Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE DUAL ENZYME IRE1 REVEALS THE BASIS FOR CATALYSIS AND REGULATION OF NON-CONVENTIONAL SPLICING
 
Authors :  K. P. Lee, M. Dey, D. Neculai, C. Cao, T. E. Dever, F. Sicheri
Date :  12 Oct 07  (Deposition) - 29 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Nucleotide Complex, Atp-Binding, Endoplasmic Reticulum, Glycoprotein, Hydrolase, Kinase, Magnesium, Membrane, Metal-Binding, Multifunctional Enzyme, Nucleotide- Binding, Phosphorylation, Serine/Threonine-Protein Kinase, Transcription, Transcription Regulation, Transferase, Transmembrane, Unfolded Protein Response (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. P. Lee, M. Dey, D. Neculai, C. Cao, T. E. Dever, F. Sicheri
Structure Of The Dual Enzyme Ire1 Reveals The Basis For Catalysis And Regulation In Nonconventional Rna Splicing.
Cell(Cambridge, Mass. ) V. 132 89 2008
PubMed-ID: 18191223  |  Reference-DOI: 10.1016/J.CELL.2007.10.057
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE/ENDORIBONUCLEASE IRE1
    ChainsA, B
    EC Number2.7.11.1, 3.1.26.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPPROEX
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentCYTOPLASMIC FRAGMENT
    GeneIRE1, ERN1
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymENDOPLASMIC RETICULUM-TO-NUCLEUS SIGNALING 1, SERINE/THREONINE-PROTEIN KINASE, ENDORIBONUCLEASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3SR2Ligand/IonSTRONTIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:145 , ASP A:171 , ADP A:1101BINDING SITE FOR RESIDUE MG A 1102
2AC2SOFTWAREASP A:171 , ADP A:1101BINDING SITE FOR RESIDUE SR A 1103
3AC3SOFTWAREASN B:145 , ASP B:171 , ADP B:2101BINDING SITE FOR RESIDUE MG B 2102
4AC4SOFTWAREASP B:171 , ADP B:2101BINDING SITE FOR RESIDUE SR B 2103
5AC5SOFTWAREGLY A:24 , TYR A:25 , GLY A:26 , SER A:27 , THR A:30 , VAL A:32 , ALA A:43 , LYS A:45 , LEU A:88 , GLU A:89 , CYS A:91 , ASN A:94 , GLN A:144 , ASN A:145 , LEU A:147 , ASP A:171 , MG A:1102 , SR A:1103BINDING SITE FOR RESIDUE ADP A 1101
6AC6SOFTWAREGLY B:24 , TYR B:25 , GLY B:26 , SER B:27 , THR B:30 , VAL B:32 , ALA B:43 , LYS B:45 , ILE B:72 , GLU B:89 , CYS B:91 , ASN B:94 , GLN B:144 , ASN B:145 , LEU B:147 , ASP B:171 , MG B:2102 , SR B:2103BINDING SITE FOR RESIDUE ADP B 2101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (13, 13)

Asymmetric/Biological Unit
No.Residues
1Phe A:240 -Gly A:241
2Asp A:322 -Pro A:323
3Arg A:360 -Lys A:361
4Gly A:393 -Pro A:394
5Val A:395 -Pro A:396
6Thr B:212 -Lys B:213
7Lys B:235 -Gly B:236
8Asp B:322 -Pro B:323
9Met B:353 -Asp B:354
10Arg B:360 -Lys B:361
11Lys B:361 -Tyr B:362
12Gly B:393 -Pro B:394
13Val B:395 -Pro B:396

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.IRE1_YEAST793-805
 
  2A:136-148
B:136-148
2KENPS51392 KEN domain profile.IRE1_YEAST983-1115
 
  2A:302-434
B:302-434

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YHR079C1YHR079C.1VIII:261593-2582463348IRE1_YEAST1-111511152A:8-434 (gaps)
B:8-434 (gaps)
451
451

(-) 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:396
 aligned with IRE1_YEAST | P32361 from UniProtKB/Swiss-Prot  Length:1115

