4OGR: P-TEFb complex with AFF4 and Tat

crystal structure of P-TEFb complex with AFF4 and Tat. Determined by X-ray diffraction at 3.0 Å resolution. Released 7 May 2014.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Homo sapiens, Human immunodeficiency virus type 1 (HXB3 ISOLATE)
Chains: 12
Atoms: 16,154
Mol. weight: 254.45 kDa
Ligands: ADN, ZN
Released: 7 May 2014

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

Secondary structure: helices and β-sheets

4OGR contains 128 α-helices and 48 β-strands across 12 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: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
α-helix	16-18	3
β-strand	19-27	9	1
β-strand	31-38	8	1
β-strand	44-50	7	1
α-helix	61-72	12
β-strand	78	1	2
β-strand	81-86	6	1
β-strand	99-104	6	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
α-helix	168-170	3
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	271-273	3
α-helix	275-283	9
α-helix	286-295	10
α-helix	306-310	5
α-helix	313-315	3
α-helix	320-321	2
α-helix	325-328	4

Chain B: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
α-helix	16-20	5
α-helix	25-27	3
α-helix	31-52	22
β-strand	55	1	4
α-helix	56-69	14
α-helix	80-94	15
α-helix	101-112	12
α-helix	117-120	4
α-helix	124-143	20
α-helix	153-163	11
α-helix	168-184	17
α-helix	187-189	3
α-helix	193-208	16
β-strand	210-211	2	5
α-helix	221-224	4
α-helix	231-246	16
α-helix	249-252	4

Chains C and L: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	6-18	13
α-helix	36-38	3
β-strand	39-40	2	5
α-helix	47-56	10
α-helix	59-61	3

Chains D, H and M: 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	38-42	5

Chain E: 21 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	6
α-helix	16-18	3
β-strand	19-25	7	6
β-strand	33-38	6	6
β-strand	44-49	6	6
α-helix	55-57	3
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
α-helix	168-170	3
β-strand	172-173	2	8
α-helix	182-183	2
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	261-264	4
α-helix	271-273	3
α-helix	275-283	9
α-helix	286-295	10
α-helix	306-310	5
α-helix	313-315	3
α-helix	320-321	2
α-helix	325-328	4

Chain F: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	16-20	5
α-helix	25-27	3
α-helix	31-52	22
β-strand	55	1	9
α-helix	56-69	14
α-helix	80-94	15
α-helix	101-112	12
α-helix	117-120	4
α-helix	124-143	20
α-helix	153-163	11
α-helix	168-184	17
α-helix	187-189	3
α-helix	193-208	16
β-strand	210-211	2	10
α-helix	221-224	4
α-helix	231-246	16

Chain G: 3 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

Chain I: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	11
α-helix	16-18	3
β-strand	19-27	9	11
β-strand	31-38	8	11
β-strand	44-50	7	11
α-helix	61-72	12
β-strand	78	1	12
β-strand	81-86	6	11
β-strand	99-104	6	11
β-strand	108-109	2	12
α-helix	110-115	6
α-helix	123-142	20
β-strand	145-146	2	13
α-helix	152-154	3
β-strand	155-157	3	12
β-strand	163-165	3	12
α-helix	168-170	3
β-strand	172-173	2	13
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	261-264	4
α-helix	275-283	9
α-helix	286-295	10
α-helix	306-310	5
α-helix	313-315	3
α-helix	320-321	2
α-helix	325-328	4

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclin-dependent kinase 9	A, E, I	protein	332	Homo sapiens	P50750 (AlphaFold model)
Cyclin-T1	B, F, K	protein	264	Homo sapiens	O60563 (AlphaFold model)
AF4/FMR2 family member 4	C, G, L	protein	75	Homo sapiens	Q9UHB7 (AlphaFold model)
Protein Tat	D, H, M	protein	58	Human immunodeficiency virus type 1 (HXB3 ISOLATE)	P69698

Sequence of entity 1 (A, E, I), FASTA

>4OGR_1 Cyclin-dependent kinase 9 (chains A, E, I)
GHMAKQYDSVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEG
FPITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVL
VKFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAK
NSQPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQL
ALISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVL
DPAQRIDSDDALNHDFFWSDPMPSDLKGMLST

Sequence of entity 2 (B, F, K), FASTA

>4OGR_2 Cyclin-T1 (chains B, F, K)
MEGERKNNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTIN
TAIVYMHRFYMIQSFTQFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPD
TRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATN
SLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHE
FLQILEKTPNRLKRIWNWRACEAA

Sequence of entity 3 (C, G, L), FASTA

>4OGR_3 AF4/FMR2 family member 4 (chains C, G, L)
SNANREDRNVLRMKERERRNQEIQQGEDAFPPSSPLFAEPYKVTSKEDKLSSRIQSMLGN
YDEMKDFIGDRSIPK

Sequence of entity 4 (D, H, M), FASTA

>4OGR_4 Protein Tat (chains D, H, M)
XMEPVDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKALGISYGRKKRRQRRR

Ligands and cofactors

ID	Name	Formula	Copies
ADN	Adenosine	C10 H13 N5 O4	3
ZN	Zinc ion	Zn	6

Primary citation

AFF4 binding to Tat-P-TEFb indirectly stimulates TAR recognition of super elongation complexes at the HIV promoter. Schulze-Gahmen, U., Lu, H., Zhou, Q. et al. Elife (2014) 3:e02375-e02375. DOI 10.7554/eLife.02375 · 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
4OR5 2.9 Å, Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4
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

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