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(-) Description

Title :  CRYSTAL STRUCTURE OF HIV-1 TAT COMPLEXED WITH HUMAN P-TEFB AND AFF4
 
Authors :  J. Gu, N. D. Babayeva, Y. Suwa, A. G. Baranovskiy, D. H. Price, T. H. Tahir
Date :  10 Feb 14  (Deposition) - 16 Apr 14  (Release) - 11 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,E,F,G,H,J
Biol. Unit 1:  A,B,C,E  (1x)
Biol. Unit 2:  F,G,H,J  (1x)
Keywords :  Cdk9, Tat, Aff4, Zinc Finger, Transcription, Rna Binding, Phosphorylation, Transferase-Transcription Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Gu, N. D. Babayeva, Y. Suwa, A. G. Baranovskiy, D. H. Price, T. H. Tahirov
Crystal Structure Of Hiv-1 Tat Complexed With Human P-Tefb And Aff4.
Cell Cycle V. 13 1788 2014
PubMed-ID: 24727379  |  Reference-DOI: 10.4161/CC.28756

(-) Compounds

Molecule 1 - CYCLIN-DEPENDENT KINASE 9
    Chains: A, F
    EC Number: 2.7.11.22, 2.7.11.23
    Engineered: YES
    Fragment: UNP RESIDUES 7-332
    Gene: CDK9, CDC2L4, TAK
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: C-2K, CELL DIVISION CYCLE 2-LIKE PROTEIN KINASE 4, CELL DIVISION PROTEIN KINASE 9, SERINE/THREONINE-PROTEIN KINASE PITALRE, TAT-ASSOCIATED KINASE COMPLEX CATALYTIC SUBUNIT
 
Molecule 2 - CYCLIN-T1
    Chains: B, G
    Engineered: YES
    Fragment: UNP RESIDUES 1-226
    Gene: CCNT1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CYCT1, CYCLIN-T
 
Molecule 3 - PROTEIN TAT
    Chains: C, H
    Engineered: YES
    Fragment: UNP RESIDUES 1-48
    Gene: TAT
    Organism Scientific: HIV-1
    Organism Taxid: 11706
    Strain: ISOLATE HXB2
    Synonym: TRANSACTIVATING REGULATORY PROTEIN
 
Molecule 4 - AF4/FMR2 FAMILY MEMBER 4
    Chains: E, J
    Engineered: YES
    Fragment: UNP RESIDUES 32-69
    Gene: AFF4, AF5Q31, MCEF, HSPC092
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALL1-FUSED GENE FROM CHROMOSOME 5Q31 PROTEIN, PROTEIN AF- 5Q31, MAJOR CDK9 ELONGATION FACTOR-ASSOCIATED PROTEIN

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCEFGHJ
Biological Unit 1 (1x): ABCE    
Biological Unit 2 (1x):     FGHJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 26)

Asymmetric Unit (4, 26)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
2TPO2Mod. Amino AcidPHOSPHOTHREONINE
3YT316Ligand/IonYTTRIUM (III) ION
4ZN4Ligand/IonZINC ION
Biological Unit 1 (3, 11)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2TPO1Mod. Amino AcidPHOSPHOTHREONINE
3YT38Ligand/IonYTTRIUM (III) ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 11)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2TPO1Mod. Amino AcidPHOSPHOTHREONINE
3YT38Ligand/IonYTTRIUM (III) ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:149 , ASP A:167 , HOH A:521 , HOH A:527BINDING SITE FOR RESIDUE YT3 A 401
02AC2SOFTWAREASP A:305 , ASP A:308 , HOH A:514BINDING SITE FOR RESIDUE YT3 A 402
03AC3SOFTWAREGLU A:266 , LYS A:269 , HOH A:505 , ASP B:169 , YT3 B:302 , YT3 E:101BINDING SITE FOR RESIDUE YT3 A 403
04AC4SOFTWARELYS A:48 , GLU A:66 , PHE A:103 , ALA A:166 , ASP A:167BINDING SITE FOR RESIDUE SO4 A 404
05AC5SOFTWAREASP B:169 , GLN B:172 , HOH B:410 , ARG E:69 , YT3 E:101BINDING SITE FOR RESIDUE YT3 B 301
06AC6SOFTWAREGLU A:266 , YT3 A:403 , ASP B:169 , ASP E:64 , YT3 E:101BINDING SITE FOR RESIDUE YT3 B 302
07AC7SOFTWAREGLU B:17 , GLU B:20 , GLU B:240 , GLN B:243BINDING SITE FOR RESIDUE YT3 B 303
08AC8SOFTWARESER B:167 , LEU B:170 , TRP B:210 , TYR E:59 , LYS E:63BINDING SITE FOR RESIDUE SO4 B 304
09AC9SOFTWARECYS C:22 , HIS C:33 , CYS C:34 , CYS C:37BINDING SITE FOR RESIDUE ZN C 101
10BC1SOFTWARECYS B:261 , CYS C:25 , CYS C:27 , CYS C:30BINDING SITE FOR RESIDUE ZN C 102
11BC2SOFTWAREGLU A:263 , GLU A:266 , YT3 A:403 , HOH A:502 , YT3 B:301 , YT3 B:302 , ARG E:69BINDING SITE FOR RESIDUE YT3 E 101
12BC3SOFTWAREGLU A:251 , GLU E:37BINDING SITE FOR RESIDUE YT3 E 102
13BC4SOFTWAREASN A:311 , HOH A:501 , ASP F:305 , ASP F:307 , ASP F:308BINDING SITE FOR RESIDUE YT3 F 401
14BC5SOFTWAREASP F:149 , ASP F:167 , HOH F:501 , HOH F:502BINDING SITE FOR RESIDUE YT3 F 402
15BC6SOFTWAREGLU B:124 , GLU F:15BINDING SITE FOR RESIDUE YT3 F 403
16BC7SOFTWAREGLU F:263 , GLU F:266BINDING SITE FOR RESIDUE YT3 F 404
17BC8SOFTWARELYS F:48 , PHE F:103 , ALA F:166 , ASP F:167BINDING SITE FOR RESIDUE SO4 F 405
18BC9SOFTWAREGLU G:17 , GLU G:20 , GLU G:240 , GLN G:243 , HOH G:412BINDING SITE FOR RESIDUE YT3 G 301
19CC1SOFTWAREASP G:169 , GLN G:172 , ARG J:69 , YT3 J:101 , HOH J:201BINDING SITE FOR RESIDUE YT3 G 302
20CC2SOFTWAREASP G:169 , ASP J:64 , YT3 J:101 , HOH J:202BINDING SITE FOR RESIDUE YT3 G 303
21CC3SOFTWARESER G:167 , ASP G:169 , LEU G:170 , TRP G:210 , TYR J:59 , LYS J:63BINDING SITE FOR RESIDUE SO4 G 304
22CC4SOFTWARECYS H:22 , HIS H:33 , CYS H:34 , CYS H:37BINDING SITE FOR RESIDUE ZN H 101
23CC5SOFTWARECYS G:261 , CYS H:25 , CYS H:27 , CYS H:30BINDING SITE FOR RESIDUE ZN H 102
24CC6SOFTWAREYT3 G:302 , YT3 G:303 , ARG J:69BINDING SITE FOR RESIDUE YT3 J 101

