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(-) Description

Title :  CRYSTAL STRUCTURE OF STABILIZED HUMAN UPAR MUTANT
 
Authors :  M. D. Huang, X. Xu, C. Yuan
Date :  13 Oct 11  (Deposition) - 18 Apr 12  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym./Biol. Unit :  U
Keywords :  Glycosylation, Hydrolase Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Xu, H. Gardsvoll, C. Yuan, L. Lin, M. Ploug, M. Huang
Crystal Structure Of The Urokinase Receptor In A Ligand-Fre Form.
J. Mol. Biol. V. 416 629 2012
PubMed-ID: 22285761  |  Reference-DOI: 10.1016/J.JMB.2011.12.058

(-) Compounds

Molecule 1 - UROKINASE PLASMINOGEN ACTIVATOR SURFACE RECEPTOR
    Cell LineS2 CELLS
    ChainsU
    EngineeredYES
    Expression SystemDROSOPHILA MELANOGASTER
    Expression System PlasmidPMT/BIP
    Expression System Taxid7227
    Expression System Vector TypePLASMID
    GeneMO3, PLAUR, UPAR
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymU-PAR, UPAR, MONOCYTE ACTIVATION ANTIGEN MO3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit U

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN U:52 , VAL U:70 , NAG U:502BINDING SITE FOR RESIDUE NAG U 501
2AC2SOFTWARENAG U:501BINDING SITE FOR RESIDUE NAG U 502
3AC3SOFTWAREASN U:200 , THR U:202 , HIS U:203BINDING SITE FOR RESIDUE NAG U 503

(-) SS Bonds  (15, 15)

Asymmetric/Biological Unit
No.Residues
1U:3 -U:24
2U:6 -U:12
3U:17 -U:45
4U:47 -U:259
5U:71 -U:76
6U:95 -U:122
7U:98 -U:105
8U:115 -U:147
9U:153 -U:170
10U:171 -U:176
11U:194 -U:222
12U:197 -U:205
13U:215 -U:241
14U:247 -U:265
15U:266 -U:271

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Cys U:153 -Pro U:154
2Ser U:282 -Gly U:283

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_016322E55GUPAR_HUMANPolymorphism4251813UE33G
2UniProtVAR_016323T86AUPAR_HUMANPolymorphism399145UT64A
3UniProtVAR_016325K220RUPAR_HUMANPolymorphism2302524UK198R
4UniProtVAR_016326N281KUPAR_HUMANPolymorphism4251921UC259K
5UniProtVAR_052698D297AUPAR_HUMANPolymorphism16976608UD275A

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

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LY6_UPARPS00983 Ly-6 / u-PAR domain signature.UPAR_HUMAN24-67
116-169
215-269
  3U:2-45
U:94-147
U:193-247

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003400931ENSE00001048170chr19:44174502-44174218285UPAR_HUMAN1-19190--
1.2ENST000003400932ENSE00000847438chr19:44171843-44171733111UPAR_HUMAN19-56381U:1-3434
1.3ENST000003400933ENSE00000494759chr19:44169611-44169468144UPAR_HUMAN56-104491U:34-8047
1.4ENST000003400934ENSE00000710867chr19:44160792-44160631162UPAR_HUMAN104-158551U:91-12939
1.5ENST000003400935ENSE00000710856chr19:44159725-44159591135UPAR_HUMAN158-203461U:140-18142
1.6ENST000003400936ENSE00000847435chr19:44156523-44156377147UPAR_HUMAN203-252501U:181-23050
1.7ENST000003400937ENSE00000847434chr19:44153295-44152732564UPAR_HUMAN252-335841U:230-28354

(-) 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 U from PDB  Type:PROTEIN  Length:263
 aligned with UPAR_HUMAN | Q03405 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:283
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302   
           UPAR_HUMAN    23 LRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDVQYRSG 305
               SCOP domains d3u74u1 U:1-80 automated matches                                                          d3u74u2 U:91-187 automated matches                                                               d3u74u3 U:188-283 automated matches                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee......eeeeeeeeeee..eeeeeeeeeee......eeeeeee..eeeeeeeeee.........----------...eeee.....hhhhhh..eeee......eeeeeeee.----------..eeeeeeee.....eeeeee....eeeeeee...........hhhhh.eeeeeeeeeee......hhhhheeeeee....eeeeeeeee.....eeeeeeee.hhhhhhhhhhhhhheeeeeeeee......hhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------G------------------------------A-------------------------------------------------------------------------------------------------------------------------------------R------------------------------------------------------------K---------------A-------- SAPs(SNPs)
                    PROSITE -LY6_UPAR  PDB: U:2-45 UniProt: 24-67        ------------------------------------------------LY6_UPAR  PDB: U:94-147 UniProt: 116-169              ---------------------------------------------LY6_UPAR  PDB: U:193-247 UniProt: 215-269              ------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2  PDB: U:1-34 [INCOMPLETE]-----------------------------------------------Exon 1.4  PDB: U:91-129 UniProt: 104-158 [INCOMPLETE]  --------------------------------------------Exon 1.6  PDB: U:181-230 UniProt: 203-252         ----------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.3  PDB: U:34-80 UniProt: 56-104           -----------------------------------------------------Exon 1.5  PDB: U:140-181 UniProt: 158-203     ------------------------------------------------Exon 1.7  PDB: U:230-283 UniProt: 252-335 [INCOMPLETE] Transcript 1 (2)
                 3u74 U   1 LRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTCSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGN----------RYLECISCGSSDMSCERGRHQSLQCRSPEEQCLDVVTHW----------DDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMCHIDVSCCTKSGCNHPDLDVQYRSG 283
                                    10        20        30        40        50        60        70        80         -|      100       110       120        |-       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280   
                                                                                                          80         91                                   129        140                                                                                                                                               

   Legend:   → Mismatch (orange background)
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  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, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U74)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U74)

(-) Gene Ontology  (35, 35)

Asymmetric/Biological Unit(hide GO term definitions)
Chain U   (UPAR_HUMAN | Q03405)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    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:0030377    urokinase plasminogen activator receptor activity    Combining with the urokinase plasminogen activator to initiate a change in cell activity.
biological process
    GO:0016255    attachment of GPI anchor to protein    A transamidation reaction that results in the cleavage of the polypeptide chain and the concomitant transfer of the GPI anchor to the newly formed carboxy-terminal amino acid of the anchored protein. The cleaved C-terminal contains the C-terminal GPI signal sequence of the newly synthesized polypeptide chain.
    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:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0006928    movement of cell or subcellular component    The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:2001268    negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of cysteine-type endopeptidase activity involved in apoptotic signaling pathway.
    GO:2001243    negative regulation of intrinsic apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway.
    GO:0043388    positive regulation of DNA binding    Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0045742    positive regulation of epidermal growth factor receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0090200    positive regulation of release of cytochrome c from mitochondria    Any process that increases the rate, frequency or extent of release of cytochrome c from mitochondria, the process in which cytochrome c is enabled to move from the mitochondrial intermembrane space into the cytosol, which is an early step in apoptosis and leads to caspase activation.
    GO:0030162    regulation of proteolysis    Any process that modulates the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
    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.
    GO:0038195    urokinase plasminogen activator signaling pathway    A series of molecular signals initiated by the binding of urokinase plasminogen activator to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0031225    anchored component of membrane    The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0071438    invadopodium membrane    The portion of the plasma membrane surrounding an invadopodium.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UPAR_HUMAN | Q034051ywh 2fd6 2i9b 3bt1 3bt2 3u73 4k24 4qti

(-) Related Entries Specified in the PDB File

2fat 3bt1 3bt2