6PUT: HIV cleaved synaptic complex (CSC) intasome

Structure of HIV cleaved synaptic complex (CSC) intasome bound with calcium. Determined by electron microscopy at 2.9 Å resolution. Released 12 Feb 2020.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2), Human immunodeficiency virus 1
Chains: 6
Atoms: 5,488
Mol. weight: 185.46 kDa
Ligands: CA, ZN
Released: 12 Feb 2020

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

Secondary structure: helices and β-sheets

6PUT contains 25 α-helices and 35 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: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	7-15	9
α-helix	19-25	7
α-helix	30-38	9
α-helix	41-43	3
β-strand	60	1	1
β-strand	64-68	5	2
β-strand	71-75	5	2
β-strand	76-78	3	3
β-strand	83-85	3	3
β-strand	89	1	2
α-helix	94-107	14
β-strand	112-115	4	1
α-helix	119-122	4
α-helix	124-133	10
β-strand	136-139	4	1
α-helix	140-141	2
α-helix	145-148	4
α-helix	149-164	16
α-helix	166-168	3
α-helix	172-185	14
α-helix	196-218	23
β-strand	241-244	4	4
β-strand	249-251	3	4
β-strand	258-260	3	4

Chain B: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	2-15	14
α-helix	19-25	7
α-helix	30-39	10
β-strand	60-68	9	5
β-strand	71-78	8	5
β-strand	84-89	6	5
α-helix	94-107	14
β-strand	112-114	3	5
α-helix	124-133	10
β-strand	136-138	3	5
α-helix	151-165	15
α-helix	166-168	3
α-helix	173-185	13
β-strand	189	1	6
β-strand	194	1	6
α-helix	196-220	25
β-strand	224	1	7
β-strand	225	1	8
β-strand	239	1	8
β-strand	240-244	5	9
β-strand	249-252	4	9
β-strand	257-260	4	9
β-strand	268	1	7

Chain C: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	214-221	8
β-strand	224-227	4	10
β-strand	236-244	9	10
β-strand	248-253	6	10
β-strand	256-261	6	10
α-helix	262-264	3
β-strand	265-268	4	10

Chain D: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	224-228	5	11
β-strand	235-244	10	11
β-strand	248-252	5	11
β-strand	257-261	5	11
α-helix	262-264	3
β-strand	265-267	3	11

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 transferred strand	F	DNA	25	Human immunodeficiency virus 1
viral DNA non-transferred strand	E	DNA	27	Human immunodeficiency virus 1

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

>6PUT_1 Chimeric Sso7d and HIV-1 integrase (chains A, B, C, D)
MGSSHHHHHHSSGLVPRGSHMATVKFKYKGEEKEVDISKIKKVWRVGKMISFTYDEGGGK
TGRGAVSEKDAPKELLQMLEKQKKGGGGGGGGGGGFLDGIDKAQEEHEKYHSNWRAMASD
FNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIE
AEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNP
QSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIA
TDIQTKELQKQITKIQNFRVYYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKA
KIIRDYGKQMAGDDCVASRQDED

Sequence of entity 2 (F), FASTA

>6PUT_2 viral DNA transferred strand (chains F)
AGCGTGGGCGGGAAAATCTCTAGCA

Sequence of entity 3 (E), FASTA

>6PUT_3 viral DNA non-transferred strand (chains E)
ACTGCTAGAGATTTTCCCGCCCACGCT

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
ZN	Zinc ion	Zn	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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