6CYT: HIV-1 TAR loop

HIV-1 TAR loop in complex with Tat:AFF4:P-TEFb. Determined by X-ray diffraction at 3.5 Å resolution. Released 12 Dec 2018.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 5
Atoms: 5,621
Mol. weight: 86.36 kDa
Ligands: ZN
Released: 12 Dec 2018

Explore 6CYT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6CYT contains 41 α-helices and 16 β-strands across 4 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	32-38	7	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	306-311	6
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	252-255	4

Chain C: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	36-38	3
β-strand	39-40	2	5
α-helix	47-55	9

Chain D: 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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclin-dependent kinase 9	A	protein	332	Homo sapiens	P50750 (AlphaFold model)
Cyclin-T1	B	protein	264	Homo sapiens	O60563 (AlphaFold model)
AF4/FMR2 family member 4	C	protein	36	Homo sapiens	Q9UHB7 (AlphaFold model)
Protein Tat	D	protein	58	Human immunodeficiency virus 1	P04608 (AlphaFold model)
RNA (5'-r(papupcpupgpapgpcpcpupgpgpgpapgpcp*u)-3')	N	RNA	20	Human immunodeficiency virus 1

Sequence of entity 1 (A), FASTA

>6CYT_1 Cyclin-dependent kinase 9 (chains A)
GHMAKQYDSVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEG
FPITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVL
VKFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAK
NSQPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQL
ALISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVL
DPAQRIDSDDALNHDFFWSDPMPSDLKGMLST

Sequence of entity 2 (B), FASTA

>6CYT_2 Cyclin-T1 (chains B)
MEGERKNNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTIN
TAIVYMHRFYMIQSFTQFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPD
TRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATN
SLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHE
FLQILEKTPNRLKRIWNWRACEAA

Sequence of entity 3 (C), FASTA

>6CYT_3 AF4/FMR2 family member 4 (chains C)
SPLFAEPYKVTSKEDYLSSRIQSMLGNYDEMKDFIG

Sequence of entity 4 (D), FASTA

>6CYT_4 Protein Tat (chains D)
XMEPVDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKALGISYGRKKRRQRRR

Sequence of entity 5 (N), FASTA

>6CYT_5 RNA (5'-R(P*AP*UP*CP*UP*GP*AP*GP*CP*CP*UP*GP*GP*GP*AP*GP*CP*U)-3') (chains N)
GAUCUGAGCCUGGGAGCUCA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Structural mechanism for HIV-1 TAR loop recognition by Tat and the super elongation complex. Schulze-Gahmen, U., Hurley, J.H. Proc Natl Acad Sci U S A (2018) 115:12973-12978. DOI 10.1073/pnas.1806438115 · 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

Browse structure collections

About this viewer

MolViewer shows 6CYT directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.