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(-) Description

Title :  CRYSTAL STRUCTURE OF ZO-1 PDZ1 BOUND TO A PHAGE-DERIVED LIGAND (WRRTTYL)
 
Authors :  B. A. Appleton, Y. Zhang, P. Wu, J. P. Yin, W. Hunziker, N. J. Skelton, S. S C. Wiesmann
Date :  18 May 06  (Deposition) - 13 Jun 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Pdz Domain, Phage Derived High Affinity Ligand, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. A. Appleton, Y. Zhang, P. Wu, J. P. Yin, W. Hunziker, N. J. Skelton, S. S. Sidhu, C. Wiesmann
Comparative Structural Analysis Of The Erbin Pdz Domain And The First Pdz Domain Of Zo-1. Insights Into Determinants Of Pdz Domain Specificity.
J. Biol. Chem. V. 281 22312 2006
PubMed-ID: 16737969  |  Reference-DOI: 10.1074/JBC.M602901200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TIGHT JUNCTION PROTEIN ZO-1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET22D
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentFIRST PDZ DOMAIN
    GeneZO1 (TJP1)
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymZONULA OCCLUDENS 1 PROTEIN, ZONA OCCLUDENS 1 PROTEIN, TIGHT JUNCTION PROTEIN 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:61 , ASN A:85 , HOH A:308BINDING SITE FOR RESIDUE ACY A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H2B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2H2B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H2B)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.ZO1_HUMAN23-110
186-264
421-502
  2A:23-110
A:113-115
-
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.ZO1_HUMAN23-110
186-264
421-502
  4A:23-110
A:113-115
-

(-) Exons   (5, 5)

Asymmetric Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2cENST000003461282cENSE00001822067chr15:30114682-30114205478ZO1_HUMAN1-990--
1.5aENST000003461285aENSE00001658526chr15:30092905-3009284957ZO1_HUMAN10-28191A:14-2815
1.7ENST000003461287ENSE00001419179chr15:30065560-30065436125ZO1_HUMAN29-70421A:29-7042
1.8ENST000003461288ENSE00001144945chr15:30064369-30064267103ZO1_HUMAN70-104351A:70-10435
1.9ENST000003461289ENSE00000673044chr15:30058745-30058469277ZO1_HUMAN105-197931A:105-112 (gaps)38
1.10ENST0000034612810ENSE00001001849chr15:30054641-30054538104ZO1_HUMAN197-231351A:113-1208
1.11ENST0000034612811ENSE00000673042chr15:30053972-30053804169ZO1_HUMAN232-288570--
1.12ENST0000034612812ENSE00001001840chr15:30053489-30053342148ZO1_HUMAN288-337500--
1.14bENST0000034612814bENSE00001001852chr15:30034985-30034846140ZO1_HUMAN337-384480--
1.15aENST0000034612815aENSE00001493913chr15:30033640-30033535106ZO1_HUMAN384-419360--
1.16ENST0000034612816ENSE00001001854chr15:30029618-30029468151ZO1_HUMAN419-469510--
1.17ENST0000034612817ENSE00000672950chr15:30026586-30026478109ZO1_HUMAN470-506370--
1.18ENST0000034612818ENSE00000912744chr15:30025517-30025298220ZO1_HUMAN506-579740--
1.19bENST0000034612819bENSE00000912743chr15:30025019-30024835185ZO1_HUMAN579-641630--
1.20aENST0000034612820aENSE00001001836chr15:30024732-3002463796ZO1_HUMAN641-673330--
1.21ENST0000034612821ENSE00000912740chr15:30020223-3002014183ZO1_HUMAN673-700280--
1.22ENST0000034612822ENSE00000912739chr15:30019195-30018985211ZO1_HUMAN701-771710--
1.23ENST0000034612823ENSE00000912738chr15:30018683-30018583101ZO1_HUMAN771-804340--
1.24ENST0000034612824ENSE00000672942chr15:30012912-30012562351ZO1_HUMAN805-9211170--
1.25ENST0000034612825ENSE00000672941chr15:30012220-30011981240ZO1_HUMAN922-1001800--
1.26ENST0000034612826ENSE00000672940chr15:30011342-30010470873ZO1_HUMAN1002-12922910--
1.27ENST0000034612827ENSE00000672939chr15:30010322-3001022598ZO1_HUMAN1293-1325330--
1.28ENST0000034612828ENSE00001001846chr15:30009042-30008815228ZO1_HUMAN1325-1401770--
1.29ENST0000034612829ENSE00001001851chr15:30003204-30003035170ZO1_HUMAN1401-1458580--
1.30ENST0000034612830ENSE00001001837chr15:30001240-30000763478ZO1_HUMAN1458-16171600--
1.31ENST0000034612831ENSE00001001845chr15:29997949-29997732218ZO1_HUMAN1617-1690740--
1.32aENST0000034612832aENSE00001001860chr15:29996509-2999642684ZO1_HUMAN1690-1718290--
1.33bENST0000034612833bENSE00001541183chr15:29993893-299915712323ZO1_HUMAN1718-1748310--

