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(-) Description

Title :  CRYSTAL STRUCTURE OF WSN/A INFLUENZA NUCLEOPROTEIN WITH BMS-885838 LIGAND BOUND
 
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 :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
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
    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: 382835
    Strain: A/WSN/1933(H1N1)
    Synonym: NUCLEOPROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): A 
Biological Unit 2 (3x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
10MR2Ligand/IonN-[4-CHLORANYL-5-[4-[[3-(2-METHOXYPHENYL)-5-METHYL-1,2-OXAZOL-4-YL]CARBONYL]PIPERAZIN-1-YL]-2-NITRO-PHENYL]PYRIDINE-2-CARBOXAMIDE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
10MR3Ligand/IonN-[4-CHLORANYL-5-[4-[[3-(2-METHOXYPHENYL)-5-METHYL-1,2-OXAZOL-4-YL]CARBONYL]PIPERAZIN-1-YL]-2-NITRO-PHENYL]PYRIDINE-2-CARBOXAMIDE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
10MR3Ligand/IonN-[4-CHLORANYL-5-[4-[[3-(2-METHOXYPHENYL)-5-METHYL-1,2-OXAZOL-4-YL]CARBONYL]PIPERAZIN-1-YL]-2-NITRO-PHENYL]PYRIDINE-2-CARBOXAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:289 , PHE A:291 , TYR A:296 , ILE A:301 , ASP A:302 , ARG A:305 , LEU A:306 , ASN A:309 , GLU A:469 , TYR B:52 , GLU B:53 , ARG B:99 , TRP B:104 , TYR B:313 , SER B:376BINDING SITE FOR RESIDUE 0MR A 601
2AC2SOFTWARETYR A:52 , GLU A:53 , ARG A:99 , TRP A:104 , TYR A:313 , SER A:376 , TYR B:289 , PHE B:291 , TYR B:296 , ILE B:301 , ASP B:302 , ARG B:305 , LEU B:306 , ASN B:309 , GLU B:469BINDING SITE FOR RESIDUE 0MR B 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DYN)

(-) 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:437
 aligned with Q1K9H2_I33A0 | Q1K9H2 from UniProtKB/TrEMBL  Length:498

    Alignment length:480
                                    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       498
         Q1K9H2_I33A0    19 RQNATEIRASVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDRNFWRGENGRRTRIAYERMCNILKGKFQTAAQRTMVDQVRESRNPGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGYDFEREGYSLVGIDPFRLLQNSQVYSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGNTNQQRASSGQISIQPTFSVQRNLPFDRPTIMAAFTGNTEGRTSDMRTEIIRLMESARPEDVSFQGRGVFELSDEKATSPIVPSFDMSNEGSYFFGDNAEEYDN 498
               SCOP domains d4dyna_ A: Nucleocapsid protein                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh----------------..eeeeeeeeee..eeeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh-------------.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhh.............hhhhhhhhhhhh.hhhhhh.....hhhhhhhhh..eeeee....hhhhhhhhhhhhhh.....hhhhhhhhhh....hhhhh...........hhhhheeeee.....ee..................................hhhhhhhh.---------.hhhhhhhhhhhh............ee..............-----.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dyn A  19 RQNATEIRASVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFD----------------PKKTGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIK-------------GRRTRIAYERMCNILKGKFQTAAQRTMVDQVRESRNPGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGYDFEREGYSLVGIDPFRLLQNSQVYSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGNTNQQRASSGQISIQPTFSVQRNLPFDRPTIMAAF---------DMRTEIIRLMESARPEDVSFQGRGVFELSDEKATSPIVPSF-----GSYFFGDNAEEYDN 498
                                    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       398       408       418       428|        -|      448       458       468       478|     |488       498
                                                                                72               89                                                                                                          198           212                                                                                                                                                                                                                      429       439                                     479   485             


Chain B from PDB  Type:PROTEIN  Length:437
 aligned with Q1K9H2_I33A0 | Q1K9H2 from UniProtKB/TrEMBL  Length:498

    Alignment length:482
                                    18        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     9 SYEQMETDGERQNATEIRASVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDRNFWRGENGRRTRIAYERMCNILKGKFQTAAQRTMVDQVRESRNPGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGYDFEREGYSLVGIDPFRLLQNSQVYSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGNTNQQRASSGQISIQPTFSVQRNLPFDRPTIMAAFTGNTEGRTSDMRTEIIRLMESARPEDVSFQGRGVFELSDEKATSPIVPSFDMSNEGSYFFG 490
               SCOP domains d4dynb_ B: Nucleocapsid protein                                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.----...eeeeeeeeee..eeeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....hhhhh........hhhhhhhhhhhhhhhhhhhhhhhh--------------.hhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhh.............hhhhhhhhhhhh.hhhhhh.....hhhhhhhhh..eeeee....hhhhhhhhhhhhhh.....hhhhhhhhhh....hhhhh...........hhhhheeeee.....ee.......--------...................hhhhhhh.------------.hhhhhhhhhh............ee.............-------..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dyn B   9 SYEQMETDGERQNATEIRASVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFDERRNKYLEEHP----DPKKTGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKR--------------RTRIAYERMCNILKGKFQTAAQRTMVDQVRESRNPGNAEFEDLIFLARSALILRGSVAHKSCLPACVYGSAVASGYDFEREGYSLVGIDPFRLLQNSQVYSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTKVVPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSG--------SSGQISIQPTFSVQRNLPFDRPTIMAA------------RTEIIRLMESARPEDVSFQGRGVFELSDEKATSPIVPS-------SYFFG 490
                                    18        28        38        48        58        68        78    |   88        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         -  |    448       458       468       478       488  
                                                                                                     83   88                                                                                                            199            214                                                                                                                                                                                393      402                       428          441                                  478     486
   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 4DYN)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 20)

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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  4dyn
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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 4dyp 4dyt 5tjw

(-) Related Entries Specified in the PDB File

4dya 4dyb 4dyp 4dys 4dyt