7ZPP: MVV CSC intasome

Cryo-EM structure of the MVV CSC intasome at 4.5A resolution. Determined by electron microscopy at 4.5 Å resolution. Released 11 May 2022.

Method: Electron microscopy
Resolution: 4.5 Å
Organisms: Visna/maedi virus EV1 KV1772, Visna lentivirus (strain 1514), Visna-maedi virus
Chains: 20
Atoms: 33,171
Mol. weight: 542.45 kDa
Released: 11 May 2022

Explore 7ZPP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZPP contains 193 α-helices and 230 β-strands across 16 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 I: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	19-26	8
α-helix	30-39	10
α-helix	42-46	5
β-strand	58	1	1
β-strand	62-70	9	2
β-strand	73-79	7	2
β-strand	86-90	5	2
α-helix	96-109	14
β-strand	114-117	4	2
α-helix	121-124	4
α-helix	126-134	9
β-strand	138-141	4	2
α-helix	142-143	2
α-helix	147-150	4
α-helix	151-167	17
α-helix	168-170	3
α-helix	174-183	10
α-helix	184-188	5
β-strand	191	1	3
β-strand	195	1	3
α-helix	197-208	12
α-helix	210-215	6
α-helix	216-218	3
β-strand	222-224	3	4
β-strand	229-230	2	5
β-strand	233-234	2	5
β-strand	241-243	3	4
β-strand	245-246	2	6
β-strand	250-255	6	6
β-strand	260-265	6	6
α-helix	266-268	3
β-strand	271	1	4
α-helix	272-275	4

Chains B and J: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	19-26	8
α-helix	30-39	10
β-strand	62-69	8	7
β-strand	74-80	7	7
β-strand	86-90	5	7
α-helix	96-109	14
β-strand	114-117	4	7
α-helix	121-124	4
α-helix	126-135	10
β-strand	138-141	4	7
α-helix	147-167	21
α-helix	168-170	3
α-helix	174-183	10
α-helix	184-188	5
β-strand	191	1	8
β-strand	195	1	8
α-helix	197-211	15
α-helix	212-216	5
β-strand	222-226	5	9
β-strand	230	1	10
β-strand	233	1	10
β-strand	238-243	6	9
β-strand	245-246	2	11
β-strand	250-255	6	11
β-strand	260-265	6	11
α-helix	266-268	3
β-strand	269-272	4	9

Chains C and K: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	4-15	12
α-helix	19-26	8
α-helix	30-39	10
α-helix	41-45	5
β-strand	62-70	9	12
β-strand	73-80	8	12
β-strand	86-91	6	12
α-helix	96-109	14
β-strand	114-117	4	12
α-helix	121-124	4
α-helix	126-135	10
β-strand	138-141	4	12
α-helix	147-167	21
α-helix	174-183	10
α-helix	184-188	5
β-strand	191	1	13
β-strand	195	1	13
α-helix	197-218	22
β-strand	223-226	4	14
β-strand	229-230	2	15
β-strand	233-234	2	15
β-strand	238-242	5	14
β-strand	245-246	2	16
β-strand	250-254	5	16
β-strand	261-265	5	16
α-helix	266-268	3
β-strand	269-272	4	14

Chains D and L: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	62-69	8	17
β-strand	74-80	7	17
β-strand	86-87	2	17
β-strand	90-91	2	17
α-helix	96-109	14
β-strand	114-116	3	17
α-helix	121-124	4
α-helix	126-134	9
β-strand	140	1	17
α-helix	147-167	21
α-helix	174-183	10
α-helix	184-188	5
β-strand	191	1	18
β-strand	195	1	18
α-helix	197-218	22
β-strand	223-226	4	19
β-strand	241-242	2	19
β-strand	245-246	2	20
β-strand	250-254	5	20
β-strand	261-265	5	20
β-strand	268	1	1
β-strand	269-272	4	19

Chain E: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	5-15	11
α-helix	19-26	8
α-helix	30-39	10
β-strand	62-65	4	21
β-strand	68-69	2	21
β-strand	74-80	7	21
β-strand	86-90	5	21
α-helix	96-109	14
β-strand	114-117	4	21
α-helix	121-124	4
α-helix	126-135	10
β-strand	138-141	4	21
α-helix	147-167	21
α-helix	174-183	10
α-helix	184-188	5
α-helix	197-218	22
β-strand	223-226	4	22
β-strand	229-230	2	23
β-strand	233-234	2	23
β-strand	238-242	5	22
β-strand	245-246	2	24
β-strand	250-255	6	24
β-strand	260-265	6	24
α-helix	266-268	3
β-strand	271	1	22