(-) Sequences/Alignments

Asymmetric 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:107
 aligned with ZO1_HUMAN | Q07157 from UniProtKB/Swiss-Prot  Length:1748

    Alignment length:193
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203   
            ZO1_HUMAN    14 EETAIWEQHTVTLHRAPGFGFGIAISGGRDNPHFQSGETSIVISDVLKGGPAEGQLQENDRVAMVNGVSMDNVEHAFAVQQLRKSGKNAKITIRRKKKVQIPVSRPDPEPVSDNEEDSYDEEIHDPRSGRSGVVNRRSEKIWPRDRSASRERSLSPRSDRRSVASSQPAKPTKVTLVKSRKNEEYGLRLASHI 206
               SCOP domains d2h2ba_ A: automated matches                                                                                                                                                                      SCOP domains
               CATH domains 2h2bA00 A:14-120  [code=2.30.42.10, no name defined]                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee........eeeee.............eeeeee..............eeeee..ee....hhhhhhhhhhh...eeeeeeeee.------------------------------..--------------------------------------------------------........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------PDZ  PDB: A:23-110 UniProt: 23-110                                                      ---------------------------------------------------------------------------PDZ  PDB: A:113-115   PROSITE
           Transcript 1 (1) Exon 1.5a      Exon 1.7  PDB: A:29-70 UniProt: 29-70     ------------------------------------------------------------------------------------------------------------------------------Exon 1.10  Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.8  PDB: A:70-104            Exon 1.9  PDB: A:105-112 (gaps) UniProt: 105-197 [INCOMPLETE]                                --------- Transcript 1 (2)
                 2h2b A  14 GSHMIWEQHTVTLHRAPGFGFGIAISGGRDNPHFQSGETSIVISDVLKGGPAEGQLQENDRVAMVNGVSMDNVEHAFAVQQLRKSGKNAKITIRRKK------------------------------GG--------------------------------------------------------GWRRTTYL 120
                                    23        33        43        53        63        73        83        93       103      |  -         -         -       ||-         -         -         -         -         -     | 117   
                                                                                                                          110                            111|                                                      113       
                                                                                                                                                          112                                                                

   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 Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H2B)

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A   (ZO1_HUMAN | Q07157)
molecular function
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    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.
biological process
    GO:0001825    blastocyst formation    The initial formation of a blastocyst from a solid ball of cells known as a morula.
    GO:0007043    cell-cell junction assembly    The aggregation, arrangement and bonding together of a set of components to form a junction between cells.
    GO:1901350    cell-cell signaling involved in cell-cell junction organization    Any cell-cell signaling that is involved in cell-cell junction organization.
    GO:0090557    establishment of endothelial intestinal barrier    The establishment of a barrier between endothelial cell layers of the intestine to exert specific and selective control over the passage of water and solutes, thus allowing formation and maintenance of compartments that differ in fluid and solute composition.
    GO:0035329    hippo signaling    The series of molecular signals mediated by the serine/threonine kinase Hippo or one of its orthologs. In Drosophila, Hippo in complex with the scaffold protein Salvador (Sav), phosphorylates and activates Warts (Wts), which in turn phosphorylates and inactivates the Yorkie (Yki) transcriptional activator. The core fly components hippo, sav, wts and mats are conserved in mammals as STK4/3 (MST1/2), SAV1/WW45, LATS1/2 and MOB1.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
cellular component
    GO:0005912    adherens junction    A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
    GO:0043296    apical junction complex    A functional unit located near the cell apex at the points of contact between epithelial cells, which in vertebrates is composed of the tight junction, the zonula adherens, and desmosomes and in some invertebrates, such as Drosophila, is composed of the subapical complex (SAC), the zonula adherens and the septate junction. Functions in the regulation of cell polarity, tissue integrity and intercellular adhesion and permeability.
    GO:0045177    apical part of cell    The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0016327    apicolateral plasma membrane    The apical end of the lateral plasma membrane of epithelial cells.
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0005923    bicellular tight junction    An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
    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: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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005921    gap junction    A cell-cell junction composed of pannexins or innexins and connexins, two different families of channel-forming proteins.
    GO:0014704    intercalated disc    A complex cell-cell junction at which myofibrils terminate in cardiomyocytes; mediates mechanical and electrochemical integration between individual cardiomyocytes. The intercalated disc contains regions of tight mechanical attachment (fasciae adherentes and desmosomes) and electrical coupling (gap junctions) between adjacent cells.
    GO:0046581    intercellular canaliculus    An extremely narrow tubular channel located between adjacent cells. An instance of this is the secretory canaliculi occurring between adjacent parietal cells in the gastric mucosa of vertebrates.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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
        ZO1_HUMAN | Q071572h2c 2h3m 2jwe 2kxr 2kxs 2rcz 3cyy 3lh5 3shu 3shw 3tsv 3tsw 3tsz 4oeo 4oep 4q2q 4yyx

(-) Related Entries Specified in the PDB File

2h2c 2h3l 2h3m