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(-) Description

Title :  STRUCTURE OF INFLUENZA A H5N1 PB2 CAP-BINDING DOMAIN WITH BOUND CAP ANALOGUE (COMPOUND 11)
 
Authors :  S. Pautus, P. Sehr, J. Lewis, A. Fortune, A. Wolkerstorfer, O. Szolar, D. Gulligay, T. Lunardi, J. L. Decout, S. Cusack
Date :  10 Oct 13  (Deposition) - 30 Oct 13  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Influenza Polymerase, M7Gtp, Cap-Binding Inhibitors (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Pautus, P. Sehr, J. Lewis, A. Fortune, A. Wolkerstorfer, O. Szolar, D. Gulligay, T. Lunardi, J. L. Decout, S. Cusack
New 7-Methyl-Guanosine Derivatives Targeting The Influenza Polymerase Pb2 Cap-Binding Domain
J. Med. Chem. V. 56 8915 2013
PubMed-ID: 24134208  |  Reference-DOI: 10.1021/JM401369Y

(-) Compounds

Molecule 1 - POLYMERASE BASIC SUBUNIT 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-M11
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: CODONPLUS RIL
    Expression System Vector Type: PLASMID
    Fragment: CAP-BINDING DOMAIN, RESIDUES 318-483
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 365107
    Strain: A/DUCK/SHANTOU/4610/2003(H5N1)
    Synonym: H5N1 INFLUENZA POLYMERASE PB2 SUBUNIT

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric Unit (2, 15)
No.NameCountTypeFull Name
129R2Ligand/Ion2,9-N,N-DI(4-CARBOXYBUTYL)-7-N-METHYLGUANINE
2IOD13Ligand/IonIODIDE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
129R1Ligand/Ion2,9-N,N-DI(4-CARBOXYBUTYL)-7-N-METHYLGUANINE
2IOD7Ligand/IonIODIDE ION
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
129R1Ligand/Ion2,9-N,N-DI(4-CARBOXYBUTYL)-7-N-METHYLGUANINE
2IOD6Ligand/IonIODIDE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:321 , PHE A:323 , HIS A:357 , GLU A:361 , PHE A:363 , LYS A:376 , PHE A:404 , GLN A:406 , IOD A:1486BINDING SITE FOR RESIDUE 29R A1483
02AC2SOFTWAREARG A:355 , MET A:431BINDING SITE FOR RESIDUE IOD A1484
03AC3SOFTWAREASN A:456BINDING SITE FOR RESIDUE IOD A1485
04AC4SOFTWAREPHE A:325 , 29R A:1483BINDING SITE FOR RESIDUE IOD A1486
05AC5SOFTWAREASN A:429 , HIS A:432BINDING SITE FOR RESIDUE IOD A1487
06AC6SOFTWARESER B:321 , PHE B:323 , SER B:337 , HIS B:357 , GLU B:361 , PHE B:363 , LYS B:376 , PHE B:404 , GLN B:406 , IOD B:1484BINDING SITE FOR RESIDUE 29R B1483
07AC7SOFTWAREPHE B:325 , 29R B:1483BINDING SITE FOR RESIDUE IOD B1484
08AC8SOFTWAREMET B:460BINDING SITE FOR RESIDUE IOD B1485
09AC9SOFTWARETHR B:378 , HOH B:2049BINDING SITE FOR RESIDUE IOD B1487
10BC1SOFTWAREHOH B:2045BINDING SITE FOR RESIDUE IOD B1489

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CB6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CB6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CB6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CB6)

(-) Exons   (0, 0)

(no "Exon" information available for 4CB6)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:165
 aligned with Q2LG68_9INFA | Q2LG68 from UniProtKB/TrEMBL  Length:759

    Alignment length:165
                                   328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478     
         Q2LG68_9INFA   319 ISSSFSFGGFTFKRTSGSSVKKEEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRVSKM 483
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeeeeee..eeeeeeee.....eeeeeeee..eeeeee...eeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhhhhhhheee........ee.....ee..eee..eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cb6 A 319 ISSSFSFGGFTFKRTSGSSVKKEEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRVSKM 483
                                   328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478     


Chain B from PDB  Type:PROTEIN  Length:163
 aligned with Q2LG68_9INFA | Q2LG68 from UniProtKB/TrEMBL  Length:759

    Alignment length:163
                                   330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480   
         Q2LG68_9INFA   321 SSFSFGGFTFKRTSGSSVKKEEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRVSKM 483
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eeeeeeee..eeeeeeee.....eeeeeeee..eeeeee...eeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhhhhhhheee........ee.....ee..eee..eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cb6 B 321 SSFSFGGFTFKRTSGSSVKKEEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRVSKM 483
                                   330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480
   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 4CB6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CB6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CB6)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q2LG68_9INFA | Q2LG68)
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: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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
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/TrEMBL
        Q2LG68_9INFA | Q2LG68: 4cb4 4cb5 4cb7

(-) Related Entries Specified in the PDB File

4cb4 STRUCTURE OF INFLUENZA A H5N1 PB2 CAP-BINDING DOMAIN WITH BOUND M7GTP
4cb5 STRUCTURE OF INFLUENZA A H5N1 PB2 CAP-BINDING DOMAIN WITH BOUND CAP ANALOGUE (COMPOUND 8F)
4cb7 STRUCTURE OF INFLUENZA A H5N1 PB2 CAP-BINDING DOMAIN WITH BOUND CAP ANALOGUE (COMPOUND 8E)