PFA8_HUMANDisease (HEMA)  ---MR2209P
14UniProtVAR_001203R2228QFA8_HUMANDisease (HEMA)137852358MR2209Q
15UniProtVAR_028697L2229FFA8_HUMANDisease (HEMA)  ---ML2210F
16UniProtVAR_001204V2242MFA8_HUMANPolymorphism782654096MV2223M
17UniProtVAR_001205W2248CFA8_HUMANDisease (HEMA)137852469MW2229C
18UniProtVAR_028698W2248SFA8_HUMANDisease (HEMA)  ---MW2229S
19UniProtVAR_028699V2251AFA8_HUMANDisease (HEMA)782479558MV2232A
20UniProtVAR_028700V2251EFA8_HUMANDisease (HEMA)  ---MV2232E
21UniProtVAR_021356M2257VFA8_HUMANPolymorphism1800297MM2238V
22UniProtVAR_028701T2264AFA8_HUMANDisease (HEMA)  ---MT2245A
23UniProtVAR_001206Q2265RFA8_HUMANDisease (HEMA)137852470MQ2246R
24UniProtVAR_028702F2279CFA8_HUMANDisease (HEMA)  ---MF2260C
25UniProtVAR_028703F2279IFA8_HUMANDisease (HEMA)782717799MF2260I
26UniProtVAR_028704I2281TFA8_HUMANDisease (HEMA)  ---MI2262T
27UniProtVAR_065323D2286GFA8_HUMANDisease (HEMA)  ---MD2267G
28UniProtVAR_028705W2290LFA8_HUMANDisease (HEMA)  ---MW2271L
29UniProtVAR_028706G2304VFA8_HUMANDisease (HEMA)  ---MG2285V
30UniProtVAR_015134D2307AFA8_HUMANDisease (HEMA)  ---MD2288A
31UniProtVAR_001207P2319LFA8_HUMANDisease (HEMA)137852472MP2300L
32UniProtVAR_001208P2319SFA8_HUMANDisease (HEMA)137852374MP2300S
33UniProtVAR_001209R2323CFA8_HUMANDisease (HEMA)137852473MR2304C
34UniProtVAR_028707R2323GFA8_HUMANDisease (HEMA)  ---MR2304G
35UniProtVAR_001210R2323HFA8_HUMANDisease (HEMA)137852474MR2304H
36UniProtVAR_028708R2323LFA8_HUMANDisease (HEMA)  ---MR2304L
37UniProtVAR_028709R2326GFA8_HUMANDisease (HEMA)  ---MR2307G
38UniProtVAR_001211R2326LFA8_HUMANDisease (HEMA)137852360MR2307L
39UniProtVAR_028710R2326PFA8_HUMANDisease (HEMA)  ---MR2307P
40UniProtVAR_001212R2326QFA8_HUMANDisease (HEMA)137852360MR2307Q
41UniProtVAR_028711Q2330PFA8_HUMANDisease (HEMA)  ---MQ2311P
42UniProtVAR_028712W2332RFA8_HUMANDisease (HEMA)  ---MW2313R
43UniProtVAR_065324I2336FFA8_HUMANDisease (HEMA)  ---MI2317F
44UniProtVAR_028713R2339TFA8_HUMANDisease (HEMA)  ---MR2320T
45UniProtVAR_008968G2344CFA8_HUMANDisease (HEMA)  ---MG2325C
46UniProtVAR_065325G2344DFA8_HUMANDisease (HEMA)  ---MG2325D
47UniProtVAR_028714G2344SFA8_HUMANDisease (HEMA)  ---MG2325S
48UniProtVAR_028715C2345SFA8_HUMANDisease (HEMA)  ---MC2326S
49UniProtVAR_028716C2345YFA8_HUMANDisease (HEMA)  ---MC2326Y

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FA58C_3PS50022 Coagulation factors 5/8 type C domain (FA58C) profile.FA8_HUMAN2040-2188
2193-2345
  1-
M:2174-2326
2FA58C_1PS01285 Coagulation factors 5/8 type C domain (FA58C) signature 1.FA8_HUMAN2080-2107
2237-2266
  1-
M:2218-2247
3FA58C_2PS01286 Coagulation factors 5/8 type C domain (FA58C) signature 2.FA8_HUMAN2172-2188
2329-2345
  1-
M:2310-2326

