6PUY: HIV cleaved synaptic complex (CSC) intasome

Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ426 (compound 4d). Determined by electron microscopy at 2.8 Å resolution. Released 12 Feb 2020.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2), Human immunodeficiency virus 1
Chains: 6
Atoms: 5,892
Mol. weight: 185.87 kDa
Ligands: OZ1, ZN, MG
Released: 12 Feb 2020

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

Secondary structure: helices and β-sheets

6PUY contains 29 α-helices and 34 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: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5
α-helix	12-15	4
α-helix	19-25	7
α-helix	30-39	10
α-helix	41-43	3
β-strand	60-68	9	1
β-strand	71-78	8	1
β-strand	84-89	6	1
α-helix	94-105	12
β-strand	112-115	4	1
α-helix	119-122	4
α-helix	124-133	10
α-helix	135	1
β-strand	136-139	4	1
α-helix	145-148	4
α-helix	149-165	17
α-helix	166-168	3
α-helix	172-185	14
β-strand	189	1	2
β-strand	194	1	2
α-helix	196-220	25
β-strand	224-227	4	3
β-strand	238-245	8	3
β-strand	248-252	5	3
β-strand	257-261	5	3
β-strand	265-267	3	3

Chain B: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	9-15	7
α-helix	19-25	7
α-helix	30-38	9
β-strand	60-68	9	4
β-strand	71-78	8	4
β-strand	84-89	6	4
α-helix	94-107	14
β-strand	112-114	3	4
α-helix	124-133	10
β-strand	136-138	3	4
α-helix	151-165	15
α-helix	166-168	3
α-helix	172-181	10
α-helix	182-186	5
β-strand	189	1	5
β-strand	194	1	5
α-helix	196-220	25
β-strand	223-227	5	6
β-strand	238-244	7	6
β-strand	248-253	6	6
β-strand	256-261	6	6
β-strand	265-269	5	6

Chain C: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	214-220	7
β-strand	224-227	4	7
α-helix	235-236	2
β-strand	239-244	6	7
β-strand	248-253	6	7
β-strand	256-261	6	7
α-helix	262-264	3
β-strand	265-268	4	7

Chain D: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	224-227	4	8
β-strand	236-244	9	8
β-strand	248-253	6	8
β-strand	256-261	6	8
α-helix	262-264	3
β-strand	265-267	3	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chimeric Sso7d and HIV-1 integrase	A, B, C, D	protein	383	Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2), Human immunodeficiency virus 1	P12497, P39476 (AlphaFold model)
viral DNA non-transferred strand	E	DNA	27	Human immunodeficiency virus 1
viral DNA transferred strand	F	DNA	25	Human immunodeficiency virus 1

Sequence of entity 1 (A, B, C, D), FASTA

>6PUY_1 Chimeric Sso7d and HIV-1 integrase (chains A, B, C, D)
MGSSHHHHHHSSGLVPRGSHMATVKFKYKGEEKEVDISKIKKVWRVGKMISFTYDEGGGK
TGRGAVSEKDAPKELLQMLEKQKKGGGGGGGGGGGFLDGIDKAQEEHEKYHSNWRAMASD
FNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIE
AEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNP
QSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIA
TDIQTKELQKQITKIQNFRVYYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKA
KIIRDYGKQMAGDDCVASRQDED

Sequence of entity 2 (E), FASTA

>6PUY_2 viral DNA non-transferred strand (chains E)
ACTGCTAGAGATTTTCCCGCCCACGCT

Sequence of entity 3 (F), FASTA

>6PUY_3 viral DNA transferred strand (chains F)
AGCGTGGGCGGGAAAATCTCTAGCA

Ligands and cofactors

ID	Name	Formula	Copies
OZ1	4-amino-N-[(2,4-difluorophenyl)methyl]-1-hydroxy-6-(6-hydroxyhexyl)-2-oxo-1,2-d…	C22 H24 F2 N4 O4	1
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	2

Primary citation

Structural basis for strand-transfer inhibitor binding to HIV intasomes. Passos, D.O., Li, M., Jozwik, I.K. et al. Science (2020) 367:810-814. DOI 10.1126/science.aay8015 · PubMed

Other PDB entries of the same protein (UniProt P12497), best resolution first:

3DS4 1.12 Å, HIV-1 capsid C-terminal domain mutant (L211S) in complex with an inhibitor of particle…
3DS2 1.2 Å, HIV-1 capsid C-terminal domain mutant (Y169A)
6T6E 1.3 Å, Crystal Structure of the C-terminal domain of the HIV-1 Integrase (PNL4-3)
2XDE 1.4 Å, Crystal structure of the complex of PF-3450074 with an engineered HIV capsid N terminal…
3L3U 1.4 Å, Crystal structure of the HIV-1 integrase core domain to 1.4A
2PWO 1.45 Å, Crystal Structure of HIV-1 CA146 A92E Psuedo Cell
3WNF 1.45 Å, Cyclic hexapeptide CKIDNC in complex with HIV-1 integrase
6OYD 1.46 Å, X-ray crystal structure of wild type HIV-1 protease in complex with GRL-004
6MCR 1.48 Å, X-ray crystal structure of wild type HIV-1 protease in complex with GRL-001
2PXR 1.5 Å, Crystal Structure of HIV-1 CA146 in the Presence of CAP-1
3WNH 1.5 Å, Cyclic hexapeptide PKZDNv in complex with HIV-1 integrase
4NX4 1.5 Å, Re-refinement of CAP-1 HIV-CA complex

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