4IMY: Cyclin-dependent kinase 9

The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat. Determined by X-ray diffraction at 2.94 Å resolution. Released 13 Mar 2013.

Method: X-ray diffraction
Resolution: 2.94 Å
Organism: Homo sapiens
Chains: 9
Atoms: 14,608
Mol. weight: 233.95 kDa
Ligands: AMP
Released: 13 Mar 2013

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

Secondary structure: helices and β-sheets

4IMY contains 109 α-helices and 42 β-strands across 9 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: 19 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	50-51	2
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
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	261-264	4
α-helix	271-273	3
α-helix	275-279	5
α-helix	286-295	10
α-helix	300-302	3
α-helix	306-310	5
α-helix	313-315	3
α-helix	320-321	2
α-helix	325-328	4

Chain B: 14 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	16-20	5
α-helix	23-26	4
α-helix	31-52	22
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	187-189	3
α-helix	193-208	16
β-strand	210-211	2	4
α-helix	221-224	4
α-helix	231-247	17
α-helix	252-255	4

Chain C: 19 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	5
α-helix	16-18	3
β-strand	19-25	7	5
β-strand	33-38	6	5
β-strand	44-49	6	5
α-helix	50-51	2
α-helix	61-72	12
β-strand	78	1	6
β-strand	81-86	6	5
β-strand	99-104	6	5
β-strand	108-109	2	6
α-helix	110-115	6
α-helix	123-142	20
β-strand	145-146	2	7
α-helix	152-154	3
β-strand	155-157	3	6
β-strand	163-165	3	6
β-strand	172-173	2	7
α-helix	192-194	3
α-helix	197-200	4
α-helix	209-224	16
α-helix	234-245	12
α-helix	261-264	4
α-helix	271-273	3
α-helix	275-279	5
α-helix	286-295	10
α-helix	300-302	3
α-helix	306-310	5
α-helix	313-315	3
α-helix	320-321	2
α-helix	325-328	4

Chain D: 14 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	16-20	5
α-helix	23-26	4
α-helix	31-52	22
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	187-189	3
α-helix	193-208	16
β-strand	210-211	2	8
α-helix	221-224	4
α-helix	231-247	17

Chain E: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	9
α-helix	16-18	3
β-strand	19-27	9	9
β-strand	32-38	7	9
β-strand	44-50	7	9
α-helix	61-72	12
β-strand	78	1	10
β-strand	81-86	6	9
β-strand	99-104	6	9
β-strand	108-109	2	10
α-helix	110-115	6
α-helix	123-142	20
β-strand	145-146	2	11
α-helix	152-154	3
β-strand	155-157	3	10
β-strand	163-165	3	10
β-strand	172-173	2	11
α-helix	192-194	3
α-helix	197-200	4
α-helix	209-224	16
α-helix	234-245	12
α-helix	261-264	4
α-helix	271-273	3
α-helix	275-279	5
α-helix	286-295	10
α-helix	300-302	3
α-helix	306-310	5
α-helix	313-315	3
α-helix	320-321	2
α-helix	325-328	4

Chain F: 14 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	16-20	5
α-helix	23-26	4
α-helix	31-52	22
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	187-189	3
α-helix	193-208	16
β-strand	210-211	2	12
α-helix	221-224	4
α-helix	231-247	17
α-helix	251-253	3

Chains G and I: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	39-40	2	4
α-helix	47-55	9
α-helix	59-62	4
α-helix	63-65	3

Chain H: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-18	15
α-helix	36-38	3
β-strand	39-40	2	8
α-helix	47-55	9
α-helix	59-62	4
α-helix	63-65	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclin-dependent kinase 9	A, C, E	protein	332	Homo sapiens	P50750 (AlphaFold model)
Cyclin-T1	B, D, F	protein	264	Homo sapiens	O60563 (AlphaFold model)
AF4/FMR2 family member 4	G, H, I	protein	75	Homo sapiens	Q9UHB7 (AlphaFold model)

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

>4IMY_1 Cyclin-dependent kinase 9 (chains A, C, E)
GHMAKQYDSVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEG
FPITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVL
VKFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAK
NSQPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQL
ALISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVL
DPAQRIDSDDALNHDFFWSDPMPSDLKGMLST

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

>4IMY_2 Cyclin-T1 (chains B, D, F)
MEGERKNNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTIN
TAIVYMHRFYMIQSFTQFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPD
TRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATN
SLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHE
FLQILEKTPNRLKRIWNWRACEAA

Sequence of entity 3 (G, H, I), FASTA

>4IMY_3 AF4/FMR2 family member 4 (chains G, H, I)
SNANREDRNVLRMKERERRNQEIQQGEDAFPPSSPLFAEPYKVTSKEDKLSSRIQSMLGN
YDEMKDFIGDRSIPK

Ligands and cofactors

ID	Name	Formula	Copies
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	3

Primary citation

The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat. Schulze-Gahmen, U., Upton, H., Birnberg, A. et al. Elife (2013) 2:e00327-e00327. DOI 10.7554/eLife.00327 · 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
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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