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(-) Description

Title :  PYRIN PRYSPRY DOMAIN
 
Authors :  C. Weinert, P. R. Mittl, M. G. Gruetter
Date :  19 Jun 09  (Deposition) - 20 Oct 09  (Release) - 17 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Amyloidosis, Polymorphism, Cytoskeleton, Actin-Binding Inflammatory Response, Metal-Binding, Signaling Protein, Disease Mutation, Pryspry (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Weinert, C. Gruetter, H. Roschitzki-Voser, P. R. Mittl, M. G. Gruetter
The Crystal Structure Of Human Pyrin B30. 2 Domain: Implications For Mutations Associated With Familial Mediterranean Fever.
J. Mol. Biol. V. 394 226 2009
PubMed-ID: 19729025  |  Reference-DOI: 10.1016/J.JMB.2009.08.059

(-) Compounds

Molecule 1 - PYRIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6P
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentPRYSPRY, RESIDUES 586-776
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMARENOSTRIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2SCN2Ligand/IonTHIOCYANATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:737 , PRO A:751 , HOH A:2127 , HOH A:2159BINDING SITE FOR RESIDUE SCN A1777
2AC2SOFTWAREILE A:612 , ARG A:708 , HOH A:2160BINDING SITE FOR RESIDUE SCN A1778
3AC3SOFTWAREALA A:595 , ALA A:597 , PRO A:646 , SER A:647 , HOH A:2020BINDING SITE FOR RESIDUE EDO A1779
4AC4SOFTWARETRP A:665 , ILE A:692 , MET A:693 , MET A:694 , GLY A:759 , THR A:760BINDING SITE FOR RESIDUE EDO A1780
5AC5SOFTWAREGLU A:589 , GLY A:592 , HIS A:596 , ARG A:652BINDING SITE FOR RESIDUE EDO A1781

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WL1)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:704 -Pro A:705

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (31, 31)

Asymmetric/Biological Unit (31, 31)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_016827I591TMEFV_HUMANUnclassified (ARFMF)11466045AI591T
02UniProtVAR_072386G632AMEFV_HUMANUnclassified  ---AG632A
03UniProtVAR_028335G632SMEFV_HUMANDisease (ARFMF)104895128AG632S
04UniProtVAR_028336I640MMEFV_HUMANDisease (ARFMF)104895115AI640M
05UniProtVAR_028337I641FMEFV_HUMANDisease (ARFMF)104895147AI641F
06UniProtVAR_028338P646LMEFV_HUMANDisease (ARFMF)104895107AP646L
07UniProtVAR_028339L649PMEFV_HUMANDisease (ARFMF)104895108AL649P
08UniProtVAR_016828R653HMEFV_HUMANDisease (ARFMF)104895085AR653H
09UniProtVAR_028340E656AMEFV_HUMANDisease (ARFMF)104895086AE656A
10UniProtVAR_028341D661NMEFV_HUMANDisease (ARFMF)104895120AD661N
11UniProtVAR_016829S675NMEFV_HUMANDisease (ARFMF)104895087AS675N
12UniProtVAR_028342G678EMEFV_HUMANDisease (ARFMF)104895088AG678E
13UniProtVAR_028343M680IMEFV_HUMANDisease (ARFMF)28940580AM680I
14UniProtVAR_016830M680LMEFV_HUMANDisease (ARFMF)104895089AM680L
15UniProtVAR_009059T681IMEFV_HUMANDisease (ARFMF)104895090AT681I
16UniProtVAR_028344Y688CMEFV_HUMANDisease (ARFMF)104895122AY688C
17UniProtVAR_009061M694IMEFV_HUMANDisease (ARFMF)28940578AM694I
18UniProtVAR_070798M694KMEFV_HUMANDisease (ARFMF)  ---AM694K
19UniProtVAR_028345M694LMEFV_HUMANDisease (ARFMF)61752717AM694L
20UniProtVAR_009062M694VMEFV_HUMANDisease (ARFMF)61752717AM694V
21UniProtVAR_028346K695MMEFV_HUMANDisease (ARFMF)104895094AK695M
22UniProtVAR_009064K695RMEFV_HUMANDisease (ARFMF)104895094AK695R
23UniProtVAR_028347S702CMEFV_HUMANPolymorphism104895166AS702C
24UniProtVAR_028348V704IMEFV_HUMANDisease (ARFMF)104895096AV704I
25UniProtVAR_028349P705SMEFV_HUMANDisease (ARFMF)104895145AP705S
26UniProtVAR_028350I720MMEFV_HUMANDisease (ARFMF)104895102AI720M
27UniProtVAR_009065V726AMEFV_HUMANDisease (ARFMF)28940579AV726A
28UniProtVAR_028351F743LMEFV_HUMANDisease (ARFMF)104895152AF743L
29UniProtVAR_009066A744SMEFV_HUMANUnclassified (ARFMF)61732874AA744S
30UniProtVAR_028352P758SMEFV_HUMANDisease (ARFMF)104895114AP758S
31UniProtVAR_009067R761HMEFV_HUMANDisease (ARFMF)104895097AR761H

