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(-) Description

Title :  CRYSTAL STRUCTURE OF HIV-1 VPR C-TERMINAL DOMAIN AND DIBB-M-IMPORTIN-ALPHA2 COMPLEX
 
Authors :  H. Miyatake, A. Sanjoh, G. Matusda, T. Murakami, H. Murakami, K. Hagiwa M. Yokoyama, H. Sato, Y. Miyamoto, N. Dohmae, Y. Aida
Date :  25 Apr 16  (Deposition) - 01 Jun 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Arm Repeat, All Alpha Protein, Nuclear Import, Importin-Beta, Nls- Cargo, Protein Transport-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Miyatake, A. Sanjoh, T. Murakami, H. Murakami, G. Matsuda, K. Hagiwara, M. Yokoyama, H. Sato, Y. Miyamoto, N. Dohmae, Y. Aida
Molecular Mechanism Of Hiv-1 Vpr For Binding To Importin-Alpha
J. Mol. Biol. V. 428 2744 2016
PubMed-ID: 27181198  |  Reference-DOI: 10.1016/J.JMB.2016.05.003

(-) Compounds

Molecule 1 - IMPORTIN SUBUNIT ALPHA-1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 70-529
    Gene: KPNA2
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: IMPORTIN ALPHA P1,KARYOPHERIN SUBUNIT ALPHA-2,PENDULIN,PORE TARGETING COMPLEX 58 KDA SUBUNIT,PTAC58,RAG COHORT PROTEIN 1,SRP1- ALPHA
 
Molecule 2 - PROTEIN VPR
    Chains: C, D, E, F
    Engineered: YES
    Fragment: C-TERMINAL DOMAIN, UNP RESIDUES 85-96
    Organism Common: HIV-1
    Organism Taxid: 401671
    Other Details: SYNTHETIC PEPTIDE
    Synonym: R ORF PROTEIN,VIRAL PROTEIN R
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5B56)

(-) Sites  (0, 0)

(no "Site" information available for 5B56)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B56)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Asn A:241 -Pro A:242
2Gln B:71 -Gly B:72
3Glu B:107 -Lys B:108
4Asn B:241 -Pro B:242
5Asn E:91 -Gly E:92

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B56)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B56)

(-) Exons   (0, 0)

(no "Exon" information available for 5B56)

(-) 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:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b56 A  70 NQGTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAIDPLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCGIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQRHENESVYKASLNLIEKYFSV 498
                                    79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489         


Chain B from PDB  Type:PROTEIN  Length:432
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5b56 B  71 QGTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAIDPLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCGIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQRHENESVYKASLNLIEKYFSVEEEE 502
                                    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       490       500  


Chain C from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5b56 C  85 QQRRTRNGASKS  96
                                    94  


Chain D from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5b56 D  85 QQRRTRNGASKS  96
                                    94  


Chain E from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5b56 E  85 QQRRTRNGASKS  96
                                    94  


Chain F from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5b56 F  85 QQRRTRNGASKS  96
                                    94
   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 5B56)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B56)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B56)

(-) Gene Ontology  (27, 28)

Asymmetric/Biological Unit(hide GO term definitions)

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  Sites
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  Cis Peptide Bonds
    Asn A:241 - Pro A:242   [ RasMol ]  
    Asn B:241 - Pro B:242   [ RasMol ]  
    Asn E:91 - Gly E:92   [ RasMol ]  
    Gln B:71 - Gly B:72   [ RasMol ]  
    Glu B:107 - Lys B:108   [ RasMol ]  
 

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  5b56
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  IMA1_MOUSE | P52293
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  VPR_HV1B9 | Q73369
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IMA1_MOUSE | P52293: 1ejl 1ejy 1ial 1iq1 1pjm 1pjn 1q1s 1q1t 1y2a 2c1m 2ynr 3btr 3knd 3l3q 3oqs 3q5u 3rz9 3rzx 3tpm 3tpo 3ukw 3ukx 3uky 3ukz 3ul0 3ul1 3uvu 3ve6 3zin 3zio 3zip 3ziq 3zir 4ba3 4htv 4mz5 4mz6 4oih 4u54 4u58 4u5l 4u5n 4u5o 4u5s 4u5u 4u5v 4uaf 4yi0 4zdu 5ctt 5d5k 5e6q 5ekf 5ekg 5fc8 5hhg 5huw 5huy 5k9s 5klr 5klt 5svz 5wum 5wun 5x8n
        VPR_HV1B9 | Q73369: 1ceu 1esx 1m8l 1vpc 1x9v 1ym6 1ymj

(-) Related Entries Specified in the PDB File

3wpt 3WPT CONTAINS HOMODIMERIC STRUCTURE OF DIBB-HUMAN-IMPORTIN-ALPHA1.