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(-) Description

Title :  HTRA1 BOUND TO AN OPTIMIZED PEPTIDE: NMR ASSIGNMENT OF PDZ DOMAIN AND LIGAND RESONANCES
 
Authors :  S. T. Runyon, Y. Zhang, B. A. Appleton, S. L. Sazinksy, P. Wu, B. Pan, C. Wiesmann, N. J. Skelton, S. S. Sidhu
Date :  01 Mar 07  (Deposition) - 20 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Pdz, Beta-Sandwich, Cyclically-Permuted, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. T. Runyon, Y. Zhang, B. A. Appleton, S. L. Sazinsky, P. Wu, B. Pan, C. Wiesmann, N. J. Skelton, S. S. Sidhu
Structural And Functional Analysis Of The Pdz Domains Of Human Htra1 And Htra3
Protein Sci. V. 16 2454 2007
PubMed-ID: 17962403  |  Reference-DOI: 10.1110/PS.073049407
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERINE PROTEASE HTRA1
    ChainsA
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VectorPET15B
    Expression System Vector TypeVECTOR
    FragmentPDZ DOMAIN, RESIDUES 379-480
    GeneHTRA1, HTRA, PRSS11
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymL56, SERINE PROTEASE 11
 
Molecule 2 - PEPTIDE H1-C1
    ChainsB
    EngineeredYES
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE PEPTIDE WAS DERIVED FROM A PHAGE-DISPLAYED LIBRARY AS AN OPTIMAL LIGAND FOR BINDING TO THE PDZ DOMAIN OF HUMAN HTRA1.
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2JOA)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JOA)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076382D450HHTRA1_HUMANUnclassified (CADASIL2)  ---AD450H

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003689841aENSE00001448527chr10:124221041-124221640600HTRA1_HUMAN1-1581580--
1.2ENST000003689842ENSE00001727698chr10:124248418-124248517100HTRA1_HUMAN158-191340--
1.3ENST000003689843ENSE00001656483chr10:124248938-124249142205HTRA1_HUMAN191-259690--
1.4ENST000003689844ENSE00001691312chr10:124266207-124266401195HTRA1_HUMAN260-324650--
1.5ENST000003689845ENSE00001099158chr10:124266886-12426691833HTRA1_HUMAN325-335110--
1.6ENST000003689846ENSE00001099160chr10:124268172-124268286115HTRA1_HUMAN336-374391A:376-3783
1.7ENST000003689847ENSE00001099153chr10:124269612-12426966958HTRA1_HUMAN374-393201A:379-39315
1.8ENST000003689848ENSE00001099157chr10:124271486-12427158196HTRA1_HUMAN393-425331A:393-42533
1.9bENST000003689849bENSE00001608082chr10:124273707-124274424718HTRA1_HUMAN425-480561A:425-48056

(-) 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:105
 aligned with HTRA1_HUMAN | Q92743 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:115
                                   375       385       395       405       415       425       435       445       455       465       475     
          HTRA1_HUMAN   366 ESHDRQAKGKAITKKKYIGIRMMSLTSSKAKELKDRHRDFPDVISGAYIIEVIPDTPAEAGGLKENDVIISINGQSVVSANDVSDVIKRESTLNMVVRRGNEDIMITVIPEEIDP 480
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------PDZ-2joaA01 A:380-463                                                               ----------------- Pfam domains
         Sec.struct. author ...----------......eeeee.hhhhhhhhhhhh.........eeeeee...hhhhhhh.....ee.........hhhhhhhhhhhh..eeeeeee..eeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------H------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6 ------------------Exon 1.8  PDB: A:393-425         ------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.7            -------------------------------Exon 1.9b  PDB: A:425-480 UniProt: 425-480               Transcript 1 (2)
                 2joa A 376 GSH----------MKKYIGIRMMSLTSSKAKELKDRHRDFPDVISGAYIIEVIPDTPAEAGGLKENDVIISINGQSVVSANDVSDVIKRESTLNMVVRRGNEDIMITVIPEEIDP 480
                              |      -   |   385       395       405       415       425       435       445       455       465       475     
                              |        379                                                                                                     
                            378                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ...eee. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 2joa B   1 DSRIWWV   7

   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 2JOA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: PDZ-like (184)
(-)
Family: PDZ (172)

(-) Gene Ontology  (24, 24)

NMR Structure(hide GO term definitions)
Chain A   (HTRA1_HUMAN | Q92743)
molecular function
    GO:0019838    growth factor binding    Interacting selectively and non-covalently with any growth factor, proteins or polypeptides that stimulate a cell or organism to grow or proliferate.
    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:0005520    insulin-like growth factor binding    Interacting selectively and non-covalently with an insulin-like growth factor, any member of a group of polypeptides that are structurally homologous to insulin and share many of its biological activities, but are immunologically distinct from it.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0060718    chorionic trophoblast cell differentiation    The process in which relatively unspecialized cells of the ectoplacental cone acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer.
    GO:0097187    dentinogenesis    The process whose specific outcome is the formation of dentin, the mineralized tissue that constitutes the major bulk of teeth. Dentin may be one of three types: primary dentin, secondary dentin, and tertiary dentin.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0030514    negative regulation of BMP signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the BMP signaling pathway.
    GO:0050687    negative regulation of defense response to virus    Any process that stops, prevents or reduces the rate or extent of antiviral mechanisms, thereby facilitating viral replication.
    GO:0030512    negative regulation of transforming growth factor beta receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway.
    GO:0001890    placenta development    The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0050679    positive regulation of epithelial cell proliferation    Any process that activates or increases the rate or extent of epithelial cell proliferation.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0001558    regulation of cell growth    Any process that modulates the frequency, rate, extent or direction of cell growth.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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: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: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
        HTRA1_HUMAN | Q927432ytw 3num 3nwu 3nzi 3tjn 3tjo 3tjq

(-) Related Entries Specified in the PDB File

2p3w CRYSTAL STRUCTURE OF THE HTRA3 PDZ DOMAIN BOUND TO A PHAGE- DERIVED LIGAND (FGRWV)