5U1C: HIV-1 Integrase, Sso7d chimera

Structure of tetrameric HIV-1 Strand Transfer Complex Intasome. Determined by electron microscopy at 3.9 Å resolution. Released 11 Jan 2017.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Sulfolobus solfataricus, Human immunodeficiency virus 1, Homo sapiens
Chains: 10
Atoms: 8,596
Mol. weight: 213.02 kDa
Ligands: ZN, MG
Released: 11 Jan 2017

Explore 5U1C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5U1C contains 42 α-helices and 50 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.

Chains A and C: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	19-25	7
α-helix	30-39	10
β-strand	56	1	1
β-strand	60-68	9	2
β-strand	71-78	8	2
β-strand	84-89	6	2
α-helix	94-105	12
β-strand	112-114	3	2
α-helix	120-122	3
α-helix	124-132	9
β-strand	136-138	3	2
α-helix	145-148	4
α-helix	149-165	17
α-helix	166-168	3
α-helix	172-181	10
α-helix	182-186	5
β-strand	189	1	3
β-strand	194	1	3
α-helix	196-203	8
β-strand	224-227	4	4
β-strand	240-244	5	5
β-strand	248-252	5	5
β-strand	257-261	5	5
α-helix	262-264	3
β-strand	265-268	4	4

Chains B and D: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	60-66	7	6
α-helix	68-70	3
β-strand	73-78	6	6
β-strand	83-88	6	6
α-helix	94-107	14
β-strand	112-114	3	6
α-helix	119-122	4
α-helix	124-133	10
α-helix	152-165	14
α-helix	166-168	3
α-helix	172-185	14
α-helix	197-203	7
β-strand	224-227	4	7
β-strand	229	1	8
β-strand	232	1	8
β-strand	239-244	6	7
β-strand	248-252	5	7
β-strand	257-261	5	7
β-strand	264	1	1
β-strand	265-268	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HIV-1 Integrase, Sso7d chimera	A, B, C, D	protein	383	Sulfolobus solfataricus, Human immunodeficiency virus 1	P39476 (AlphaFold model)
DNA (11-mer)	G, H	DNA	11	Homo sapiens
DNA (23-mer)	E, I	DNA	23	Human immunodeficiency virus 1
DNA (37-mer)	F, J	DNA	37	Human immunodeficiency virus 1, Homo sapiens

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

>5U1C_1 HIV-1 Integrase, Sso7d chimera (chains A, B, C, D)
MGSSHHHHHHSSGLVPRGSHMATVKFKYKGEEKEVDISKIKKVWRVGKMISFTYDEGGGK
TGRGAVSEKDAPKELLQMLEKQKKGGGGGGGGGGGFLDGIDKAQEEHEKYHSNWRAMASD
FNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIE
AEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNP
QSQGVIQSMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIA
TDIQTKELQKQITKIQNFRVYYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKA
KIIRDYGKQMAGDDCVASRQDED

Sequence of entity 2 (G, H), FASTA

>5U1C_2 DNA (11-MER) (chains G, H)
GTACGCTGACT

Sequence of entity 3 (E, I), FASTA

>5U1C_3 DNA (23-MER) (chains E, I)
ACTGCTAGAGATTTTCCACACTG

Sequence of entity 4 (F, J), FASTA

>5U1C_4 DNA (37-MER) (chains F, J)
CAGTGTGGAAAATCTCTAGCAGTTACAGTCAGCGTAC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	2

Primary citation

Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome. Passos, D.O., Li, M., Yang, R. et al. Science (2017) 355:89-92. DOI 10.1126/science.aah5163 · PubMed

Other PDB entries of the same protein (UniProt P39476 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1C8C 1.45 Å, Crystal structures of the chromosomal proteins SSO7D/SAC7D bound to DNA containing T-G…
1BNZ 2.0 Å, SSO7D hyperthermophile protein/dna complex
5B02 2.21 Å, Structure of the prenyltransferase MoeN5 with a fusion protein tag of Sso7d
6J8V 2.23 Å, Structure of MOEN5-SSO7D fusion protein in complex with ligand 2
5B0I 2.26 Å, Structure of MoeN5-Sso7d fusion protein in complex with beta-octyl glucoside
5GWW 2.3 Å, Structure of MoeN5-Sso7d fusion protein in complex with a permethylated substrate analogue
6J8W 2.35 Å, Structure of MOEN5-SSO7D fusion protein in complex with lig 1
5GWV 2.4 Å, Structure of MoeN5-Sso7d fusion protein in complex with a substrate analogue
5B0J 2.5 Å, Structure of MoeN5-Sso7d fusion protein in complex with beta-undecyl maltoside
5B03 2.6 Å, Structure of MoeN5-Sso7d fusion protein in complex with geranyl pyrophosphate
5B0K 2.75 Å, Structure of MoeN5-Sso7d fusion protein in complex with beta-decyl maltoside
5B0L 2.8 Å, Structure of MoeN5-Sso7d fusion protein in complex with beta-nonyl glucoside

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