7U32: MVV cleaved synaptic complex (CSC) intasome

MVV cleaved synaptic complex (CSC) intasome at 3.4 A resolution. Determined by electron microscopy at 3.46 Å resolution. Released 11 May 2022.

Method: Electron microscopy
Resolution: 3.46 Å
Organisms: Visna/maedi virus EV1 KV1772, synthetic construct
Chains: 20
Atoms: 32,150
Mol. weight: 553.2 kDa
Ligands: ZN, CA
Released: 11 May 2022

Explore 7U32 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7U32 contains 172 α-helices and 200 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: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	19-26	8
α-helix	30-38	9
α-helix	41-45	5
α-helix	47-50	4
β-strand	62-69	8	1
β-strand	74-80	7	1
β-strand	86-90	5	1
α-helix	96-109	14
β-strand	114-117	4	1
α-helix	126-135	10
β-strand	138-141	4	1
α-helix	142-143	2
α-helix	147-150	4
α-helix	151-167	17
α-helix	174-186	13
α-helix	197-207	11
α-helix	210-213	4
β-strand	223-230	8	2
β-strand	233-242	10	2
β-strand	246	1	3
β-strand	250-255	6	3
β-strand	260-265	6	3
α-helix	266-268	3
β-strand	269-271	3	2
α-helix	272-275	4

Chains B and J: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	4-15	12
α-helix	19-26	8
α-helix	30-38	9
α-helix	41-45	5
β-strand	62-70	9	4
β-strand	73-80	8	4
β-strand	86-90	5	4
α-helix	96-109	14
β-strand	114-117	4	4
α-helix	126-135	10
β-strand	138-141	4	4
α-helix	149-167	19
α-helix	174-183	10
α-helix	184-188	5
β-strand	191	1	5
β-strand	195	1	5
α-helix	199-215	17

Chains C and K: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	19-26	8
α-helix	30-38	9
α-helix	41-44	4
β-strand	62-69	8	6
β-strand	74-80	7	6
β-strand	86-87	2	6
β-strand	90	1	6
α-helix	96-109	14
β-strand	114-117	4	6
α-helix	128-135	8
β-strand	138-141	4	6
α-helix	147-162	16
α-helix	174-182	9
α-helix	183-188	6
β-strand	191	1	7
β-strand	195	1	7
α-helix	197-215	19
β-strand	223-226	4	8
β-strand	230	1	9
β-strand	233	1	9
β-strand	238-242	5	8
β-strand	250-254	5	10
β-strand	261-265	5	10
α-helix	266-268	3
β-strand	272	1	8

Chains D and L: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	62-70	9	11
β-strand	73-80	8	11
β-strand	86-91	6	11
α-helix	96-109	14
β-strand	114-116	3	11
α-helix	126-134	9
β-strand	139-140	2	11
α-helix	147-166	20
α-helix	168-170	3
α-helix	175-188	14
β-strand	191	1	12
β-strand	195	1	12
α-helix	197-213	17
α-helix	215-218	4
β-strand	223-226	4	13
β-strand	229-230	2	14
β-strand	233-234	2	14
β-strand	238-242	5	13
β-strand	243-246	4	15
β-strand	250-254	5	15
β-strand	261-265	5	15
α-helix	266-268	3
β-strand	269-272	4	13

Chains E and M: 12 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	62-66	5	16
β-strand	69-70	2	16
β-strand	73-80	8	16
β-strand	86-91	6	16
α-helix	96-108	13
β-strand	114-117	4	16
α-helix	126-135	10
β-strand	140-141	2	16
α-helix	147-165	19
α-helix	180-183	4
α-helix	184-188	5
β-strand	191	1	17
β-strand	195	1	17
α-helix	197-214	18
α-helix	215-218	4
β-strand	224-226	3	18
β-strand	230	1	19
β-strand	233	1	19
β-strand	238-241	4	18
β-strand	245-246	2	20
β-strand	250-255	6	20
β-strand	260-265	6	20
α-helix	266-268	3
β-strand	269-270	2	18

Chains F and N: 12 helices, 13 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	64-70	7	21
β-strand	73-79	7	21
β-strand	86-91	6	21
α-helix	96-108	13
β-strand	114-117	4	21
α-helix	126-134	9
β-strand	138-141	4	21
α-helix	147-162	16
α-helix	163-166	4
α-helix	175-185	11
α-helix	197-214	18
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	250-254	5	24
β-strand	261-265	5	24
α-helix	266-268	3
β-strand	269-272	4	22
α-helix	273-275	3

Chains G and O: 9 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	63-70	8	25
β-strand	73-80	8	25
β-strand	86-87	2	25
β-strand	90	1	25
α-helix	96-106	11
β-strand	114-116	3	26
α-helix	130-133	4
β-strand	138-140	3	26
α-helix	147-167	21
α-helix	174-186	13
β-strand	191	1	27
β-strand	195	1	27
α-helix	197-214	18

Chains H and P: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	62-69	8	28
β-strand	74-80	7	28
β-strand	86-91	6	28
α-helix	96-109	14
β-strand	114-117	4	28
α-helix	126-135	10
β-strand	138-141	4	28
α-helix	147-164	18
α-helix	174-188	15
β-strand	191	1	29
β-strand	195	1	29
α-helix	197-206	10
α-helix	210-213	4
β-strand	223-224	2	30
β-strand	229-230	2	31
β-strand	233-234	2	31
β-strand	241-242	2	30
β-strand	243-246	4	32
β-strand	250-254	5	32
β-strand	261-265	5	32
α-helix	266-268	3
α-helix	270	1
β-strand	271	1	30
α-helix	272-275	4

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
DNA EV273	X, Y	DNA	29	synthetic construct
DNA EV272	W, Z	DNA	27	synthetic construct

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

>7U32_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 (X, Y), FASTA

>7U32_2 DNA EV273 (chains X, Y)
GCTGCGAGATCCGCTCCGGTGTTGCACGG

Sequence of entity 3 (W, Z), FASTA

>7U32_3 DNA EV272 (chains W, Z)
CCGTGCAACACCGGAGCGGATCTCGCA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	12
CA	Calcium ion	Ca	2

Primary citation

Multivalent interactions essential for lentiviral integrase function. Ballandras-Colas, A., Chivukula, V., Gruszka, D.T. et al. Nat Commun (2022) 13:2416-2416. DOI 10.1038/s41467-022-29928-8 · 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…
7Z1Z 3.5 Å, MVV strand transfer complex (STC) intasome in complex with LEDGF/p75 at 3.5 A resolution
7ZPP 4.5 Å, Cryo-EM structure of the MVV CSC intasome at 4.5A resolution
5M0R 8.2 Å, Cryo-EM reconstruction of the maedi-visna virus (MVV) strand transfer complex

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