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 :  CRYSTAL STRUCTURE OF THE ASYMMETRIC HUMAN METAPNEUMOVIRUS M2-1 TETRAMER, FORM 2
 
Authors :  C. Leyrat, M. Renner, K. Harlos, J. M. Grimes
Date :  05 Mar 14  (Deposition) - 28 May 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,E
Keywords :  Viral Protein, Antiterminator, Transcription Elongation, Rna-Binding, Modular Protein, Asymmetric Tetramer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Leyrat, M. Renner, K. Harlos, J. T. Huiskonen, J. M. Grimes
Drastic Changes In Conformational Dynamics Of The Antiterminator M2-1 Regulate Transcription Efficiency In Pneumovirinae.
Elife V. 3 02674 2014
PubMed-ID: 24842877  |  Reference-DOI: 10.7554/ELIFE.02674

(-) Compounds

Molecule 1 - M2-1
    Chains: A, B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POPINF
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA2
    Expression System Vector Type: PLASMID
    Organism Scientific: HUMAN METAPNEUMOVIRUS
    Organism Taxid: 162145
    Other Details: ZN ION COORDINATED BY C7, C15, C21 AND H25
    Strain: NL1-00 (A1)
 
Molecule 2 - M2-1
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POPINF
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA2
    Expression System Vector Type: PLASMID
    Organism Scientific: HUMAN METAPNEUMOVIRUS
    Organism Taxid: 162145
    Other Details: ZN ION COORDINATED BY C7, C15, C21 AND H25
    Strain: NL1-00 (A1)

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS E:7 , CYS E:15 , CYS E:21 , HIS E:25BINDING SITE FOR RESIDUE ZN E1177
2AC2SOFTWARECYS A:7 , CYS A:15 , CYS A:21 , HIS A:25BINDING SITE FOR RESIDUE ZN A1171
3AC3SOFTWARECYS B:7 , CYS B:15 , CYS B:21 , HIS B:25BINDING SITE FOR RESIDUE ZN B1169
4AC4SOFTWARECYS C:7 , CYS C:15 , CYS C:21 , HIS C:25BINDING SITE FOR RESIDUE ZN C1173

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CS8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CS8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CS8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CS8)

(-) Exons   (0, 0)

(no "Exon" information available for 4CS8)

(-) 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:159
 aligned with Q8QN58_9MONO | Q8QN58 from UniProtKB/TrEMBL  Length:187

    Alignment length:168
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162        
         Q8QN58_9MONO     3 RKAPCKYEVRGKCNRGSECKFNHNYWSWPDRYLLIRSNYLLNQLLRNTDRADGLSIISGAGREDRTQDFVLGSTNVVQGYIDDNQSITKAAACYSLHNIIKQLQEVEVRQARDNKLSDSKHVALHNLVLSYMEMSKTPASLINNLKRLPREKLKKLAKLIIDLSAGAE 170
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhh..---------hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4cs8 A   3 RKAPCKYEVRGKCNRGSECKFNHNYWSWPDRYLLIRSNYLLNQLLRNTDRA---------GREDRTQDFVLGSTNVVQGYIDDNQSITKAAACYSLHNIIKQLQEVEVRQARDNKLSDSKHVALHNLVLSYMEMSKTPASLINNLKRLPREKLKKLAKLIIDLSAGAE 170
                                    12        22        32        42        52|        -|       72        82        92       102       112       122       132       142       152       162        
                                                                             53        63                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:164
 aligned with Q8QN58_9MONO | Q8QN58 from UniProtKB/TrEMBL  Length:187

