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(-) Description

Title :  INFLUENZA A VIRUS NUCLEOPROTEIN NP AT 3.2A RESOLUTION
 
Authors :  Q. Ye, Y. J. Tao
Date :  13 Oct 06  (Deposition) - 26 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Oligomerization, Rna Binding, Nls, Polymerase Binding, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Ye, R. M. Krug, Y. J. Tao
The Mechanism By Which Influenza A Virus Nucleoprotein Forms Oligomers And Binds Rna.
Nature V. 444 1078 2006
PubMed-ID: 17151603  |  Reference-DOI: 10.1038/NATURE05379
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEOCAPSID PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTATM 2(DE3) SINGLESTM
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP
    Organism Scientific: INFLUENZA A VIRUS (A/WILSON- SMITH/1933(H1N1))
    Organism Taxid: 381518
    Strain: A/WILSON-SMITH/1933(H1N1)

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2IQH)

(-) Sites  (0, 0)

(no "Site" information available for 2IQH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2IQH)

(-) 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:426
 aligned with Q1K9H2_I33A0 | Q1K9H2 from UniProtKB/TrEMBL  Length:498

    Alignment length:469
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480         
         Q1K9H2_I33A0    21 NATEIRASVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDRNFWRGENGRRTRIAYERMCNILKGKFQTAAQRTMVDQVRESRNPGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGYDFEREGYSLVGIDPFRLLQNSQVYSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGNTNQQRASSGQISIQPTFSVQRNLPFDRPTIMAAFTGNTEGRTSDMRTEIIRLMESARPEDVSFQGRGVFELSDEKATSPIVPSFDMSNEGSYFF 489
               SCOP domains d2iqha1 A:21-489 Nucleocapsid protein                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.-------------------.eeeeeee....eeeeeee.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhh.........hhhhhh..hhhhhhhhhhhhhhhhhh----------.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhh.............hhhhhhhhhhh..hhhhhh....hhhhhhhh.....eeee....hhhhhhhhhhhhhhh....hhhhhhhhhh.........................eeee..................-----..............ee...hhhhhh..---------.hhhhhhhhhhhhh....ee.......................eee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iqh A  21 NATEIRASVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFD-------------------TGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGIN----------RRTRIAYERMCNILKGKFQTAAQRTMVDQVRESRNPGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGYDFEREGYSLVGIDPFRLLQNSQVYSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGNT-----SSGQISIQPTFSVQRNLPFDRPTIMAA---------SDMRTEIIRLMESARPEDVSFQGRGVFELSDEKATSPIVPSFDMSNEGSYFF 489
                                    30        40        50        60        70 |       -         - |     100       110       120       130       140       150       160       170       180       190       200 |       -  |    220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390     |   - |     410       420       | -       440       450       460       470       480         
                                                                              72                  92                                                                                                           202        213                                                                                                                                                                                    396   402                       428       438                                                   


Chain B from PDB  Type:PROTEIN  Length:426
 aligned with Q1K9H2_I33A0 | Q1K9H2 from UniProtKB/TrEMBL  Length:498

    Alignment length:469
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480         
         Q1K9H2_I33A0    21 NATEIRASVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDRNFWRGENGRRTRIAYERMCNILKGKFQTAAQRTMVDQVRESRNPGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGYDFEREGYSLVGIDPFRLLQNSQVYSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGNTNQQRASSGQISIQPTFSVQRNLPFDRPTIMAAFTGNTEGRTSDMRTEIIRLMESARPEDVSFQGRGVFELSDEKATSPIVPSFDMSNEGSYFF 489
               SCOP domains d2iqhb1 B:21-489 Nucleocapsid protein                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.-------------------.eeeeeeee..eeeeeeee....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhh.....hhhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhhh----------hhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhh.............hhhhhhhhhhhh.hhhhhh....hhhhhhhhhhh..eeee....hhhhhhhhhhhhhh.....hhhhhhhhhh.........................eeee..................-----..............ee...hhhhhhh.---------.hhhhhhhhhhhh.....ee..................eee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iqh B  21 NATEIRASVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFD-------------------TGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGIN----------RRTRIAYERMCNILKGKFQTAAQRTMVDQVRESRNPGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGYDFEREGYSLVGIDPFRLLQNSQVYSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGNT-----SSGQISIQPTFSVQRNLPFDRPTIMAA---------SDMRTEIIRLMESARPEDVSFQGRGVFELSDEKATSPIVPSFDMSNEGSYFF 489
                                    30        40        50        60        70 |       -         - |     100       110       120       130       140       150       160       170       180       190       200 |       -  |    220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390     |   - |     410       420       | -       440       450       460       470       480         
                                                                              72                  92                                                                                                           202        213                                                                                                                                                                                    396   402                       428       438                                                   


Chain C from PDB  Type:PROTEIN  Length:436
 aligned with Q1K9H2_I33A0 | Q1K9H2 from UniProtKB/TrEMBL  Length:498

    Alignment length:469
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480         
         Q1K9H2_I33A0    21 NATEIRASVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDRNFWRGENGRRTRIAYERMCNILKGKFQTAAQRTMVDQVRESRNPGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGYDFEREGYSLVGIDPFRLLQNSQVYSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGNTNQQRASSGQISIQPTFSVQRNLPFDRPTIMAAFTGNTEGRTSDMRTEIIRLMESARPEDVSFQGRGVFELSDEKATSPIVPSFDMSNEGSYFF 489
               SCOP domains d2iqhc1 C:21-489 Nucleocapsid protein                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..-------------------.eee..eee..eee..eee.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhh....hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh..hhhhhh....hhhhhhhhhh...eeee......hhhhhhhhhhhhh....hhhhhhhhh.....hhhhh................eeee......ee..........-----..............ee...hhhhhhh.---------hhhhhhhhhhhhhh....ee......ee........................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iqh C  21 NATEIRASVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFD-------------------TGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDRNFWRGENGRRTRIAYERMCNILKGKFQTAAQRTMVDQVRESRNPGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGYDFEREGYSLVGIDPFRLLQNSQVYSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGNT-----SSGQISIQPTFSVQRNLPFDRPTIMAA---------SDMRTEIIRLMESARPEDVSFQGRGVFELSDEKATSPIVPSFDMSNEGSYFF 489
                                    30        40        50        60        70 |       -         - |     100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390     |   - |     410       420       | -       440       450       460       470       480         
                                                                              72                  92                                                                                                                                                                                                                                                                                                             396   402                       428       438
   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, 3)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IQH)

(-) Gene Ontology  (10, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (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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  2iqh
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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: 2ymn 3ro5 3tg6 4bbl 4dya 4dyb 4dyn 4dyp 4dyt 5tjw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2IQH)