4OR5: HIV-1 Tat

Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4. Determined by X-ray diffraction at 2.9 Å resolution. Released 16 Apr 2014.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Homo sapiens, HIV-1
Chains: 8
Atoms: 10,895
Mol. weight: 159.54 kDa
Ligands: ZN, YT3
Released: 16 Apr 2014

Explore 4OR5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4OR5 contains 81 α-helices and 32 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
α-helix	16-18	3
β-strand	19-24	6	1
β-strand	33-38	6	1
β-strand	44-49	6	1
α-helix	61-70	10
β-strand	78	1	2
β-strand	81-87	7	1
β-strand	98-104	7	1
β-strand	108-109	2	2
α-helix	110-115	6
α-helix	123-142	20
β-strand	145-146	2	3
α-helix	152-154	3
β-strand	155-157	3	2
β-strand	163-165	3	2
β-strand	172-173	2	3
α-helix	192-194	3
α-helix	197-200	4
α-helix	209-224	16
α-helix	234-245	12
α-helix	256-258	3
α-helix	262-264	3
α-helix	275-283	9
α-helix	286-295	10
α-helix	304-305	2
α-helix	306-309	4
α-helix	313-315	3
α-helix	320-321	2

Chain B: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	16-19	4
α-helix	23-26	4
α-helix	31-52	22
β-strand	55	1	4
α-helix	56-72	17
α-helix	80-94	15
α-helix	101-112	12
α-helix	124-143	20
α-helix	153-163	11
α-helix	168-184	17
α-helix	187-189	3
α-helix	193-207	15
β-strand	210-211	2	5
α-helix	213-215	3
α-helix	221-224	4
α-helix	231-247	17
α-helix	252-254	3

Chain C: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	14	1
β-strand	15	1	4
α-helix	28-31	4
α-helix	35-37	3
α-helix	38-43	6

Chain E: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	36-38	3
β-strand	39-40	2	5
α-helix	47-56	10
α-helix	59-62	4

Chain F: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	6
α-helix	16-18	3
β-strand	19-24	6	6
β-strand	33-38	6	6
β-strand	44-49	6	6
α-helix	61-72	12
β-strand	78	1	7
β-strand	81-86	6	6
β-strand	99-104	6	6
β-strand	108-109	2	7
α-helix	110-115	6
α-helix	123-142	20
β-strand	145-146	2	8
α-helix	152-154	3
β-strand	155-157	3	7
β-strand	163-165	3	7
β-strand	172-173	2	8
α-helix	192-194	3
α-helix	197-200	4
α-helix	209-224	16
α-helix	234-245	12
α-helix	256-258	3
α-helix	260-264	5
α-helix	275-283	9
α-helix	286-295	10
α-helix	300-302	3
α-helix	306-310	5
α-helix	313-316	4
α-helix	320-321	2

Chain G: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	18-20	3
α-helix	25-27	3
α-helix	31-51	21
β-strand	55	1	9
α-helix	56-69	14
α-helix	80-94	15
α-helix	101-112	12
α-helix	124-143	20
α-helix	153-163	11
α-helix	168-184	17
α-helix	187-190	4
α-helix	193-207	15
β-strand	210-211	2	10
α-helix	212-215	4
α-helix	221-224	4
α-helix	231-246	16
α-helix	252-254	3

Chain H: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15	1	9
α-helix	21-22	2
α-helix	28-32	5
α-helix	35-36	2
α-helix	37-42	6

Chain J: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	36-38	3
β-strand	39-40	2	10
α-helix	47-56	10
α-helix	59-62	4
α-helix	63-65	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclin-dependent kinase 9	A, F	protein	326	Homo sapiens	P50750 (AlphaFold model)
Cyclin-T1	B, G	protein	266	Homo sapiens	O60563 (AlphaFold model)
Protein Tat	C, H	protein	48	HIV-1	P04608 (AlphaFold model)
AF4/FMR2 family member 4	E, J	protein	43	Homo sapiens	Q9UHB7 (AlphaFold model)

Sequence of entity 1 (A, F), FASTA

>4OR5_1 Cyclin-dependent kinase 9 (chains A, F)
SVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEGFPITALRE
IKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVLVKFTLSEI
KRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKNSQPNRYT
NRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLALISQLCG
SITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDPAQRIDS
DDALNHDFFWSDPMPSDLKGMLSTHL

Sequence of entity 2 (B, G), FASTA

>4OR5_2 Cyclin-T1 (chains B, G)
MEGERKNNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTIN
TAIVYMHRFYMIQSFTQFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPD
TRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATN
SLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHE
FLQILEKTPNRLKRIWNWRACEAAKK

Sequence of entity 3 (C, H), FASTA

>4OR5_3 Protein Tat (chains C, H)
MEPVDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKALGISYG

Sequence of entity 4 (E, J), FASTA

>4OR5_4 AF4/FMR2 family member 4 (chains E, J)
EQIGGSPLFAEPYKVTSKEDKLSSRIQSMLGNYDEMKDFIGDR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
YT3	Yttrium (III) ion	Y	16

Water and common crystallization additives (SO4) are not listed.

Primary citation

Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4. Gu, J., Babayeva, N.D., Suwa, Y. et al. Cell Cycle (2014) 13:1788-1797. DOI 10.4161/cc.28756 · PubMed

Other PDB entries of the same protein (UniProt P50750 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MI9 2.1 Å, Crystal structure of HIV-1 Tat complexed with human P-TEFb
3BLH 2.48 Å, Crystal Structure of Human CDK9/cyclinT1
3BLR 2.8 Å, Crystal Structure of Human CDK9/cyclinT1 in complex with Flavopiridol
3MY1 2.8 Å, Structure of CDK9/cyclinT1 in complex with DRB
7NWK 2.81 Å, Crystal structure of CDK9-Cyclin T1 bound by compound 6
3BLQ 2.9 Å, Crystal Structure of Human CDK9/cyclinT1 in Complex with ATP
4IMY 2.94 Å, The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat
3TN8 2.95 Å, CDK9/cyclin T in complex with CAN508
4BCH 2.96 Å, Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine…
3LQ5 3.0 Å, Structure of CDK9/CyclinT in complex with S-CR8
3MIA 3.0 Å, Crystal structure of HIV-1 Tat complexed with ATP-bound human P-TEFb
4OGR 3.0 Å, crystal structure of P-TEFb complex with AFF4 and Tat

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