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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MAM-IG MODULE OF RECEPTOR PROTEIN TYROSINE PHOSPHATASE MU
 
Authors :  A. R. Aricescu, W. C. Hon, C. Siebold, W. Lu, P. A. Van Der Merwe, E. Y. J
Date :  09 Dec 05  (Deposition) - 19 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycoprotein, Hydrolase, Immunoglobulin Domain, Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. R. Aricescu, W. C. Hon, C. Siebold, W. Lu, P. A. Van Der Merwe, E. Y. Jones
Molecular Analysis Of Receptor Protein Tyrosine Phosphatase Mu-Mediated Cell Adhesion.
Embo J. V. 25 701 2006
PubMed-ID: 16456543  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600974

(-) Compounds

Molecule 1 - RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE MU
    ChainsA
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK-293T
    Expression System PlasmidPHL
    Expression System Taxid9606
    FragmentMAM-IG MODULE RESIDUES 21-279
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRECEPTOR PROTEIN TYROSINE PHOSPHATASE MU, R-PTP-MU

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 13)

Asymmetric/Biological Unit (6, 13)
No.NameCountTypeFull Name
1FUL1Ligand/IonBETA-L-FUCOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3MSE3Mod. Amino AcidSELENOMETHIONINE
4NA2Ligand/IonSODIUM ION
5NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMSE A:63 , ASN A:72 , SER A:74 , TYR A:169 , NAG A:1281BINDING SITE FOR RESIDUE NAG A1280
02AC2SOFTWARESER A:164 , HIS A:166 , NAG A:1280 , MAN A:1282BINDING SITE FOR RESIDUE NAG A1281
03AC3SOFTWARENAG A:1281 , MAN A:1283BINDING SITE FOR RESIDUE MAN A1282
04AC4SOFTWAREMAN A:1282BINDING SITE FOR RESIDUE MAN A1283
05AC5SOFTWARELYS A:90 , ASN A:92 , TRP A:151 , NDG A:1285 , FUL A:1286BINDING SITE FOR RESIDUE NAG A1284
06AC6SOFTWARETRP A:151 , LYS A:231 , GLU A:232 , ILE A:233 , NAG A:1284 , FUL A:1286BINDING SITE FOR RESIDUE NDG A1285
07AC7SOFTWARENAG A:1284 , NDG A:1285BINDING SITE FOR RESIDUE FUL A1286
08AC8SOFTWAREASN A:131 , ARG A:263BINDING SITE FOR RESIDUE NAG A1287
09AC9SOFTWAREGLN A:40 , SER A:41 , ASP A:44 , PHE A:46 , ASN A:47 , HIS A:83BINDING SITE FOR RESIDUE NA A1288
10BC1SOFTWARELEU A:28 , SER A:67 , ASP A:173BINDING SITE FOR RESIDUE NA A1289

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:27 -A:36
2A:96 -A:182
3A:206 -A:260

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:151 -Pro A:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_046634S39RPTPRM_HUMANPolymorphism35224276AS39R

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MAM_2PS50060 MAM domain profile.PTPRM_HUMAN25-184  1A:25-184
2MAM_1PS00740 MAM domain signature.PTPRM_HUMAN66-105  1A:66-105

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003321751ENSE00001308921chr18:7567817-756788973PTPRM_HUMAN1-25251A:21-255
1.3ENST000003321753ENSE00001688331chr18:7774147-7774269123PTPRM_HUMAN25-66421A:25-6642
1.4ENST000003321754ENSE00001747026chr18:7888104-7888375272PTPRM_HUMAN66-156911A:66-15691
1.5ENST000003321755ENSE00001782251chr18:7906503-790658179PTPRM_HUMAN157-183271A:157-18327
1.6ENST000003321756ENSE00001612827chr18:7926566-7926681116PTPRM_HUMAN183-221391A:183-22139
1.8ENST000003321758ENSE00001732355chr18:7949179-7949353175PTPRM_HUMAN222-280591A:222-27958
1.9ENST000003321759ENSE00001651616chr18:7955119-7955412294PTPRM_HUMAN280-378990--
1.10ENST0000033217510ENSE00001638021chr18:8069684-8069992309PTPRM_HUMAN378-4811040--
1.11ENST0000033217511ENSE00001650489chr18:8076453-8076562110PTPRM_HUMAN481-517370--
1.12ENST0000033217512ENSE00001728904chr18:8085669-8085870202PTPRM_HUMAN518-585680--
1.13ENST0000033217513ENSE00001800642chr18:8088747-8088849103PTPRM_HUMAN585-619350--
1.14ENST0000033217514ENSE00001777562chr18:8113484-8113757274PTPRM_HUMAN619-710920--
1.15ENST0000033217515ENSE00001725303chr18:8114789-811482537PTPRM_HUMAN711-723130--
1.16ENST0000033217516ENSE00001751923chr18:8143645-8143777133PTPRM_HUMAN723-767450--
1.17ENST0000033217517ENSE00001788248chr18:8244056-8244207152PTPRM_HUMAN767-818520--
1.18ENST0000033217518ENSE00001690528chr18:8247843-824791775PTPRM_HUMAN818-843260--
1.21ENST0000033217521ENSE00001735424chr18:8253225-8253412188PTPRM_HUMAN843-905630--
1.22ENST0000033217522ENSE00001785900chr18:8296366-829645388PTPRM_HUMAN906-935300--
1.23ENST0000033217523ENSE00001611771chr18:8314779-831485577PTPRM_HUMAN935-960260--
1.24ENST0000033217524ENSE00001645096chr18:8319176-831921237PTPRM_HUMAN961-973130--
1.25ENST0000033217525ENSE00001602094chr18:8343421-834351898PTPRM_HUMAN973-1005330--
1.26ENST0000033217526ENSE00001610861chr18:8370888-8371004117PTPRM_HUMAN1006-1044390--
1.27ENST0000033217527ENSE00001783729chr18:8376044-8376198155PTPRM_HUMAN1045-1096520--
1.28ENST0000033217528ENSE00001732392chr18:8376460-8376595136PTPRM_HUMAN1096-1141460--
1.29ENST0000033217529ENSE00001797057chr18:8378263-8378412150PTPRM_HUMAN1142-1191500--
1.30ENST0000033217530ENSE00001188168chr18:8379165-8379338174PTPRM_HUMAN1192-1249580--
1.31ENST0000033217531ENSE00001143060chr18:8380294-8380425132PTPRM_HUMAN1250-1293440--
1.32ENST0000033217532ENSE00001143052chr18:8384559-8384684126PTPRM_HUMAN1294-1335420--
1.33ENST0000033217533ENSE00001143044chr18:8387070-8387233164PTPRM_HUMAN1336-1390550--
1.34ENST0000033217534ENSE00001148347chr18:8394474-8394609136PTPRM_HUMAN1390-1435460--
1.35bENST0000033217535bENSE00001541394chr18:8406107-8406859753PTPRM_HUMAN1436-1452170--