    Alignment length:451
                                   674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114 
          IRE1_YEAST    665 NFEQSLKNLVVSEKILGYGSSGTVVFQGSFQGRPVAVKRMLIDFCDIALMEIKLLTESDDHPNVIRYYCSETTDRFLYIALELCNLNLQDLVESKNVSDENLKLQKEYNPISLLRQIASGVAHLHSLKIIHRDLKPQNILVSTSSRFTADQQTGAENLRILISDFGLCKKLDSGQSSFRTNLNNPSGTSGWRAPELLEESNNLQCQVETEHSSSRHTVVSSDSFYDPFTKRRLTRSIDIFSMGCVFYYILSKGKHPFGDKYSRESNIIRGIFSLDEMKCLHDRSLIAEATDLISQMIDHDPLKRPTAMKVLRHPLFWPKSKKLEFLLKVSDRLEIENRDPPSALLMKFDAGSDFVIPSGDWTVKFDKTFMDNLERYRKYHSSKLMDLLRALRNKYHHFMDLPEDIAELMGPVPDGFYDYFTKRFPNLLIGVYMIVKENLSDDQILREFLYS 1115
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeee.....eeeeee....eeeeeeee..hhhhhhhhhhhhhhhh.......eeeeee...eeeeee....eehhhhhhh.------------.hhhhhhhhhhhhhhhhhhh.ee....hhh.eeee.hhhhhh.........eeee......ee...--------------.....hhhhhh......------------------------......hhhhhhhhhhhhhhhhh..........hhhhhhhhh...........hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhh......-----......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KEN  PDB: A:302-434 UniProt: 983-1115                                                                                                 PROSITE
               Transcript 1 Exon 1.1  PDB: A:8-434 (gaps) UniProt: 1-1115 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                          Transcript 1
                2rio A    8 NFEQSLKNLVVSEKILGYGSSGTVVFQGSFQGRPVAVKRMLIDFCDIALMEIKLLTESDDHPNVIRYYCSETTDRFLYIALELCNLNLQDLVESK------------YNPISLLRQIASGVAHLHSLKIIHRDLKPQNILVSTSSRFTADQQTGAENLRILISDFGLCKKLDS--------------TSGWRAPELLEESNNLQ------------------------TKRRLTRSIDIFSMGCVFYYILSKGKHPFGDKYSRESNIIRGIFSLDEMKCLHDRSLIAEATDLISQMIDHDPLKRPTAMKVLRHPLFWPKSKKLEFLLKVSDRLEIENRDPPSALLMKFDAGSDFVIPSGDWTVKFDKTFMD-----RKYHSSKLMDLLRALRNKYHHFMDLPEDIAELMGPVPDGFYDYFTKRFPNLLIGVYMIVKENLSDDQILREFLYS  434
                                    17        27        37        47        57        67        77        87        97    |    -       117       127       137       147       157       167       177  |      -       197       207   |     -         -       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353|     |363       373       383       393       403       413       423       433 
                                                                                                                        102          115                                                              180            195             211                      212                                                                                                                                           354   360                                                                          

Chain B from PDB  Type:PROTEIN  Length:395
 aligned with IRE1_YEAST | P32361 from UniProtKB/Swiss-Prot  Length:1115

