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(-) Description

Title :  CRYSTAL STRUCTURE OF WSN/A INFLUENZA NUCLEOPROTEIN WITH THREE MUTATIONS (E53D, Y289H, Y313V)
 
Authors :  H. A. Lewis, E. T. Baldwin, S. Steinbacher, K. Maskos, M. Mortl, R. Kiefe S. Edavettal, P. A. Mcdonnell, B. C. Pearce, D. R. Langley
Date :  29 Feb 12  (Deposition) - 06 Mar 13  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. A. Lewis, E. T. Baldwin, S. Steinbacher, K. Maskos, M. Mortl, R. Kiefersauer, S. Edavettal, P. A. Mcdonnell, B. C. Pearce, D. R. Langley
To Be Determined
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NUCLEOCAPSID PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP
    Mutation: YES
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 382835
    Strain: A/WSN/1933(H1N1)
    Synonym: NUCLEOPROTEIN

 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 4DYT)

(-) Sites  (0, 0)

(no "Site" information available for 4DYT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DYT)

(-) 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:432
 aligned with Q1K9H2_I33A0 | Q1K9H2 from UniProtKB/TrEMBL  Length:498

    Alignment length:471
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488 
         Q1K9H2_I33A0    19 RQNATEIRASVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDRNFWRGENGRRTRIAYERMCNILKGKFQTAAQRTMVDQVRESRNPGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGYDFEREGYSLVGIDPFRLLQNSQVYSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGNTNQQRASSGQISIQPTFSVQRNLPFDRPTIMAAFTGNTEGRTSDMRTEIIRLMESARPEDVSFQGRGVFELSDEKATSPIVPSFDMSNEGSYFF 489
               SCOP domains d4dyta_ A: Nucleocapsid protein                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..---------------..eeeeee..ee..ee..eeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhh.....hhhhh..........hhhhhh.hhhhhhhhhhhhh.....----------...hhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh.hhhhhh.....hhhhhhhhhh..eeee....hhhhhhhhhhhhhh.....hhhhhhhhhh....hhhhh................eeee......ee..........-----..............ee...hhhhhh..---------.hhhhhhhhhh...............ee........................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dyt A  19 RQNATEIRASVGKMIDGIGRFYIQMCTELKLSDYDGRLIQNSLTIERMVLSAFDE---------------PKKTGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGIN----------RRTRIAYERMCNILKGKFQTAAQRTMVDQVRESRNPGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGHDFEREGYSLVGIDPFRLLQNSQVVSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGNT-----SSGQISIQPTFSVQRNLPFDRPTIMAA---------SDMRTEIIRLMESARPEDVSFQGRGVFELSDEKATSPIVPSFDMSNEGSYFF 489
                                    28        38        48        58        68    |    -         -|       98       108       118       128       138       148       158       168       178       188       198   |     -    |  218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       | -   |   408       418       428       438       448       458       468       478       488 
                                                                                 73              89                                                                                                              202        213                                                                                                                                                                                    396   402                       428       438                                                   


Chain B from PDB  Type:PROTEIN  Length:429
 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 d4dytb_ B: Nucleocapsid protein                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..-------------------......eee..eee........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhh...hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.....------..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhh.............hhhhhhhhhhh..hhhhhh.....hhhhhhhhh...eeee....hhhhhhhhhhhhhh.....hhhhhhhhhh.........................eeee......ee.........------...................hhhhhhh.---------.hhhhhhhhhhh......ee......ee........................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dyt B  21 NATEIRASVGKMIDGIGRFYIQMCTELKLSDYDGRLIQNSLTIERMVLSAFD-------------------TGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDR------NGRRTRIAYERMCNILKGKFQTAAQRTMVDQVRESRNPGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGHDFEREGYSLVGIDPFRLLQNSQVVSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGN------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                                                                                                             204    211                                                                                                                                                                                     395    402                       428       438                                                   


Chain C from PDB  Type:PROTEIN  Length:433
 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 d4dytc_ C: Nucleocapsid protein                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh...--------------------..................hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhhhh...................hhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh............hhhhhhhhh...............hhhhhhhhh...eeee......hhhhhhhhhhh........hhhhhhh..........................eeee......ee..........-----..............ee...hhhhhhh.---------.hhhhhhhhhhhhh....ee......ee.................--..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dyt C  21 NATEIRASVGKMIDGIGRFYIQMCTELKLSDYDGRLIQNSLTIERMVLSAFDE--------------------GPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDRNFWRGENGRRTRIAYERMCNILKGKFQTAAQRTMVDQVRESRNPGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGHDFEREGYSLVGIDPFRLLQNSQVVSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGNT-----SSGQISIQPTFSVQRNLPFDRPTIMAA---------SDMRTEIIRLMESARPEDVSFQGRGVFELSDEKATSPIVPSFDMS--GSYFF 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 |  |    
                                                                               73                   94                                                                                                                                                                                                                                                                                                           396   402                       428       438                                         482  |    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          485
   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 4DYT)

(-) Pfam Domains  (0, 0)

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

(-) 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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 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 3ro5 3tg6 4bbl 4dya 4dyb 4dyn 4dyp 5tjw

(-) Related Entries Specified in the PDB File

4dya 4dyb 4dyn 4dyp 4dys