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(-) Description

Title :  CRYSTAL STRUCTURE OF INFLUENZA A VIRUS NUCLEOPROTEIN WITH LIGAND
 
Authors :  B. C. Pearce, S. Edavettal, P. A. Mcdonnell, H. A. Lewis, S. Steinbacher E. T. Baldwin, D. R. Langley, K. Maskos, M. Mortl, R. Kiefersauer
Date :  25 Apr 11  (Deposition) - 14 Sep 11  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.66
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Influenza Nucleoprotein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. W. Gerritz, C. Cianci, S. Kim, B. C. Pearce, C. Deminie, L. Discotto, B. Mcauliffe, B. F. Minassian, S. Shi, S. Zhu, W. Zhai, A. Pendri, G. Li, M. A. Poss, S. Edavettal, P. A. Mcdonnell, H. A. Lewis, K. Maskos, M. Mortl, R. Kiefersauer, S. Steinbacher, E. T. Baldwin, W. Metzler, J. Bryson, M. D. Healy, T. Philip, M. Zoeckler, R. Schartman, M. Sinz, V. H. Leyva-Grado, H. H. Hoffmann, D. R. Langley, N. A. Meanwell, M. Krystal
Inhibition Of Influenza Virus Replication Via Small Molecules That Induce The Formation Of Higher-Order Nucleoprotein Oligomers.
Proc. Natl. Acad. Sci. Usa V. 108 15366 2011
PubMed-ID: 21896751  |  Reference-DOI: 10.1073/PNAS.1107906108

(-) Compounds

Molecule 1 - NUCLEOCAPSID PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 381518
    Strain: A/WILSON-SMITH/1933 H1N1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1LGH2Ligand/Ion[4-(2-CHLORO-4-NITROPHENYL)PIPERAZIN-1-YL][3-(2-METHOXYPHENYL)-5-METHYL-1,2-OXAZOL-4-YL]METHANONE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1LGH6Ligand/Ion[4-(2-CHLORO-4-NITROPHENYL)PIPERAZIN-1-YL][3-(2-METHOXYPHENYL)-5-METHYL-1,2-OXAZOL-4-YL]METHANONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:289 , GLU A:294 , TYR A:296 , ASP A:302 , ARG A:305 , LEU A:306 , ASN A:309 , TYR B:52 , GLU B:53 , ARG B:99 , TRP B:104 , TYR B:313 , SER B:376BINDING SITE FOR RESIDUE LGH B 1
2AC2SOFTWARETYR A:52 , GLU A:53 , ARG A:99 , TRP A:104 , TYR A:313 , SER A:376 , TYR B:289 , GLU B:294 , TYR B:296 , ASP B:302 , ARG B:305 , LEU B:306 , ASN B:309BINDING SITE FOR RESIDUE LGH B 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RO5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RO5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RO5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RO5)

(-) Exons   (0, 0)

(no "Exon" information available for 3RO5)

(-) 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:430
 aligned with Q1K9H2_I33A0 | Q1K9H2 from UniProtKB/TrEMBL  Length:498

    Alignment length:476
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491      
         Q1K9H2_I33A0    22 ATEIRASVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDRNFWRGENGRRTRIAYERMCNILKGKFQTAAQRTMVDQVRESRNPGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGYDFEREGYSLVGIDPFRLLQNSQVYSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGNTNQQRASSGQISIQPTFSVQRNLPFDRPTIMAAFTGNTEGRTSDMRTEIIRLMESARPEDVSFQGRGVFELSDEKATSPIVPSFDMSNEGSYFFGDNAEEYD 497
               SCOP domains d3ro5a_ A: Nucleocapsid protein                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh-------------------.eeeeeeeee..eeeeeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhh.....hhhhh.........hhhhhhhhhhhhhhhhhhhhhh-------------.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhh.............hhhhhhhhhhhh.hhhhhh.....hhhhhhhhh..eeeee....hhhhhhhhhhhhhh.....hhhhhhhhhh....hhhhh...........hhhhheeeee.........................................hhhhhhhh.---------hhhhhhhhhhhhh............................-----............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ro5 A  22 ATEIRASVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAF-------------------KTGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIK-------------GRRTRIAYERMCNILKGKFQTAAQRTMVDQVRESRNPGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGYDFEREGYSLVGIDPFRLLQNSQVYSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGNTNQQRASSGQISIQPTFSVQRNLPFDRPTIMAAF---------DMRTEIIRLMESARPEDVSFQGRGVFELSDEKATSPIVPSF-----GSYFFGDNAEEYD 497
                                    31        41        51        61        71         -        91       101       111       121       131       141       151       161       171       181       191      |  -         -|      221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       | -       441       451       461       471       | -   |   491      
                                                                            71                  91                                                                                                        198           212                                                                                                                                                                                                                      429       439                                     479   485            


Chain B from PDB  Type:PROTEIN  Length:423
 aligned with Q1K9H2_I33A0 | Q1K9H2 from UniProtKB/TrEMBL  Length:498

    Alignment length:470
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491
         Q1K9H2_I33A0    22 ATEIRASVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDRNFWRGENGRRTRIAYERMCNILKGKFQTAAQRTMVDQVRESRNPGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGYDFEREGYSLVGIDPFRLLQNSQVYSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGNTNQQRASSGQISIQPTFSVQRNLPFDRPTIMAAFTGNTEGRTSDMRTEIIRLMESARPEDVSFQGRGVFELSDEKATSPIVPSFDMSNEGSYFFGD 491
               SCOP domains d3ro5b_ B: Nucleocapsid protein                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.----...eeeeeeeeee..eeeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh--------------hhhhhhhhhhhhhhh...hhhhhhhhhhhhh..-.hhhhhhhhhhhhhhh.............hhhhhhhhhhhh.hhhhhh.....hhhhhhhhh..eeeee....hhhhhhhhhhhhhh.....hhhhhhhhhh....hhhhh...........hhhhheeeee..............----------.................hhhhhhh.------------hhhhhhhhhhh............................------...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ro5 B  22 ATEIRASVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFDERRNKYLEEHP----DPKKTGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKR--------------RTRIAYERMCNILKGKFQTAAQRTMVDQVRESR-PGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGYDFEREGYSLVGIDPFRLLQNSQVYSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSG----------GQISIQPTFSVQRNLPFDRPTIMAA------------RTEIIRLMESARPEDVSFQGRGVFELSDEKATSPIVPSF------SYFFGD 491
                                    31        41        51        61        71        81 |    | 91       101       111       121       131       141       151       161       171       181       191       | -         -  |    221       231       241    | |251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 |       -  |    411       421      |  -       441       451       461       471       | -    |  491
                                                                                        83   88                                                                                                            199            214                             246 |                                                                                                                                              393        404                     428          441                                   479    486     
                                                                                                                                                                                                                                                            248
   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, 2)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RO5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RO5)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q1K9H2_I33A0 | Q1K9H2)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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.
biological process
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0075732    viral penetration into host nucleus    The crossing by the virus of the host nuclear membrane, either as naked viral genome or for small viruses as an intact capsid.
    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.
cellular component
    GO:0019029    helical viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles; the subunits are arranged to form a protein helix with the genetic material contained within. Tobacco mosaic virus has such a capsid structure.
    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:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019013    viral nucleocapsid    The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
    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
        Q1K9H2_I33A0 | Q1K9H2: 3zdp 4iry 5b7b
UniProtKB/TrEMBL
        Q1K9H2_I33A0 | Q1K9H2: 2iqh 2ymn 3tg6 4bbl 4dya 4dyb 4dyn 4dyp 4dyt 5tjw

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