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(-) Description

Title :  CRYSTAL STRUCTURE OF THE D1596A MUTANT OF AN ENGINEERED VWF A2 DOMAIN (N1493C AND C1670S)
 
Authors :  M. Zhou, X. Dong, C. Zhong, J. Ding
Date :  25 Nov 10  (Deposition) - 04 May 11  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Von Willebrand Factor, Vwa Domain, Protein Unfolding, And Adamts13 Cleavage, Rossmann Fold, Coagulation, Cell Adhesion, Cleavage, Glycosylation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Zhou, X. Dong, C. Baldauf, H. Chen, Y. Zhou, T. A. Springer, X. Luo, C. Zhong, F. Grater, J. Ding
A Novel Calcium-Binding Site Of Von Willebrand Factor A2 Domain Regulates Its Cleavage By Adamts13
Blood V. 117 4623 2011
PubMed-ID: 21385852  |  Reference-DOI: 10.1182/BLOOD-2010-11-321596

(-) Compounds

Molecule 1 - VON WILLEBRAND FACTOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System StrainBL21(DE3) CODON PLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentVWFA 2 DOMAIN, UNP RESIDUES 1488-1674
    GeneF8VWF, VWF
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymVWF, VON WILLEBRAND ANTIGEN 2, VON WILLEBRAND ANTIGEN II

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:101 , ASP A:1498 , ARG A:1597 , ALA A:1600 , ASN A:1602BINDING SITE FOR RESIDUE NA A 1

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:1493 -A:1669

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:1644 -Pro A:1645

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (16, 16)

Asymmetric/Biological Unit (16, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_005808F1514CVWF_HUMANDisease (VWD2)61750101AF1514C
02UniProtVAR_005809L1540PVWF_HUMANDisease (VWD2)267607342AL1540P
03UniProtVAR_014630V1565LVWF_HUMANPolymorphism1800385AV1565L
04UniProtVAR_036276Y1570CVWF_HUMANUnclassified  ---AY1570C
05CancerSNPVAR_VWF_HUMAN_CCDS8539_1_01 *Y1570CVWF_HUMANDisease (Breast cancer)  ---AY1570C
06UniProtVAR_005810Y1584CVWF_HUMANPolymorphism1800386AY1584C
07UniProtVAR_005811R1597GVWF_HUMANDisease (VWD2)61750117AR1597G
08UniProtVAR_005812R1597QVWF_HUMANDisease (VWD2)61750577AR1597Q
09UniProtVAR_005813R1597WVWF_HUMANDisease (VWD2)61750117AR1597W
10UniProtVAR_005814V1607DVWF_HUMANDisease (VWD2)61750579AV1607D
11UniProtVAR_005815G1609RVWF_HUMANDisease (VWD2)61750580AG1609R
12UniProtVAR_005816S1613PVWF_HUMANDisease (VWD2)61750581AS1613P
13UniProtVAR_005817I1628TVWF_HUMANDisease (VWD2)61750584AI1628T
14UniProtVAR_005818E1638KVWF_HUMANDisease (VWD2)61750588AE1638K
15UniProtVAR_005819P1648SVWF_HUMANDisease (VWD2)61750590AP1648S
16UniProtVAR_005820V1665EVWF_HUMANDisease (VWD2)61750596AV1665E
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VWFAPS50234 VWFA domain profile.VWF_HUMAN1498-1665
1277-1453
1691-1871
  1A:1498-1665
-
-

