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(-) Description

Title :  STRUCTURE OF THE CAP-BINDING DOMAIN OF INFLUENZA VIRUS POLYMERASE SUBUNIT PB2 WITH BOUND M7GTP
 
Authors :  D. Guilligay, F. Tarendeau, P. Resa-Infante, R. Coloma, T. Crepin, P. Sehr, J. Lewis, R. W. H. Ruigrok, J. Ortin, D. J. Hart, S. Cusack
Date :  21 Mar 08  (Deposition) - 13 May 08  (Release) - 19 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,D,E,F
Keywords :  Rna-Dependent Rna Polymerase, Transcription, Pb2 Subunit, Influenza Virus, Cap-Binding Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Guilligay, F. Tarendeau, P. Resa-Infante, R. Coloma, T. Crepin, P. Sehr, J. Lewis, R. W. H. Ruigrok, J. Ortin, D. J. Hart, S. Cusack
The Structural Basis For Cap Binding By Influenza Virus Polymerase Subunit Pb2.
Nat. Struct. Mol. Biol. V. 15 500 2008
PubMed-ID: 18454157  |  Reference-DOI: 10.1038/NSMB.1421

(-) Compounds

Molecule 1 - POLYMERASE BASIC PROTEIN 2
    Chains: A, B, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-CODONPLUS-RIL
    Expression System Taxid: 511693
    Expression System Vector: PET-M11
    Fragment: CAP-BINDING DOMAIN, RESIDUES 318-483
    Mutation: YES
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
    Strain: A/VICTORIA/3/1975(H3N2)
    Synonym: RNA-DIRECTED RNA POLYMERASE SUBUNIT P3, PB2 CAP-BINDING DOMAIN

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 55)

Asymmetric/Biological Unit (2, 55)
No.NameCountTypeFull Name
1MGT5Ligand/Ion7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
2MSE50Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:323 , LYS A:339 , ARG A:355 , HIS A:357 , GLU A:361 , PHE A:363 , LYS A:376 , PHE A:404 , GLN A:406 , ASN A:429 , MSE A:431 , HIS A:432 , HOH A:2065BINDING SITE FOR RESIDUE MGT A1483
2AC2SOFTWAREPHE B:323 , ARG B:332 , LYS B:339 , ARG B:355 , HIS B:357 , GLU B:361 , PHE B:363 , LYS B:376 , PHE B:404 , GLN B:406 , ASN B:429 , MSE B:431 , HIS B:432 , HOH B:2066BINDING SITE FOR RESIDUE MGT B1483
3AC3SOFTWARESER D:320 , PHE D:323 , LYS D:339 , ARG D:355 , HIS D:357 , GLU D:361 , PHE D:363 , LYS D:376 , PHE D:404 , GLN D:406 , ASN D:429 , MSE D:431 , HIS D:432BINDING SITE FOR RESIDUE MGT D1483
4AC4SOFTWAREGLN D:392 , SER E:320 , PHE E:323 , LYS E:339 , ARG E:355 , HIS E:357 , GLU E:361 , PHE E:363 , LYS E:376 , PHE E:404 , ASN E:429 , MSE E:431 , HIS E:432 , HOH E:2049 , HOH E:2050 , HOH E:2051BINDING SITE FOR RESIDUE MGT E1483
5AC5SOFTWAREPHE F:323 , SER F:324 , ARG F:355 , HIS F:357 , GLU F:361 , PHE F:363 , LYS F:376 , PHE F:404 , GLN F:406 , MSE F:431 , HIS F:432BINDING SITE FOR RESIDUE MGT F1483

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VQZ)

(-) 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:164
 aligned with PB2_I75A3 | P31345 from UniProtKB/Swiss-Prot  Length:759

    Alignment length:164
                                   329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479    
            PB2_I75A3   320 SSSFSFGGFTFKRTSGSSIKREEEVLTGNLQTLKIRVHEGYEEFTMVGKRATAILRKATRRLVQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEHIDNVMGMVGVLPDMTPSTEMSMRGIRVSKM 483
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeeeeee..eeeeeeee.....eeeeeeee..eeeeee...eeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhhhhhh.eee......eeee.....ee..eee..eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vqz A 320 SSSFSFGGFTFKRTSGSSIKREEEVLTGNLQTLKIRVHEGYEEFTmVGKRATAILRKATRRLVQLIVSGKDEQSIAEAIIVAmVFSQEDCmIKAVRGDLNFVNRANQRLNPmHQLLRHFQKDAKVLFQNWGIEHIDNVmGmVGVLPDmTPSTEmSmRGIRVSKm 483
                                   329       339       349       359     | 369       379       389       399  |    409|      419       429 |     439       449       459|      469   | | 479   |
                                                                       365-MSE                              402-MSE 410-MSE              431-MSE                    458-MSE    |     | |     483-MSE
                                                                                                                                                                      460-MSE  |     | |        
                                                                                                                                                                             467-MSE | |        
                                                                                                                                                                                   473-MSE      
                                                                                                                                                                                     475-MSE    


