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(-) Description

Title :  CRYSTAL STRUCTURE OF HIV-1 NEF-SF2 CORE DOMAIN IN COMPLEX WITH THE SRC FAMILY KINASE HCK SH3-SH2 TANDEM REGULATORY DOMAINS
 
Authors :  J. J. Alvarado, J. I. Yeh, T. E. Smithgall
Date :  25 Jul 14  (Deposition) - 20 Aug 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hck, Sh3-Sh2 Regulatory Domains, Sh3, Sh2, Src Family Kinase, Sfk, Hiv-1, Nef, Virus, Protein-Protein Complex, Nef-Hck Complex, Viral Protein-Transferase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Alvarado, S. Tarafdar, J. I. Yeh, T. E. Smithgall
Interaction With The Src Homology (Sh3-Sh2) Region Of The Src-Family Kinase Hck Structures The Hiv-1 Nef Dimer For Kinase Activation And Effector Recruitment.
J. Biol. Chem. V. 289 28539 2014
PubMed-ID: 25122770  |  Reference-DOI: 10.1074/JBC.M114.600031

(-) Compounds

Molecule 1 - PROTEIN NEF
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B(+)
    Expression System Strain: ROSETTA2(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 62-209
    Gene: NEF
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid: 11685
    Strain: ISOLATE ARV2/SF2
    Synonym: 3'ORF,NEGATIVE FACTOR,F-PROTEIN
 
Molecule 2 - TYROSINE-PROTEIN KINASE HCK
    Chains: B, D
    EC Number: 2.7.10.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A(+)
    Expression System Strain: ROSETTA2(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SH3-SH2 DOMAIN, UNP RESIDUES 72-242
    Gene: HCK
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HEMATOPOIETIC CELL KINASE,HEMOPOIETIC CELL KINASE,P59- HCK/P60-HCK,P59HCK,P61HCK

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1IOD6Ligand/IonIODIDE ION
2MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:81 , HOH A:452 , ASP B:99 , TYR B:131binding site for residue MPD A 301
2AC2SOFTWAREGLN A:77 , VAL A:78 , PRO A:79 , HOH A:440 , HOH A:442 , ASN B:135 , HOH B:416 , GLU D:225binding site for residue MPD A 302
3AC3SOFTWAREARG A:110 , ILE A:113 , LEU C:104 , ARG C:110binding site for residue MPD A 303
4AC4SOFTWAREPRO A:82 , THR D:219 , IOD D:302 , HOH D:435binding site for residue IOD A 304
5AC5SOFTWAREGLN B:224binding site for residue IOD B 301
6AC6SOFTWARELEU C:80 , PRO C:82binding site for residue IOD C 301
7AC7SOFTWARELYS D:231binding site for residue IOD D 301
8AC8SOFTWAREIOD A:304 , HOH A:443 , LEU D:207 , ASN D:209 , HOH D:424binding site for residue IOD D 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U5W)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:134 -Pro A:135
2Phe C:72 -Pro C:73
3Gly C:134 -Pro C:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U5W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U5W)

(-) Exons   (0, 0)

(no "Exon" information available for 4U5W)

(-) 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:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh.......................eeeee............eeeee.hhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 4u5w A  72 FPVRPQVPLRPMTYKAALDISHFLKEKGGLEGLIWSQRRQEILDLWIYHTQGYFPDWQNYTPGPGIRYPLTFGWCFKLVPVEPEKVEEANEVLVWRFDSKLAFHHMARELHPEYYK 208
                                    81        91       101       111       121       131       141       151       161|      192       202      
                                                                                                                   161|                         
                                                                                                                    183                         


Chain B from PDB  Type:PROTEIN  Length:163
                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..................eeeeee....eeeeee.....eeeee...eee..hhhhh..ee...hhhhhhhhhhh.......eeeee.......eeeeeeeee...eeeeeeeeeee.....ee.....ee.hhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u5w B  83 DIIVVALYDYEAIHHEDLSFQKGDQMVVLEESGEWWKARSLATRKEGYIPSNYVARVDSLETEEWFFKGISRKDAERQLLAPGNMLGSFMIRDSETTKGSYSLSVRDYDPRQGDTVKHYKIRTLDNGGFYISPRSTFSTLQELVDHYKKGNDGLCQKLSVPCM 246
                                    92       102       112 ||    123       133       143       153       163       173       183       193       203       213       223       233       243   
                                                         114|                                                                                                                                  
                                                          116                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.......................eeeee......eeeee.hhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4u5w C  71 GFPVRPQVPLRPMTYKAALDISHFLKEKGGLEGLIWSQRRQEILDLWIYHTQGYFPDWQNYTPGPGIRYPLTFGWCFKLVPVEPKEVLVWRFDSKLAFHHMARELHPEYYK 208
                                    80        90       100       110       120       130       140       150   ||  187       197       207 
                                                                                                             154|                          
                                                                                                              182                          


Chain D from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..................eeeeee....eeeeee.....eeeee...eee.hhh..........hhhhhhhhhhh.......eeee...eeeeeeeee...eeeeeeeeeee.....ee........hhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u5w D  83 DIIVVALYDYEAIHHEDLSFQKGDQMVVLEESGEWWKARSLATRKEGYIPSNYVARVDSLETEEWFFKGISRKDAERQLLAPGNMLGSFMIRDGSYSLSVRDYDPRQGDTVKHYKIRTLDNGGFYISPRSTFSTLQELVDHYKKGNDGLCQKLSVPCMLE 248
                                    92       102       112 ||    123       133       143       153       163       173  ||   188       198       208       218       228       238       248
                                                         114|                                                         176|                                                                  
                                                          116                                                          182
   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 4U5W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U5W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U5W)

(-) Gene Ontology  (74, 77)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:134 - Pro A:135   [ RasMol ]  
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    Phe C:72 - Pro C:73   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        HCK_HUMAN | P08631: 1ad5 1bu1 1qcf 2c0i 2c0o 2c0t 2hck 2hk5 2oi3 2oj2 3hck 3nhn 3rbb 3rea 3reb 3vry 3vrz 3vs0 3vs1 3vs2 3vs3 3vs4 3vs5 3vs6 3vs7 4hck 4lud 4lue 4orz 5hck
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(-) Related Entries Specified in the PDB File

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