    Alignment length:451
                                   674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114 
          IRE1_YEAST    665 NFEQSLKNLVVSEKILGYGSSGTVVFQGSFQGRPVAVKRMLIDFCDIALMEIKLLTESDDHPNVIRYYCSETTDRFLYIALELCNLNLQDLVESKNVSDENLKLQKEYNPISLLRQIASGVAHLHSLKIIHRDLKPQNILVSTSSRFTADQQTGAENLRILISDFGLCKKLDSGQSSFRTNLNNPSGTSGWRAPELLEESNNLQCQVETEHSSSRHTVVSSDSFYDPFTKRRLTRSIDIFSMGCVFYYILSKGKHPFGDKYSRESNIIRGIFSLDEMKCLHDRSLIAEATDLISQMIDHDPLKRPTAMKVLRHPLFWPKSKKLEFLLKVSDRLEIENRDPPSALLMKFDAGSDFVIPSGDWTVKFDKTFMDNLERYRKYHSSKLMDLLRALRNKYHHFMDLPEDIAELMGPVPDGFYDYFTKRFPNLLIGVYMIVKENLSDDQILREFLYS 1115
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------Pkinase-2rioB01 B:17-299                                                                                                                                                                                                                                                                                           ----Ribonuc_2-5A-2rioB03 B:304-434                                                                                                      Pfam domains (1)
           Pfam domains (2) ---------Pkinase-2rioB02 B:17-299                                                                                                                                                                                                                                                                                           ----Ribonuc_2-5A-2rioB04 B:304-434                                                                                                      Pfam domains (2)
         Sec.struct. author ........eeeeeeeeee.....eeeeeee..eeeeeeeee..hhhhhhhhhhhhhhhh.......eeeeee...eeeeee....eehhhhhhh-------------.hhhhhhhhhhhhhhhhhhh.ee....hhh.eeee.hhhhhh.........eeee......ee...--------------.....hhhhhh......------------------------......hhhhhhhhhhhhhhhhh..........hhhhhhhh............hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhh......-----......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KEN  PDB: B:302-434 UniProt: 983-1115                                                                                                 PROSITE
               Transcript 1 Exon 1.1  PDB: B:8-434 (gaps) UniProt: 1-1115 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                          Transcript 1
                2rio B    8 NFEQSLKNLVVSEKILGYGSSGTVVFQGSFQGRPVAVKRMLIDFCDIALMEIKLLTESDDHPNVIRYYCSETTDRFLYIALELCNLNLQDLVES-------------YNPISLLRQIASGVAHLHSLKIIHRDLKPQNILVSTSSRFTADQQTGAENLRILISDFGLCKKLDS--------------TSGWRAPELLEESNNLQ------------------------TKRRLTRSIDIFSMGCVFYYILSKGKHPFGDKYSRESNIIRGIFSLDEMKCLHDRSLIAEATDLISQMIDHDPLKRPTAMKVLRHPLFWPKSKKLEFLLKVSDRLEIENRDPPSALLMKFDAGSDFVIPSGDWTVKFDKTFMD-----RKYHSSKLMDLLRALRNKYHHFMDLPEDIAELMGPVPDGFYDYFTKRFPNLLIGVYMIVKENLSDDQILREFLYS  434
                                    17        27        37        47        57        67        77        87        97   |     -       117       127       137       147       157       167       177  |      -       197       207   |     -         -       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353|     |363       373       383       393       403       413       423       433 
                                                                                                                       101           115                                                              180            195             211                      212                                                                                                                                           354   360                                                                          

   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 2RIO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (38, 38)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (IRE1_YEAST | P32361)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    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:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    GO:0036498    IRE1-mediated unfolded protein response    A series of molecular signals mediated by the endoplasmic reticulum stress sensor IRE1 (Inositol-requiring transmembrane kinase/endonuclease). Begins with activation of IRE1 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. One target of activated IRE1 is the transcription factor HAC1 in yeast, or XBP1 in mammals; IRE1 cleaves an intron of a mRNA coding for HAC1/XBP1 to generate an activated HAC1/XBP1 transcription factor, which controls the up regulation of UPR-related genes. At least in mammals, IRE1 can also signal through additional intracellular pathways including JNK and NF-kappaB.
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0030968    endoplasmic reticulum unfolded protein response    The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation.
    GO:0031505    fungal-type cell wall organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the fungal-type cell wall.
    GO:0006020    inositol metabolic process    The chemical reactions and pathways involving inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0000042    protein targeting to Golgi    The process of directing proteins towards the Golgi; usually uses signals contained within the protein.
    GO:0036290    protein trans-autophosphorylation    The phosphorylation by a protein of a residue on an identical protein. For example, phosphorylation by the other kinase within a homodimer.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0034976    response to endoplasmic reticulum stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
    GO:0006986    response to unfolded protein    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 an unfolded protein stimulus.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0030176    integral component of endoplasmic reticulum membrane    The component of the endoplasmic reticulum 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: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: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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:360 - Lys A:361   [ RasMol ]  
    Arg B:360 - Lys B:361   [ RasMol ]  
    Asp A:322 - Pro A:323   [ RasMol ]  
    Asp B:322 - Pro B:323   [ RasMol ]  
    Gly A:393 - Pro A:394   [ RasMol ]  
    Gly B:393 - Pro B:394   [ RasMol ]  
    Lys B:235 - Gly B:236   [ RasMol ]  
    Lys B:361 - Tyr B:362   [ RasMol ]  
    Met B:353 - Asp B:354   [ RasMol ]  
    Phe A:240 - Gly A:241   [ RasMol ]  
    Thr B:212 - Lys B:213   [ RasMol ]  
    Val A:395 - Pro A:396   [ RasMol ]  
    Val B:395 - Pro B:396   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2rio
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  IRE1_YEAST | P32361
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.11.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
  3.1.26.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  IRE1_YEAST | P32361
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        IRE1_YEAST | P323612be1 3fbv 3lj0 3lj1 3lj2 3sdj 3sdm

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2RIO)