7Z1Z: MVV strand transfer complex (STC) intasome

MVV strand transfer complex (STC) intasome in complex with LEDGF/p75 at 3.5 A resolution. Determined by electron microscopy at 3.5 Å resolution. Released 11 May 2022.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Visna/maedi virus EV1 KV1772, Homo sapiens, DNA molecule
Chains: 24
Atoms: 35,605
Mol. weight: 599.89 kDa
Ligands: ZN
Released: 11 May 2022

Explore 7Z1Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Z1Z contains 180 α-helices and 202 β-strands across 18 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: 14 helices, 13 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	63-69	7	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	127-135	9
β-strand	138-141	4	1
α-helix	147-150	4
α-helix	151-167	17
α-helix	174-186	13
α-helix	197-207	11
α-helix	211-215	5
β-strand	223-225	3	2
β-strand	229-230	2	3
β-strand	233-234	2	3
β-strand	240-242	3	2
β-strand	243-246	4	4
β-strand	250-255	6	4
β-strand	260-265	6	4
α-helix	266-268	3
β-strand	270-271	2	2
α-helix	272-275	4

Chains B and J: 10 helices, 7 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	62-69	8	5
β-strand	74-80	7	5
β-strand	86-90	5	5
α-helix	96-109	14
β-strand	114-117	4	5
α-helix	126-135	10
β-strand	138-141	4	5
α-helix	147-167	21
α-helix	174-183	10
α-helix	184-188	5
β-strand	191	1	6
β-strand	195	1	6
α-helix	197-215	19

Chains C and K: 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	62-70	9	7
β-strand	73-80	8	7
β-strand	86-91	6	7
α-helix	96-106	11
β-strand	114-117	4	7
α-helix	126-135	10
β-strand	138-141	4	7
α-helix	147-167	21
α-helix	174-182	9
α-helix	183-187	5
α-helix	197-210	14
α-helix	212-218	7
β-strand	223-226	4	8
β-strand	230	1	9
β-strand	233	1	9
β-strand	238-242	5	8
β-strand	245-246	2	10
β-strand	250-254	5	10
β-strand	261-265	5	10
α-helix	266-268	3
β-strand	269-271	3	8

Chains D and L: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	4-14	11
α-helix	19-25	7
α-helix	30-34	5
β-strand	63-70	8	11
β-strand	73-80	8	11
β-strand	86-87	2	11
β-strand	90-91	2	11
α-helix	96-109	14
β-strand	114-117	4	11
α-helix	126-135	10
β-strand	138-140	3	11
α-helix	147-167	21
α-helix	174-187	14
β-strand	191	1	12
β-strand	195	1	12
α-helix	197-219	23
β-strand	223-226	4	13
β-strand	230	1	14
β-strand	233	1	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: 11 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	41-44	4
β-strand	63-69	7	16
β-strand	74-80	7	16
β-strand	86-91	6	16
α-helix	96-109	14
β-strand	116-117	2	16
α-helix	126-135	10
β-strand	140-141	2	16
α-helix	147-167	21
α-helix	174-183	10
α-helix	184-188	5
β-strand	191	1	17
β-strand	195	1	17
α-helix	197-215	19
β-strand	224-230	7	18
β-strand	233-241	9	18
β-strand	245-246	2	19
β-strand	250-255	6	19
β-strand	260-265	6	19
α-helix	266-268	3
β-strand	269-270	2	18

Chains F and N: 11 helices, 15 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	63-69	7	20
β-strand	74-80	7	20
β-strand	86-91	6	20
α-helix	96-109	14
β-strand	114-117	4	20
α-helix	126-134	9
β-strand	138-141	4	20
α-helix	147-164	18
α-helix	174-187	14
β-strand	191	1	21
β-strand	195	1	21
α-helix	197-217	21
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	1	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: 10 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	90-91	2	25
α-helix	96-109	14
β-strand	114-117	4	25
α-helix	131-135	5
β-strand	138-141	4	25
α-helix	149-167	19
α-helix	174-183	10
α-helix	184-188	5
β-strand	191	1	26
β-strand	195	1	26
α-helix	197-214	18

Chains H and P: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	62-69	8	27
β-strand	74-80	7	27
β-strand	86-91	6	27
α-helix	96-109	14
β-strand	114-117	4	27
α-helix	126-135	10
β-strand	138-141	4	27
α-helix	147-164	18
α-helix	174-188	15
β-strand	191	1	28
β-strand	195	1	28
α-helix	197-206	10
α-helix	210-214	5
β-strand	223-224	2	29
β-strand	229-230	2	30
β-strand	233-234	2	30
β-strand	241-242	2	29
β-strand	245-246	2	31
β-strand	250-254	5	31
β-strand	261-265	5	31
α-helix	266-268	3
β-strand	271	1	29
α-helix	272-274	3

2 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
Pol polyprotein	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	protein	281	Visna/maedi virus EV1 KV1772	P35956
PC4 and SFRS1-interacting protein	Q, R	protein	95	Homo sapiens	O75475 (AlphaFold model)
DNA (5'-d(gpcptpgpcpgpapgpaptpcpcpgpcptpcpcpgpgptp*g)-3')	X, Y	DNA	23	DNA molecule
DNA (37-mer)	W, Z	DNA	50	DNA molecule
DNA (5'-d(ptptpgpaptptpapgpgpgptpg)-3')	U, a	DNA	23	DNA molecule

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

>7Z1Z_1 Pol polyprotein (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, R), FASTA

>7Z1Z_2 PC4 and SFRS1-interacting protein (chains Q, R)
SMDSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRF
KVSQVIMEKSTMLYNKFKNMFLVGEGDSVLEVLFQ

Sequence of entity 3 (X, Y), FASTA

>7Z1Z_3 DNA (5'-D(*GP*CP*TP*GP*CP*GP*AP*GP*AP*TP*CP*CP*GP*CP*TP*CP*CP*GP*GP*TP*G)-3') (chains X, Y)
GCTGCGAGATCCGCTCCGGTGTT

Sequence of entity 4 (W, Z), FASTA

>7Z1Z_4 DNA (37-MER) (chains W, Z)
AACACCGGAGCGGATCTCGCAGTCGACCACCCTAATCAAGTTTTTTGGGG

Sequence of entity 5 (U, a), FASTA

>7Z1Z_5 DNA (5'-D(P*TP*TP*GP*AP*TP*TP*AP*GP*GP*GP*TP*G)-3') (chains U, a)
CCCCAAAAAACTTGATTAGGGTG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	12

Primary citation

Multivalent interactions essential for lentiviral integrase function. Ballandras-Colas, A., Chivukula, V., Gruszka, D.T. et al. Nat Commun (2022) 13:2416. DOI 10.1038/s41467-022-29928-8

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
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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