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002614051ENSE00001184496chr12:6233836-6233587250VWF_HUMAN-00--
1.2ENST000002614052ENSE00001653826chr12:6232362-623230855VWF_HUMAN1-19190--
1.4ENST000002614054ENSE00001261893chr12:6230504-6230340165VWF_HUMAN19-74560--
1.5ENST000002614055ENSE00001261546chr12:6220134-6220032103VWF_HUMAN74-108350--
1.6ENST000002614056ENSE00002152539chr12:6219748-6219540209VWF_HUMAN108-178710--
1.7aENST000002614057aENSE00001676171chr12:6204750-6204626125VWF_HUMAN178-219420--
1.8ENST000002614058ENSE00001682720chr12:6184717-6184501217VWF_HUMAN220-292730--
1.9ENST000002614059ENSE00001640051chr12:6182907-6182785123VWF_HUMAN292-333420--
1.10ENST0000026140510ENSE00001656280chr12:6181608-6181497112VWF_HUMAN333-370380--
1.11ENST0000026140511ENSE00001700039chr12:6180509-618046347VWF_HUMAN370-386170--
1.12ENST0000026140512ENSE00001674584chr12:6174439-6174303137VWF_HUMAN386-431460--
1.13ENST0000026140513ENSE00001645253chr12:6173550-6173412139VWF_HUMAN432-478470--
1.14ENST0000026140514ENSE00001679915chr12:6172220-6172120101VWF_HUMAN478-511340--
1.15ENST0000026140515ENSE00001640163chr12:6167210-6167015196VWF_HUMAN512-577660--
1.16ENST0000026140516ENSE00001727074chr12:6166238-6166023216VWF_HUMAN577-649730--
1.17bENST0000026140517bENSE00000936967chr12:6161949-6161709241VWF_HUMAN649-729810--
1.18ENST0000026140518ENSE00000936968chr12:6155983-615588995VWF_HUMAN729-761330--
1.19ENST0000026140519ENSE00000936969chr12:6153617-6153457161VWF_HUMAN761-814540--
1.20ENST0000026140520ENSE00000936970chr12:6145657-6145554104VWF_HUMAN815-849350--
1.21ENST0000026140521ENSE00000936971chr12:6143992-6143854139VWF_HUMAN849-895470--
1.22ENST0000026140522ENSE00000936972chr12:6140744-6140610135VWF_HUMAN896-940450--
1.23ENST0000026140523ENSE00000936973chr12:6138654-6138508147VWF_HUMAN941-989490--
1.24ENST0000026140524ENSE00000936974chr12:6135212-6135072141VWF_HUMAN990-1036470--
1.25ENST0000026140525ENSE00001731504chr12:6134859-6134746114VWF_HUMAN1037-1074380--
1.26ENST0000026140526ENSE00000936976chr12:6132953-6132797157VWF_HUMAN1075-1127530--
1.27ENST0000026140527ENSE00001792722chr12:6132064-6131906159VWF_HUMAN1127-1180540--
1.28ENST0000026140528ENSE00001679248chr12:6131201-6131066136VWF_HUMAN1180-1225460--
1.29ENST0000026140529ENSE00001749068chr12:6128909-61275311379VWF_HUMAN1225-16854611A:1493-1676184
1.30ENST0000026140530ENSE00001676963chr12:6126036-6125920117VWF_HUMAN1685-1724400--
1.31ENST0000026140531ENSE00001646337chr12:6125822-6125682141VWF_HUMAN1724-1771480--
1.32ENST0000026140532ENSE00001603271chr12:6125398-6125255144VWF_HUMAN1771-1819490--
1.33ENST0000026140533ENSE00000936983chr12:6122811-6122647165VWF_HUMAN1819-1874560--
1.34ENST0000026140534ENSE00001761241chr12:6121296-612125344VWF_HUMAN1874-1888150--
1.35ENST0000026140535ENSE00001622286chr12:6120960-6120783178VWF_HUMAN1889-1948600--
1.36ENST0000026140536ENSE00001261636chr12:6105388-6105168221VWF_HUMAN1948-2021740--
1.37ENST0000026140537ENSE00000866874chr12:6103773-6103581193VWF_HUMAN2022-2086650--
1.38ENST0000026140538ENSE00000866873chr12:6103369-6103028342VWF_HUMAN2086-22001150--
1.39ENST0000026140539ENSE00001328745chr12:6101184-6100985200VWF_HUMAN2200-2266670--
1.40ENST0000026140540ENSE00001261609chr12:6094831-6094729103VWF_HUMAN2267-2301350--
1.41ENST0000026140541ENSE00001261603chr12:6094285-609421175VWF_HUMAN2301-2326260--
1.42ENST0000026140542ENSE00000866869chr12:6092420-6092316105VWF_HUMAN2326-2361360--
1.43ENST0000026140543ENSE00001309185chr12:6091157-6090952206VWF_HUMAN2361-2429690--
1.44ENST0000026140544ENSE00000866867chr12:6085426-6085277150VWF_HUMAN2430-2479500--
1.45ENST0000026140545ENSE00001261579chr12:6080875-6080765111VWF_HUMAN2480-2516370--
1.46ENST0000026140546ENSE00001316394chr12:6078557-6078377181VWF_HUMAN2517-2577610--
1.47ENST0000026140547ENSE00000866864chr12:6077333-607729341VWF_HUMAN2577-2590140--
1.48ENST0000026140548ENSE00001289624chr12:6076768-6076652117VWF_HUMAN2591-2629390--
1.49ENST0000026140549ENSE00001312819chr12:6062760-606266299VWF_HUMAN2630-2662330--
1.50ENST0000026140550ENSE00001326641chr12:6061685-6061557129VWF_HUMAN2663-2705430--
1.51ENST0000026140551ENSE00001307387chr12:6061049-606101040VWF_HUMAN2706-2719140--
1.52aENST0000026140552aENSE00001293437chr12:6059049-605895298VWF_HUMAN2719-2751330--
1.53bENST0000026140553bENSE00001314535chr12:6058369-6058040330VWF_HUMAN2752-2813620--

