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(-) Description

Title :  HIV CAPSID C-TERMINAL DOMAIN
 
Authors :  A. Lampel, O. Yaniv, O. Berger, E. Bachrach, E. Gazit, F. Frolow
Date :  10 Jan 13  (Deposition) - 16 Oct 13  (Release) - 16 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Biol. Unit 4:  C  (1x)
Biol. Unit 5:  D  (1x)
Keywords :  Viral Protein, Capsid, Core Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Lampel, O. Yaniv, O. Berger, E. Bacharach, E. Gazit, F. Frolow
A Triclinic Crystal Structure Of The Carboxy-Terminal Domai Of Hiv-1 Capsid Protein With Four Molecules In The Asymmetric Unit Reveals A Novel Packing Interface.
Acta Crystallogr. , Sect. F V. 69 602 2013
PubMed-ID: 23722834  |  Reference-DOI: 10.1107/S1744309113011871

(-) Compounds

Molecule 1 - CAPSID PROTEIN P24
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: WISP97-7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET11A
    Fragment: C-TERMINAL DOMAIN, RESIDUES 278-363
    Gene: GAG-POL
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid: 11698
    Strain: NEW YORK-5 ISOLATE
    Synonym: CA

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): A   
Biological Unit 3 (1x):  B  
Biological Unit 4 (1x):   C 
Biological Unit 5 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:202 , LYS A:203 , GLY A:206 , ALA A:209 , MET A:214 , HOH A:410 , HOH A:425 , HOH A:453BINDING SITE FOR RESIDUE EDO A 301

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:198 -A:218
2B:198 -B:218
3C:198 -C:218
4D:198 -D:218

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Val A:230 -Leu A:231
2Gly B:222 -Gly B:223
3Gly C:222 -Gly C:223

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IPY)

(-) 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:85
                                                                                                                     
               SCOP domains d4ipya_ A: HIV capsid protein, dimerisation domain                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 4ipy A 147 PTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL 231
                                   156       166       176       186       196       206       216       226     


Chain B from PDB  Type:PROTEIN  Length:85
                                                                                                                     
               SCOP domains d4ipyb_ B: HIV capsid protein, dimerisation domain                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 4ipy B 147 PTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL 231
                                   156       166       176       186       196       206       216       226     


Chain C from PDB  Type:PROTEIN  Length:85
                                                                                                                     
               SCOP domains d4ipyc_ C: HIV capsid protein, dimerisation domain                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 4ipy C 147 PTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL 231
                                   156       166       176       186       196       206       216       226     


Chain D from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains d4ipyd_ D: HIV capsid protein, dimerisation domain                          SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4ipy D 147 PTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGV 221
                                   156       166       176       186       196       206       216
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IPY)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (48, 48)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        POL_HV1N5 | P12497: 1a43 1a8o 1afv 1ak4 1aum 1b92 1b9d 1b9f 1baj 1bhl 1bi4 1bis 1biu 1biz 1bl3 1gwp 1hiw 1hyv 1hyz 1itg 1k6y 1m9d 1qs4 1uph 1wjb 1wjd 1wkn 1za9 2b4j 2gol 2gon 2h3f 2h3i 2h3q 2h3v 2h3z 2hmx 2hvp 2itg 2jpr 2jyg 2jyl 2lf4 2lya 2lyb 2m3z 2m8l 2m8n 2m8p 2ont 2pwm 2pwo 2pxr 2x2d 2xde 2xv6 2xxm 3av9 3ava 3avb 3avc 3avf 3avg 3avh 3avi 3avj 3avk 3avl 3avm 3avn 3dik 3dph 3ds0 3ds1 3ds2 3ds3 3ds4 3ds5 3dtj 3gv2 3h47 3h4e 3l3u 3l3v 3lpt 3lpu 3lry 3mge 3nf6 3nf7 3nf8 3nf9 3nfa 3p05 3p0a 3s85 3wne 3wnf 3wng 3wnh 4ah9 4ahr 4ahs 4aht 4ahu 4ahv 4coc 4cop 4dga 4dge 4dmn 4e1m 4e1n 4e91 4e92 4gvm 4gw6 4id1 4jlh 4jmu 4lqw 4nx4 4o0j 4o55 4o5b 4phv 4qnb 4wym 4zhr 5hvp 9hvp

(-) Related Entries Specified in the PDB File

1a8o HIV CAPSID C-TERMINAL DOMAIN CRYSTALLISED WITH ONE MOLECULE IN ASYMMETRIC UNIT