Chain B from PDB  Type:PROTEIN  Length:162
 aligned with PB2_I75A3 | P31345 from UniProtKB/Swiss-Prot  Length:759

    Alignment length:164
                                   329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479    
            PB2_I75A3   320 SSSFSFGGFTFKRTSGSSIKREEEVLTGNLQTLKIRVHEGYEEFTMVGKRATAILRKATRRLVQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEHIDNVMGMVGVLPDMTPSTEMSMRGIRVSKM 483
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeeeeee..eeeeeeee.....eeeeeeee..eeeeee...eeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.........--.....hhhhhhhhhhhhhhhhhhhhh.eee......eeee.....ee..eee..eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vqz B 320 SSSFSFGGFTFKRTSGSSIKREEEVLTGNLQTLKIRVHEGYEEFTmVGKRATAILRKATRRLVQLIVSGKDEQSIAEAIIVAmVFSQEDCmIKAVRGDLNFV--ANQRLNPmHQLLRHFQKDAKVLFQNWGIEHIDNVmGmVGVLPDmTPSTEmSmRGIRVSKm 483
                                   329       339       349       359     | 369       379       389       399  |    409|      419 |  |  429 |     439       449       459|      469   | | 479   |
                                                                       365-MSE                              402-MSE 410-MSE    421  |      |                        458-MSE    |     | |     483-MSE
                                                                                                                                  424      |                          460-MSE  |     | |        
                                                                                                                                         431-MSE                             467-MSE | |        
                                                                                                                                                                                   473-MSE      
                                                                                                                                                                                     475-MSE    


Chain D from PDB  Type:PROTEIN  Length:165
 aligned with PB2_I75A3 | P31345 from UniProtKB/Swiss-Prot  Length:759

    Alignment length:165
                                   328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478     
            PB2_I75A3   319 ISSSFSFGGFTFKRTSGSSIKREEEVLTGNLQTLKIRVHEGYEEFTMVGKRATAILRKATRRLVQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEHIDNVMGMVGVLPDMTPSTEMSMRGIRVSKM 483
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeeeeee..eeeeeeee.....eeeeeeee..eeeeee...eeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh.eee......eeee.....ee..eee..eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vqz D 319 ISSSFSFGGFTFKRTSGSSIKREEEVLTGNLQTLKIRVHEGYEEFTmVGKRATAILRKATRRLVQLIVSGKDEQSIAEAIIVAmVFSQEDCmIKAVRGDLNFVNRANQRLNPmHQLLRHFQKDAKVLFQNWGIEHIDNVmGmVGVLPDmTPSTEmSmRGIRVSKm 483
                                   328       338       348       358      |368       378       388       398   |   408 |     418       428  |    438       448       458 |     468    | |478    |
                                                                        365-MSE                              402-MSE 410-MSE              431-MSE                    458-MSE    |     | |     483-MSE
                                                                                                                                                                       460-MSE  |     | |        
                                                                                                                                                                              467-MSE | |        
                                                                                                                                                                                    473-MSE      
                                                                                                                                                                                      475-MSE    


Chain E from PDB  Type:PROTEIN  Length:160
 aligned with PB2_I75A3 | P31345 from UniProtKB/Swiss-Prot  Length:759

    Alignment length:164
                                   329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479    
            PB2_I75A3   320 SSSFSFGGFTFKRTSGSSIKREEEVLTGNLQTLKIRVHEGYEEFTMVGKRATAILRKATRRLVQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEHIDNVMGMVGVLPDMTPSTEMSMRGIRVSKM 483
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeeeeee..eeeeeeee.....eeeeeeee..eeeeee...eeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhh.hhhhhh..........----..hhhhhhhhhhhhhhhhhhhhh.eee......eeee.....ee..eee..eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vqz E 320 SSSFSFGGFTFKRTSGSSIKREEEVLTGNLQTLKIRVHEGYEEFTmVGKRATAILRKATRRLVQLIVSGKDEQSIAEAIIVAmVFSQEDCmIKAVRGDLNFVN----RLNPmHQLLRHFQKDAKVLFQNWGIEHIDNVmGmVGVLPDmTPSTEmSmRGIRVSKm 483
                                   329       339       349       359     | 369       379       389       399  |    409|      419  |    429 |     439       449       459|      469   | | 479   |
                                                                       365-MSE                              402-MSE 410-MSE     422  427   |                        458-MSE    |     | |     483-MSE
                                                                                                                                         431-MSE                      460-MSE  |     | |        
                                                                                                                                                                             467-MSE | |        
                                                                                                                                                                                   473-MSE      
                                                                                                                                                                                     475-MSE    


