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(-) Description

Title :  SOLUTION STRUCTURE OF THE MAJOR FACTOR VIII BINDING REGION ON VON WILLEBRAND FACTOR
 
Authors :  N. Shiltagh, J. Kirkpatrick, L. D. Cabrita, T. A. J. Mckinnon, K. Thalas E. G. D. Tuddenham, D. F. Hansen
Date :  02 Dec 13  (Deposition) - 14 May 14  (Release) - 14 May 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
NMR Structure *:  A  (1x)
Keywords :  Von Willebrand Factor, Factor Viii, Ensemble Refinement, Blood Clotting (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Shiltagh, J. Kirkpatrick, L. D. Cabrita, T. A. J. Mckinnon, K. Thalassinos, E. G. D. Tuddenham, D. F. Hansen
Solution Structure Of The Major Factor Viii Binding Region On Von Willebrand Factor
Blood 2014
PubMed-ID: 24700780  |  Reference-DOI: 10.1182/BLOOD-2013-07-517086

(-) Compounds

Molecule 1 - VON WILLEBRAND FACTOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainK12
    Expression System Taxid562
    Expression System VariantSHUFFLE
    Expression System VectorPET32B+
    Expression System Vector TypeVECTOR
    FragmentDOMAINS TIL' AND E', UNP RESIDUES 766-864
    GeneVWF, F8VWF
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymVWF, VON WILLEBRAND ANTIGEN 2, VON WILLEBRAND ANTIGEN II

 Structural Features

(-) Chains, Units

  1
NMR Structure (10x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2MHQ)

(-) Sites  (0, 0)

(no "Site" information available for 2MHQ)

(-) SS Bonds  (8, 8)

NMR Structure
No.Residues
1A:6 -A:47
2A:15 -A:43
3A:27 -A:38
4A:31 -A:66
5A:49 -A:60
6A:68 -A:90
7A:85 -A:102
8A:88 -A:97

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2MHQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (7, 7)

NMR Structure (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_009141C788YVWF_HUMANDisease (VWD2)61748476AC27Y
2UniProtVAR_005785T789AVWF_HUMANPolymorphism1063856AT28A
3UniProtVAR_005786T791MVWF_HUMANDisease (VWD2)61748477AT30M
4UniProtVAR_005787R816WVWF_HUMANDisease (VWD2)121964894AR55W
5UniProtVAR_005788Q852RVWF_HUMANPolymorphism216321AR91R
6UniProtVAR_005789R854QVWF_HUMANDisease (VWD2)41276738AR93Q
7UniProtVAR_005790N857DVWF_HUMANPolymorphism  ---AN96D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_009141C788YVWF_HUMANDisease (VWD2)61748476AC27Y
2UniProtVAR_005785T789AVWF_HUMANPolymorphism1063856AT28A
3UniProtVAR_005786T791MVWF_HUMANDisease (VWD2)61748477AT30M
4UniProtVAR_005787R816WVWF_HUMANDisease (VWD2)121964894AR55W
5UniProtVAR_005788Q852RVWF_HUMANPolymorphism216321AR91R
6UniProtVAR_005789R854QVWF_HUMANDisease (VWD2)41276738AR93Q
7UniProtVAR_005790N857DVWF_HUMANPolymorphism  ---AN96D

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2MHQ)

(-) Exons   (4, 4)

NMR Structure (4, 4)
 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_HUMAN729-761331A:1-44
1.19ENST0000026140519ENSE00000936969chr12:6153617-6153457161VWF_HUMAN761-814541A:5-5349
1.20ENST0000026140520ENSE00000936970chr12:6145657-6145554104VWF_HUMAN815-849351A:54-8835
1.21ENST0000026140521ENSE00000936971chr12:6143992-6143854139VWF_HUMAN849-895471A:88-10316
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_HUMAN1225-16854610--
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

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:103
 aligned with VWF_HUMAN | P04275 from UniProtKB/Swiss-Prot  Length:2813

    Alignment length:123
                                   751       761       771       781       791       801       811       821       831       841       851       861   
            VWF_HUMAN   742 GVPGSLLPDAVLSSPLSHRSKRSLSCRPPMVKLVCPADNLRAEGLECTKTCQNYDLECMSMGCVSGCLCPPGMVRHENRCVALERCPCFHQGKEYAPGETVKIGCNTCVCQDRKWNCTDHVCD 864
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....--------------------.................................................eee..eee..................eeee..eeeeee..eeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------YA-M------------------------W-----------------------------------R-Q--D------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.18  PDB: A:1------------------------------------------------------Exon 1.20  PDB: A:54-88            --------------- Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.19  PDB: A:5-53 UniProt: 761-814 [INCOMPLETE]  ----------------------------------Exon 1.21        Transcript 1 (2)
                 2mhq A   1 GAMG--------------------SCRPPMVKLVCPADNLRAEGLECTKTCQNYDLECMSMGCVSGCLCPPGMVRHENRCVALERCPCFHQGKEYAPGETVKIGCNTCVCRDRKWNCTDHVCD 103
                               |     -         -    |   10        20        30        40        50        60        70        80        90       100   
                               4                    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  (0, 0)

(no "SCOP Domain" information available for 2MHQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2MHQ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

NMR Structure(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 3gxb 3hxo 3hxq 3ppv 3ppw 3ppx 3ppy 3zqk 4c29 4c2a 4c2b 4dmu 4nt5 5bv8

(-) Related Entries Specified in the PDB File

2mhp