    Alignment length:166
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162      
         Q8QN58_9MONO     3 RKAPCKYEVRGKCNRGSECKFNHNYWSWPDRYLLIRSNYLLNQLLRNTDRADGLSIISGAGREDRTQDFVLGSTNVVQGYIDDNQSITKAAACYSLHNIIKQLQEVEVRQARDNKLSDSKHVALHNLVLSYMEMSKTPASLINNLKRLPREKLKKLAKLIIDLSAG 168
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh...hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...--......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cs8 B   3 RKAPCKYEVRGKCNRGSECKFNHNYWSWPDRYLLIRSNYLLNQLLRNTDRAD--SIISGAGREDRTQDFVLGSTNVVQGYIDDNQSITKAAACYSLHNIIKQLQEVEVRQARDNKLSDSKHVALHNLVLSYMEMSKTPASLINNLKRLPREKLKKLAKLIIDLSAG 168
                                    12        22        32        42        52 |  |   62        72        82        92       102       112       122       132       142       152       162      
                                                                              54 57                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:162
 aligned with Q8QN58_9MONO | Q8QN58 from UniProtKB/TrEMBL  Length:187

    Alignment length:170
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
         Q8QN58_9MONO     3 RKAPCKYEVRGKCNRGSECKFNHNYWSWPDRYLLIRSNYLLNQLLRNTDRADGLSIISGAGREDRTQDFVLGSTNVVQGYIDDNQSITKAAACYSLHNIIKQLQEVEVRQARDNKLSDSKHVALHNLVLSYMEMSKTPASLINNLKRLPREKLKKLAKLIIDLSAGAEND 172
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh...hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh..--------..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cs8 C   3 RKAPCKYEVRGKCNRGSECKFNHNYWSWPDRYLLIRSNYLLNQLLRDTDRA--------AGREDRTQDFVLGSTNVVQGYIDDNQSITKAAACYSLHNIIKQLQEVEVRQARDNKLSDSKHVALHNLVLSYMEMSKTPASLINNLKRLPREKLKKLAKLIIDLSAGAEND 172
                                    12        22        32        42        52|       62        72        82        92       102       112       122       132       142       152       162       172
                                                                             53       62                                                                                                              


Chain E from PDB  Type:PROTEIN  Length:161
 aligned with Q8QN58_9MONO | Q8QN58 from UniProtKB/TrEMBL  Length:187

    Alignment length:173
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173   
         Q8QN58_9MONO     4 KAPCKYEVRGKCNRGSECKFNHNYWSWPDRYLLIRSNYLLNQLLRNTDRADGLSIISGAGREDRTQDFVLGSTNVVQGYIDDNQSITKAAACYSLHNIIKQLQEVEVRQARDNKLSDSKHVALHNLVLSYMEMSKTPASLINNLKRLPREKLKKLAKLIIDLSAGAENDSSYA 176
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..------------hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cs8 E   4 KAPCKYEVRGKCNRGSECKFNHNYWSWPDRYLLIRSNYLLNQLLRNTDR------------EDRTQDFVLGSTNVVQGYIDDNQSITKAAACYSLHNIIKQLQEVEVRQARDNKLSDSKHVALHNLVLSYMEMSKTPASLINNLKRLPREKLKKLAKLIIDLSAGAENDSSYA 176
                                    13        23        33        43        |-         - |      73        83        93       103       113       123       133       143       153       163       173   
                                                                           52           65
   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 4CS8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CS8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CS8)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,E   (Q8QN58_9MONO | Q8QN58)
molecular function
    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:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
    GO:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
    GO:0046782    regulation of viral transcription    Any process that modulates the frequency, rate or extent of the transcription of the viral genome.
    GO:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
cellular component
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

 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
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4cs8)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4cs8
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q8QN58_9MONO | Q8QN58
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q8QN58_9MONO | Q8QN58
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8QN58_9MONO | Q8QN58: 4cs7 4cs9 4csa

(-) Related Entries Specified in the PDB File

4cs7 CRYSTAL STRUCTURE OF THE ASYMMETRIC HUMAN METAPNEUMOVIRUS M2-1 TETRAMER, FORM 1
4cs9 CRYSTAL STRUCTURE OF THE ASYMMETRIC HUMAN METAPNEUMOVIRUS M2-1 TETRAMER BOUND TO ADENOSINE MONOPHOSPHATE
4csa CRYSTAL STRUCTURE OF THE ASYMMETRIC HUMAN METAPNEUMOVIRUS M2-1 TETRAMER BOUND TO A DNA 4-MER