(-) 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:184
 aligned with VWF_HUMAN | P04275 from UniProtKB/Swiss-Prot  Length:2813

    Alignment length:184
                                  1502      1512      1522      1532      1542      1552      1562      1572      1582      1592      1602      1612      1622      1632      1642      1652      1662      1672    
           VWF_HUMAN   1493 NSMVLDVAFVLEGSDKIGEADFNRSKEFMEEVIQRMDVGQDSIHVTVLQYSYMVTVEYPFSEAQSKGDILQRVREIRYQGGNRTNTGLALRYLSDHSFLVSQGDREQAPNLVYMVTGNPASDEIKRLPGDIQVVPIGVGPNANVQELERIGWPNAPILIQDFETLPREAPDLVLQRCCSGEGLQ 1676
               SCOP domains d3ppwa_ A: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----VWA-3ppwA01 A:1498-1659                                                                                                                                           ----------------- Pfam domains
         Sec.struct. author ....eeeeeeee.....hhhhhhhhhhhhhhhhhhh......eeeeeeee...eeeee......hhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh......eeeeeee..............eeeeeeee....hhhhhhhhhh....eee....hhhhhhhhhhhhhhhhh.... Sec.struct. author
             SAPs(SNPs) (1) ---------------------C-------------------------P------------------------L----C-------------C------------G---------D-R---P--------------T---------K---------S----------------E----------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------C--------------------------Q------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) --------------------------------------------------------------------------------------------------------W------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE -----VWFA  PDB: A:1498-1665 UniProt: 1498-1665                                                                                                                               ----------- PROSITE
               Transcript 1 Exon 1.29  PDB: A:1493-1676 UniProt: 1225-1685 [INCOMPLETE]                                                                                                                              Transcript 1
                3ppw A 1493 CSMVLDVAFVLEGSDKIGEADFNRSKEFMEEVIQRMDVGQDSIHVTVLQYSYMVTVEYPFSEAQSKGDILQRVREIRYQGGNRTNTGLALRYLSDHSFLVSQGAREQAPNLVYMVTGNPASDEIKRLPGDIQVVPIGVGPNANVQELERIGWPNAPILIQDFETLPREAPDLVLQRCSSGEGLE 1676
                                  1502      1512      1522      1532      1542      1552      1562      1572      1582      1592      1602      1612      1622      1632      1642      1652      1662      1672    

   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  (0, 0)

(no "CATH Domain" information available for 3PPW)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: vWA-like (60)
(-)
Family: VWA (50)
1aVWA-3ppwA01A:1498-1659

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VWF_HUMAN | P04275)
molecular function
    GO:0051087    chaperone binding    Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
    GO:0005518    collagen binding    Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0019865    immunoglobulin binding    Interacting selectively and non-covalently with an immunoglobulin.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
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: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:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0031589    cell-substrate adhesion    The attachment of a cell to the underlying substrate via adhesion molecules.
    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:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    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.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0035902    response to immobilization stress    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 being rendered immobile.
    GO:0009611    response to wounding    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 indicating damage to the organism.
cellular component
    GO:0033093    Weibel-Palade body    A large, elongated, rod-shaped secretory granule characteristic of vascular endothelial cells that contain a number of structurally and functionally distinct proteins, of which the best characterized are von Willebrand factor (VWF) and P-selectin. Weibel-Palade bodies are formed from the trans-Golgi network in a process that depends on VWF, which is densely packed in a highly organized manner, and on coat proteins that remain associated with the granules. Upon cell stimulation, regulated exocytosis releases the contained proteins to the cell surface, where they act in the recruitment of platelets and leukocytes and in inflammatory and vasoactive responses.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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: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.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VWF_HUMAN | P042751ao3 1atz 1auq 1fe8 1fns 1ijb 1ijk 1m10 1oak 1sq0 1u0n 1uex 2adf 2mhp 2mhq 3gxb 3hxo 3hxq 3ppv 3ppx 3ppy 3zqk 4c29 4c2a 4c2b 4dmu 4nt5 5bv8

(-) Related Entries Specified in the PDB File

3gxb 3ppv 3ppx 3ppy