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1G:261 -H:30

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:318 -Pro A:319
2Asp F:318 -Pro F:319

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OR5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OR5)

(-) Exons   (0, 0)

(no "Exon" information available for 4OR5)

(-) 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:320
                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhh.eeeeee........eeeeee.....eeeeee..........hhhhhhhhhhhh.........eeeeeee......eeeeeee...eehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.................hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh........hhhhh.hhhhh........hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4or5 A   8 VECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEGFPITALREIKILQLLKHENVVNLIEICRTKASPKGSIYLVFDFCEHDLAGLLSNVLVKFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKNSQPNRYtNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLALISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDPAQRIDSDDALNHDFFWSDPMPSDLKGMLSTH 331
                                    17        27        37        47        57        67        77        87   ||  101       111       121       131       141       151       161       171       181    |  191       201       211       221       231       241       251       261       271       281       291       301       311       321       331
                                                                                                              91|                                                                                       186-TPO                                                                                                                                             
                                                                                                               96                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.ee........hhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4or5 B   7 NNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQILEKTPNRLKRIWNWRACE 262
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256      


Chain C from PDB  Type:PROTEIN  Length:48
                                                                                
               SCOP domains ------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhh.............hhhhhh.hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                 4or5 C   1 MEPVDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKALGISYG  48
                                    10        20        30        40        


Chain E from PDB  Type:PROTEIN  Length:38
                                                                      
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author .......ee.....hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 4or5 E  32 SPLFAEPYKVTSKEDKLSSRIQSMLGNYDEMKDFIGDR  69
                                    41        51        61        


Chain F from PDB  Type:PROTEIN  Length:325
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhh.eeeeee........eeeeee.....eeeeee..........hhhhhhhhhhhhhh.......eeeeee............eeeeee...eehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.................hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh........hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4or5 F   8 VECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEGFPITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVLVKFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKNSQPNRYtNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLALISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDPAQRIDSDDALNHDFFWSDPMPSDLKGMLSTHL 332
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327     
                                                                                                                                                                                                            186-TPO                                                                                                                                              


Chain G from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee........hhhhhh....hhhhhhhhhhhhhhhhhh...hhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4or5 G   7 NNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQILEKTPNRLKRIWNWRAC 261
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256     


Chain H from PDB  Type:PROTEIN  Length:48
                                                                                
               SCOP domains ------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                 4or5 H   1 MEPVDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKALGISYG  48
                                    10        20        30        40        


Chain J from PDB  Type:PROTEIN  Length:38
                                                                      
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author .......ee.....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 4or5 J  32 SPLFAEPYKVTSKEDKLSSRIQSMLGNYDEMKDFIGDR  69
                                    41        51        61
   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 4OR5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OR5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OR5)

(-) Gene Ontology  (76, 108)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        AFF4_HUMAN | Q9UHB7: 4imy 4ogr 5jw9 5l1z
        CCNT1_HUMAN | O60563: 2pk2 3blh 3blq 3blr 3lq5 3mi9 3mia 3my1 3tn8 3tnh 3tni 4bcf 4bcg 4bch 4bci 4bcj 4ec8 4ec9 4imy 4ogr 5l1z
        CDK9_HUMAN | P50750: 1pf6 3blh 3blq 3blr 3lq5 3mi9 3mia 3my1 3tn8 3tnh 3tni 4bcf 4bcg 4bch 4bci 4bcj 4ec8 4ec9 4imy 4ogr 5l1z
        TAT_HV1H2 | P04608: 3mi9 3mia

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4OR5)