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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HIV-1 REV DIMER
 
Authors :  M. D. Daugherty
Date :  05 Feb 10  (Deposition) - 08 Dec 10  (Release) - 08 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Helix-Loop-Helix, Rna-Binding Arginine Rich Motif, Protein Oligomerization, Aids, Host Cytoplasm, Host Nucleus, Host-Virus Interaction, Mrna Transport, Phosphoprotein, Rna-Binding, Transport, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. Daugherty, B. Liu, A. D. Frankel
Structural Basis For Cooperative Rna Binding And Export Complex Assembly By Hiv Rev.
Nat. Struct. Mol. Biol. V. 17 1337 2010
PubMed-ID: 20953181  |  Reference-DOI: 10.1038/NSMB.1902

(-) Compounds

Molecule 1 - PROTEIN REV
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21/DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: OLIGOMERIZATION AND RNA-BINDING DOMAINS, RESIDUES 1-70
    Gene: REV
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid: 11707
    Strain: HXB3
    Synonym: REGULATOR OF EXPRESSION OF VIRAL PROTEINS, ANTI-REPRESSION TRANSACTIVATOR, ART/TRS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1BR13Ligand/IonBROMIDE ION
2MLI2Ligand/IonMALONATE ION
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2MLI2Ligand/IonMALONATE ION
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2MLI-1Ligand/IonMALONATE ION
3SO4-1Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:39 , ARG A:42 , ARG A:46 , HOH A:78 , HOH A:92 , ARG C:42 , ARG C:46BINDING SITE FOR RESIDUE SO4 A 71
02AC2SOFTWAREARG A:41 , ARG A:44 , ARG A:48 , ARG B:58BINDING SITE FOR RESIDUE SO4 A 72
03AC3SOFTWAREARG A:42 , MLI A:76BINDING SITE FOR RESIDUE BR A 73
04AC4SOFTWAREGLY A:65 , ARG D:60BINDING SITE FOR RESIDUE BR D 71
05AC5SOFTWAREHOH A:94BINDING SITE FOR RESIDUE BR A 74
06AC6SOFTWAREALA A:37 , ASN A:40 , ARG A:43 , ARG A:44 , HOH A:82BINDING SITE FOR RESIDUE BR A 75
07AC7SOFTWARETHR B:34BINDING SITE FOR RESIDUE BR B 71
08AC8SOFTWAREARG B:17 , HOH B:87BINDING SITE FOR RESIDUE BR B 72
09AC9SOFTWAREARG B:60BINDING SITE FOR RESIDUE BR B 73
10BC1SOFTWAREARG B:60 , LYS C:20BINDING SITE FOR RESIDUE BR B 74
11BC2SOFTWAREHOH B:88BINDING SITE FOR RESIDUE BR D 72
12BC3SOFTWAREHOH D:81BINDING SITE FOR RESIDUE BR C 73
13BC4SOFTWAREARG C:46BINDING SITE FOR RESIDUE BR C 74
14BC5SOFTWAREPRO A:31 , ARG A:35 , ARG A:38 , ARG A:42 , BR A:73 , TRP C:45 , GLN C:49 , HIS C:53BINDING SITE FOR RESIDUE MLI A 76
15BC6SOFTWAREGLN B:36 , ALA B:37 , ASN B:40 , ARG B:44BINDING SITE FOR RESIDUE MLI B 75

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LPH)

(-) 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:62
 aligned with REV_HV1H3 | P69718 from UniProtKB/Swiss-Prot  Length:116

    Alignment length:62
                                    18        28        38        48        58        68  
             REV_HV1H3    9 DEDLLKAVRLIKFLYQSNPPPNPEGTRQARRNRRRRWRERQRQIHSISERILSTYLGRSAEP 70
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  3lph A  9 DEDSLKAVRLIKFLYQSNPPPNPEGTRQARRNRRRRWRERQRQIHSISERIRSTYLGRSAEP 70
                                    18        28        38        48        58        68  


Chain B from PDB  Type:PROTEIN  Length:55
 aligned with REV_HV1H3 | P69718 from UniProtKB/Swiss-Prot  Length:116

    Alignment length:55
                                    18        28        38        48        58     
             REV_HV1H3    9 DEDLLKAVRLIKFLYQSNPPPNPEGTRQARRNRRRRWRERQRQIHSISERILSTY 63
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  3lph B  9 DEDSLKAVRLIKFLYQSNPPPNPEGTRQARRNRRRRWRERQRQIHSISERIRSTY 63
                                    18        28        38        48        58     


Chain C from PDB  Type:PROTEIN  Length:58
 aligned with REV_HV1H3 | P69718 from UniProtKB/Swiss-Prot  Length:116

    Alignment length:58
                                    17        27        37        47        57        
             REV_HV1H3    8 SDEDLLKAVRLIKFLYQSNPPPNPEGTRQARRNRRRRWRERQRQIHSISERILSTYLG 65
               SCOP domains ---------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  3lph C  8 SDEDSLKAVRLIKFLYQSNPPPNPEGTRQARRNRRRRWRERQRQIHSISERIRSTYLG 65
                                    17        27        37        47        57        


Chain D from PDB  Type:PROTEIN  Length:57
 aligned with REV_HV1H3 | P69718 from UniProtKB/Swiss-Prot  Length:116

    Alignment length:57
                                    17        27        37        47        57       
             REV_HV1H3    8 SDEDLLKAVRLIKFLYQSNPPPNPEGTRQARRNRRRRWRERQRQIHSISERILSTYL 64
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
           Pfam domains (1) REV-3lphD01 D:8-64                                        Pfam domains (1)
           Pfam domains (2) REV-3lphD02 D:8-64                                        Pfam domains (2)
           Pfam domains (3) REV-3lphD03 D:8-64                                        Pfam domains (3)
           Pfam domains (4) REV-3lphD04 D:8-64                                        Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                  3lph D  8 SDEDSLKAVRLIKFLYQSNPPPNPEGTRQARRNRRRRWRERQRQIHSISERIRSTYL 64
                                    17        27        37        47        57
   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 3LPH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: REV] (4)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (REV_HV1H3 | P69718)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0051028    mRNA transport    The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    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:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044196    host cell nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic host cells.
    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.

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 Related Entries

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

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        REV_HV1H3 | P69718: 4pmi 5dhx

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