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WL1)

(-) Exons   (0, 0)

(no "Exon" information available for 2WL1)

(-) 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:191
 aligned with MEFV_HUMAN | O15553 from UniProtKB/Swiss-Prot  Length:781

    Alignment length:191
                                   595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775 
           MEFV_HUMAN   586 NVPELIGAQAHAVNVILDAETAYPNLIFSDDLKSVRLGNKWERLPDGPQRFDSCIIVLGSPSFLSGRRYWEVEVGDKTAWILGACKTSISRKGNMTLSPENGYWVVIMMKENEYQASSVPPTRLLIKEPPKRVGIFVDYRVGSISFYNVTARSHIYTFASCSFSGPLQPIFSPGTRDGGKNTAPLTICPVG 776
               SCOP domains d2wl1a_ A: automated matches                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------PRY-2wl1A01 A:600-648                            -SPRY-2wl1A02 A:650-775                                                                                                        - Pfam domains
         Sec.struct. author ...hhhhhhh.....ee........eee.....eeee...................eeee......eeeeeee......eeeeeee...........hhhh.eeeeeeee..eeee.....ee........eeeeeee....eeeeee....eeeeee........eeeeee...hhhhh....eeee... Sec.struct. author
             SAPs(SNPs) (1) -----T----------------------------------------A-------MF----L--P---H--A----N-------------N--E-II------C-----IM------C-IS--------------M-----A----------------LS-------------S--H--------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------S-----------------------------------------------L-------------KR--------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ------------------------------------------------------------------------------------------------------------L---------------------------------------------------------------------------------- SAPs(SNPs) (3)
             SAPs(SNPs) (4) ------------------------------------------------------------------------------------------------------------V---------------------------------------------------------------------------------- SAPs(SNPs) (4)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wl1 A 586 NVPELIGAQAHAVNVILDAETAYPNLIFSDDLKSVRLGNKWERLPDGPQRFDSCIIVLGSPSFLSGRRYWEVEVGDKTAWILGACKTSISRKGNMTLSPENGYWVVIMMKENEYQASSVPPTRLLIKEPPKRVGIFVDYRVGSISFYNVTARSHIYTFASCSFSGPLQPIFSPGTRDGGKNTAPLTICPVG 776
                                   595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775 

   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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WL1)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MEFV_HUMAN | O15553)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:1900226    negative regulation of NLRP3 inflammasome complex assembly    Any process that stops, prevents or reduces the frequency, rate or extent of NLRP3 inflammasome complex assembly.
    GO:1900016    negative regulation of cytokine production involved in inflammatory response    Any process that stops, prevents or reduces the frequency, rate or extent of cytokine production involved in inflammatory response.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0032691    negative regulation of interleukin-1 beta production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-1 beta production.
    GO:0032695    negative regulation of interleukin-12 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-12 production.
    GO:0071641    negative regulation of macrophage inflammatory protein 1 alpha production    Any process that stops, prevents, or reduces the frequency, rate, or extent of production of macrophage inflammatory protein 1 alpha.
    GO:0010508    positive regulation of autophagy    Any process that activates, maintains or increases the rate of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:2001056    positive regulation of cysteine-type endopeptidase activity    Any process that activates or increases the frequency, rate or extent of cysteine-type endopeptidase activity.
    GO:0034341    response to interferon-gamma    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 interferon-gamma stimulus. Interferon-gamma is also known as type II interferon.
cellular component
    GO:0005776    autophagosome    A double-membrane-bounded compartment that engulfs endogenous cellular material as well as invading microorganisms to target them to the vacuole/lysosome for degradation as part of macroautophagy.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0005875    microtubule associated complex    Any multimeric complex connected to a microtubule.
    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:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MEFV_HUMAN | O155532mpc 4cg4

(-) Related Entries Specified in the PDB File

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