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003602562aENSE00001645223X:154251028-154250685344FA8_HUMAN1-48480--
1.3ENST000003602563ENSE00001422135X:154227875-154227754122FA8_HUMAN48-89420--
1.4ENST000003602564ENSE00001096342X:154225370-154225248123FA8_HUMAN89-130420--
1.5bENST000003602565bENSE00002195289X:154221423-154221211213FA8_HUMAN130-201720--
1.6ENST000003602566ENSE00001633063X:154215580-15421551269FA8_HUMAN201-224240--
1.7bENST000003602567bENSE00002147243X:154213078-154212962117FA8_HUMAN224-263400--
1.8ENST000003602568ENSE00001653886X:154197827-154197606222FA8_HUMAN263-337750--
1.9aENST000003602569aENSE00001776938X:154194962-154194701262FA8_HUMAN337-424880--
1.10aENST0000036025610aENSE00001708410X:154194416-154194245172FA8_HUMAN424-481580--
1.11ENST0000036025611ENSE00001607410X:154189443-15418935094FA8_HUMAN482-513320--
1.12ENST0000036025612ENSE00001748476X:154185446-154185232215FA8_HUMAN513-584720--
1.13ENST0000036025613ENSE00001769821X:154182317-154182167151FA8_HUMAN585-635510--
1.14ENST0000036025614ENSE00001591329X:154176182-154175973210FA8_HUMAN635-705710--
1.15bENST0000036025615bENSE00001311652X:154159951-1541568463106FA8_HUMAN705-174010360--
1.16ENST0000036025616ENSE00001096353X:154134848-154134695154FA8_HUMAN1740-1791520--
1.17ENST0000036025617ENSE00001096366X:154133298-154133086213FA8_HUMAN1792-1862710--
1.18ENST0000036025618ENSE00001096327X:154132799-154132571229FA8_HUMAN1863-1939770--
1.19ENST0000036025619ENSE00001096346X:154132363-154132181183FA8_HUMAN1939-2000620--
1.20ENST0000036025620ENSE00001297698X:154130442-154130326117FA8_HUMAN2000-2039400--
1.21ENST0000036025621ENSE00001413135X:154129717-15412964672FA8_HUMAN2039-2063250--
1.22ENST0000036025622ENSE00001411839X:154128226-15412814186FA8_HUMAN2063-2091290--
1.23ENST0000036025623ENSE00001403942X:154124507-154124352156FA8_HUMAN2092-2143520--
1.25ENST0000036025625ENSE00001308463X:154091502-154091358145FA8_HUMAN2144-2192491M:2171-21733
1.26ENST0000036025626ENSE00001096349X:154090141-154089993149FA8_HUMAN2192-2241501M:2173-222250
1.27ENST0000036025627ENSE00001096386X:154088883-154088707177FA8_HUMAN2242-2300591M:2223-228159
1.28aENST0000036025628aENSE00001878069X:154066027-1540640701958FA8_HUMAN2301-2351511M:2282-233049

(-) 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 M from PDB  Type:PROTEIN  Length:160
 aligned with FA8_HUMAN | P00451 from UniProtKB/Swiss-Prot  Length:2351

    Alignment length:160
                                  2199      2209      2219      2229      2239      2249      2259      2269      2279      2289      2299      2309      2319      2329      2339      2349
           FA8_HUMAN   2190 LNSCSMPLGMESKAISDAQITASSYFTNMFATWSPSKARLHLQGRSNAWRPQVNNPKEWLQVDFQKTMKVTGVTTQGVKSLLTSMYVKEFLISSSQDGHQWTLFFQNGKVKVFQGNQDSFTPVVNSLDPPLLTRYLRIHPQSWVHQIALRMEVLGCEAQD 2349
               SCOP domains d1d7pm_ M: C2 domain of factor VIII                                                                                                                              SCOP domains
               CATH domains 1d7pM00 M:2171-2329 Galactose-binding domain-like                                                                                                              - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhh.......eee..eeehhhhh..................................................................ee..ee.................................................. Sec.struct. author
             SAPs(SNPs) (1) --IG--R-V-D---T----N-P--------P---L---GF------------M-----C--A-----V------AR-------------C-T----G---L-------------V--A-----------L---C--G---P-R---F--T----CS---- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------L-------------------S--E---------------------------I---------------------------------------S---G--L-----------------DY---- SAPs(SNPs) (2)
             SAPs(SNPs) (3) --------------------------------------P----------------------------------------------------------------------------------------------H--P-----------------S----- SAPs(SNPs) (3)
             SAPs(SNPs) (4) --------------------------------------Q----------------------------------------------------------------------------------------------L--Q----------------------- SAPs(SNPs) (4)
                PROSITE (1) ---FA58C_3  PDB: M:2174-2326 UniProt: 2193-2345                                                                                                             ---- PROSITE (1)
                PROSITE (2) -----------------------------------------------FA58C_1  PDB: M:2218-2247     --------------------------------------------------------------FA58C_2          ---- PROSITE (2)
           Transcript 1 (1) 1.2-------------------------------------------------Exon 1.27  PDB: M:2223-2281 UniProt: 2242-2300             Exon 1.28a  PDB: M:2282-2330 UniProt: 2301-2351   Transcript 1 (1)
           Transcript 1 (2) --Exon 1.26  PDB: M:2173-2222 UniProt: 2192-2241    ------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                1d7p M 2171 LNSCSMPLGMESKAISDAQITASSYFTNMFATWSPSKARLHLQGRSNAWRPQVNNPKEWLQVDFQKTMKVTGVTTQGVKSLLTSMYVKEFLISSSQDGHQWTLFFQNGKVKVFQGNQDSFTPVVNCLDPPLLTRYLRIHPQSWVHQIALRMEVLGCEAQC 2330
                                  2180      2190      2200      2210      2220      2230      2240      2250      2260      2270      2280      2290      2300      2310      2320      2330

   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1D7P)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain M   (FA8_HUMAN | P00451)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    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).
biological process
    GO:0048208    COPII vesicle coating    The addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.
    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:0006953    acute-phase response    An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
    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:0007597    blood coagulation, intrinsic pathway    A protein activation cascade that contributes to blood coagulation and consists of the interactions among high molecular weight kininogen, prekallikrein, and factor XII that lead to the activation of clotting factor X.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    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:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
cellular component
    GO:0030134    COPII-coated ER to Golgi transport vesicle    A vesicle with a coat formed of the COPII coat complex proteins. The COPII coat complex is formed by the Sec23p/Sec24p and the Sec13p/Sec31p heterodimers. COPII-associated vesicles transport proteins from the rough endoplasmic reticulum to the Golgi apparatus (anterograde transport).
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0033116    endoplasmic reticulum-Golgi intermediate compartment membrane    The lipid bilayer surrounding any of the compartments of the endoplasmic reticulum (ER)-Golgi intermediate compartment system.
    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: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
        FA8_HUMAN | P004511cfg 1fac 1iqd 2r7e 3cdz 3hnb 3hny 3hob 3j2q 3j2s 4bdv 4ki5 4pt6 4xzu 5k8d

(-) Related Entries Specified in the PDB File

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