Chain F from PDB  Type:PROTEIN  Length:160
 aligned with PB2_I75A3 | P31345 from UniProtKB/Swiss-Prot  Length:759

    Alignment length:162
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481  
            PB2_I75A3   322 SFSFGGFTFKRTSGSSIKREEEVLTGNLQTLKIRVHEGYEEFTMVGKRATAILRKATRRLVQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEHIDNVMGMVGVLPDMTPSTEMSMRGIRVSKM 483
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Flu_PB2-2vqzF01 F:322-483                                                                                                                                          Pfam domains (1)
           Pfam domains (2) Flu_PB2-2vqzF02 F:322-483                                                                                                                                          Pfam domains (2)
           Pfam domains (3) Flu_PB2-2vqzF03 F:322-483                                                                                                                                          Pfam domains (3)
           Pfam domains (4) Flu_PB2-2vqzF04 F:322-483                                                                                                                                          Pfam domains (4)
           Pfam domains (5) Flu_PB2-2vqzF05 F:322-483                                                                                                                                          Pfam domains (5)
         Sec.struct. author .eee..eeeeeeee..eeeeeeee.....eeeeeeee..eeeeee...eeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhh.hhhhhh..........--....hhhhhhhhhhhhhhhhhhhhhheee......eeee.....ee..eee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vqz F 322 SFSFGGFTFKRTSGSSIKREEEVLTGNLQTLKIRVHEGYEEFTmVGKRATAILRKATRRLVQLIVSGKDEQSIAEAIIVAmVFSQEDCmIKAVRGDLNFVN--NQRLNPmHQLLRHFQKDAKVLFQNWGIEHIDNVmGmVGVLPDmTPSTEmSmRGIRVSKm 483
                                   331       341       351       361   |   371       381       391       401|      411       421|  |   431       441       451      |461     | 471 | |   481 |
                                                                     365-MSE                              402-MSE 410-MSE     422  |     |                        458-MSE    |     | |     483-MSE
                                                                                                                                 425     |                          460-MSE  |     | |        
                                                                                                                                       431-MSE                             467-MSE | |        
                                                                                                                                                                                 473-MSE      
                                                                                                                                                                                   475-MSE
   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 2VQZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 5)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Flu_PB2] (8)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,D,E,F   (PB2_I75A3 | P31345)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003968    RNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
biological process
    GO:0006370    7-methylguanosine mRNA capping    Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
    GO:0075526    cap snatching    A transcription initiation process during which a nucleotide sequence between 10 and 20 nucleotides in size is cleaved from the 5' end of host mRNAs by a viral RNA-dependent polymerase. The capped leader sequence obtained is subsequently used to prime transcription on the viral genome, which ultimately leads to the synthesis of capped, translatable viral mRNAs.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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:0039545    suppression by virus of host MAVS activity    Any process in which a virus stops, prevents, or reduces the activity of MAVS (mitochondrial antiviral signaling protein), a signal transducer that lies downstream of the viral RNA receptors MDA-5 and RIG-I to coordinate host innate immune responses.
    GO:0039523    suppression by virus of host RNA polymerase II activity    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host RNA polymerase II activity.
    GO:0039657    suppression by virus of host gene expression    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
    GO:0039503    suppression by virus of host innate immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019083    viral transcription    The process by which a viral genome, or part of a viral genome, is transcribed within the host cell.
cellular component
    GO:0033650    host cell mitochondrion    A semiautonomous, self replicating organelle as found in host cells that occurs in varying numbers, shapes, and sizes in the cell cytoplasm. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PB2_I75A3 | P31345: 2gmo 2jdq 2vy6 2vy7 2vy8 4nce 4ncm 4p1u 4uad 4uae 4uaf

(-) Related Entries Specified in the PDB File

2jdq C-TERMINAL DOMAIN OF INFLUENZA A VIRUS POLYMERASE PB2 SUBUNIT IN COMPLEX WITH HUMAN IMPORTIN ALPHA5