(-) 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:259
 aligned with PTPRM_HUMAN | P28827 from UniProtKB/Swiss-Prot  Length:1452

    Alignment length:259
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
          PTPRM_HUMAN    21 ETFSGGCLFDEPYSTCGYSQSEGDDFNWEQVNTLTKPTSDPWMPSGSFMLVNASGRPEGQRAHLLLPQLKENDTHCIDFHYFVSSKSNSPPGLLNVYVKVNNGPLGNPIWNISGDPTRTWNRAELAISTFWPNFYQVIFEVITSGHQGYLAIDEVKVLGHPCTRTPHFLRIQNVEVNAGQFATFQCSAIGRTVAGDRLWLQGIDVRDAPLKEIKVTSSRRFIASFNVVNTTKRDAGKYRCMIRTEGGVGISNYAELVVK 279
               SCOP domains d2c9aa2 A:21-183 Receptor-type tyrosine-protein phosphatase mu                                                                                                     d2c9aa1 A:184-279 Receptor-type tyrosine-protein phosphatase mu                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhh.ee........eeee..............eeeeee........eeeee..........eeeeeeeee.......eeeeeeeee.........eee.......eeeeeeee.......eeeeeeeee.....eeeeeeeeee........ee.....eee.....eeeeeeee.......eeeeee.......eeeeeeee..eeeeeeee...hhhhh.eeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------R------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----MAM_2  PDB: A:25-184 UniProt: 25-184                                                                                                                            ----------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------MAM_1  PDB: A:66-105 UniProt: 66-105    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) 1.1  ----------------------------------------Exon 1.4  PDB: A:66-156 UniProt: 66-156                                                    Exon 1.5  PDB: A:157-183   --------------------------------------Exon 1.8  PDB: A:222-279 UniProt: 222-280 [INCOMPLETE]     Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.3  PDB: A:25-66 UniProt: 25-66     --------------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:183-221               ---------------------------------------------------------- Transcript 1 (2)
                 2c9a A  21 ETFSGGCLFDEPYSTCGYSQSEGDDFNWEQVNTLTKPTSDPWmPSGSFmLVNASGRPEGQRAHLLLPQLKENDTHCIDFHYFVSSKSNSPPGLLNVYVKVNNGPLGNPIWNISGDPTRTWNRAELAISTFWPNFYQVIFEVITSGHQGYLAIDEVKVLGHPCTRTPHFLRIQNVEVNAGQFATFQCSAIGRTVAGDRLWLQGIDVRDAPLKEIKVTSSRRFIASFNVVNTTKRDAGKYRCmIRTEGGVGISNYAELVVK 279
                                    30        40        50        60  |     70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260|      270         
                                                                     63-MSE |                                                                                                                                                                                             261-MSE              
                                                                           69-MSE                                                                                                                                                                                                              

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C9A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C9A)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PTPRM_HUMAN | P28827)
molecular function
    GO:0045296    cadherin binding    Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    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:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0005001    transmembrane receptor protein tyrosine phosphatase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    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:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0007156    homophilic cell adhesion via plasma membrane adhesion molecules    The attachment of a plasma membrane adhesion molecule in one cell to an identical molecule in an adjacent cell.
    GO:0016525    negative regulation of angiogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
    GO:0010596    negative regulation of endothelial cell migration    Any process that decreases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    GO:0001937    negative regulation of endothelial cell proliferation    Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation.
    GO:0031175    neuron projection development    The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0010842    retina layer formation    The process in which the vertebrate retina is organized into three laminae: the outer nuclear layer (ONL), which contains photoreceptor nuclei; the inner nuclear layer (INL), which contains amacrine, bipolar and horizontal cells; and the retinal ganglion cell (RGC) layer. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells. The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells. Spanning all layers of the retina are the radially oriented Mueller glia.
    GO:0031290    retinal ganglion cell axon guidance    The process in which the migration of an axon growth cone of a retinal ganglion cell (RGC) is directed to its target in the brain in response to a combination of attractive and repulsive cues.
    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.
cellular component
    GO:0005913    cell-cell adherens junction    An adherens junction which connects a cell to another cell.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PTPRM_HUMAN | P288271rpm 2v5y

(-) Related Entries Specified in the PDB File

1rpm HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE MU, DOMAIN 1