Chains F and N: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	19-26	8
α-helix	30-39	10
α-helix	41-45	5
β-strand	63-65	3	25
β-strand	68-70	3	25
β-strand	73-80	8	25
β-strand	86-91	6	25
α-helix	96-108	13
β-strand	114-117	4	25
α-helix	121-124	4
α-helix	126-135	10
β-strand	138-141	4	25
α-helix	147-167	21
α-helix	168-170	3
α-helix	174-183	10
α-helix	184-188	5
β-strand	191	1	26
β-strand	195	1	26
α-helix	197-217	21
β-strand	223-226	4	27
β-strand	229-230	2	28
β-strand	233-234	2	28
α-helix	235-237	3
β-strand	238-242	5	27
β-strand	243-246	4	29
β-strand	250-255	6	29
β-strand	260-265	6	29
α-helix	266-268	3
β-strand	270-272	3	27

Chains G and O: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	19-26	8
α-helix	30-39	10
α-helix	41-45	5
β-strand	62-70	9	30
β-strand	73-80	8	30
β-strand	86-87	2	30
β-strand	90-91	2	30
α-helix	96-109	14
β-strand	114-117	4	30
α-helix	121-124	4
α-helix	126-135	10
β-strand	138-141	4	30
α-helix	147-167	21
α-helix	174-183	10
α-helix	184-188	5
β-strand	191	1	31
β-strand	195	1	31
α-helix	197-218	22

Chains H and P: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	62-69	8	32
β-strand	74-80	7	32
β-strand	86-87	2	32
β-strand	90-91	2	32
α-helix	96-109	14
β-strand	114-117	4	32
α-helix	121-124	4
α-helix	126-135	10
β-strand	138-141	4	32
α-helix	147-167	21
α-helix	174-183	10
α-helix	184-188	5
β-strand	191	1	33
β-strand	195	1	33
α-helix	197-207	11
α-helix	210-218	9
β-strand	223-226	4	34
β-strand	229-230	2	35
β-strand	233-234	2	35
β-strand	238-242	5	34
β-strand	245-246	2	36
β-strand	250-254	5	36
β-strand	261-265	5	36
α-helix	266-268	3
β-strand	269-271	3	34
α-helix	272-275	4

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrase	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	protein	281	Visna/maedi virus EV1 KV1772	P35956
vDNA, non-transferred strand	Q, S	DNA	21	Visna lentivirus (strain 1514)
vDNA, transferred strand	R, T	DNA	19	Visna-maedi virus

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P), FASTA

>7ZPP_1 Integrase (chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P)
WIENIPLAEEEHNKWHQDAVSLHLEFGIPRTAAEDIVQQCDVCQENKMPSTLRGSNKRGI
DHWQVDYTHYEDKIILVWVETNSGLIYAERVKGETGQEFRVQTMKWYAMFAPKSLQSDNG
PAFVAESTQLLMKYLGIEHTTGIPWNPQSQALVERTHQTLKNTLEKLIPMFNAFESALAG
TLITLNIKRKGGLGTSPMDIFIFNKEQQRIQQQSKSKQEKIRFCYYRTRKRGHPGEWQGP
TQVLWGGDGAIVVKDRGTDRYLVIANKDVKFIPPPKEIQKE

Sequence of entity 2 (Q, S), FASTA

>7ZPP_2 vDNA, non-transferred strand (chains Q, S)
GCTGCGAGATCCGCTCCGGTG

Sequence of entity 3 (R, T), FASTA

>7ZPP_3 vDNA, transferred strand (chains R, T)
CACCGGAGCGGATCTCGCA

Primary citation

A supramolecular assembly mediates lentiviral DNA integration. Ballandras-Colas, A., Maskell, D.P., Serrao, E. et al. Science (2017) 355:93-95. DOI 10.1126/science.aah7002 · PubMed

Other PDB entries of the same protein (UniProt P35956), best resolution first:

5LLJ 1.78 Å, Maedi-Visna virus (MVV) integrase C-terminal domain (residues 220-276)
5T3A 2.5 Å, Maedi-Visna virus (MVV) integrase CCD-CTD (residues 60-275)
3HPH 2.64 Å, Closed tetramer of Visna virus integrase (residues 1-219) in complex with LEDGF IBD
9S28 2.8 Å, MVV STC intasome in complex with LEDGF
9S29 2.8 Å, MVV CSC intasome in complex with LEDGF
3HPG 3.28 Å, Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open…
7U32 3.46 Å, MVV cleaved synaptic complex (CSC) intasome at 3.4 A resolution
7Z1Z 3.5 Å, MVV strand transfer complex (STC) intasome in complex with LEDGF/p75 at 3.5 A resolution
5M0R 8.2 Å, Cryo-EM reconstruction of the maedi-visna virus (MVV) strand transfer complex

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