9S28: MVV STC intasome

MVV STC intasome in complex with LEDGF. Determined by electron microscopy at 2.8 Å resolution. Released 5 Aug 2026.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Visna/maedi virus EV1 KV1772, Homo sapiens, synthetic construct
Chains: 32
Atoms: 41,690
Mol. weight: 1198.66 kDa
Ligands: ZN
Released: 5 Aug 2026

Explore 9S28 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9S28 contains 238 α-helices and 214 β-strands across 26 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 g: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	348-362	15
α-helix	365-367	3
α-helix	370-381	12
α-helix	387-392	6
α-helix	394-403	10
α-helix	410-425	16

Chains A and I: 13 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	41-45	5
α-helix	48-50	3
β-strand	62-69	8	1
β-strand	74-80	7	1
β-strand	86-91	6	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	147-150	4
α-helix	151-167	17
α-helix	174-186	13
β-strand	191	1	2
β-strand	195	1	2
α-helix	197-213	17
β-strand	223-226	4	3
β-strand	229-230	2	4
β-strand	233-234	2	4
β-strand	240-242	3	3
β-strand	243-246	4	5
β-strand	250-255	6	5
β-strand	260-265	6	5
α-helix	266-268	3
β-strand	269-271	3	3
α-helix	272-275	4

Chains b and h: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	348-362	15
α-helix	365-367	3
α-helix	370-381	12
α-helix	387-392	6
α-helix	394-403	10
α-helix	410-424	15

Chains B and J: 11 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	6
β-strand	74-80	7	6
β-strand	86-91	6	6
α-helix	96-109	14
β-strand	114-117	4	6
α-helix	126-135	10
β-strand	138-141	4	6
α-helix	147-167	21
α-helix	168-170	3
α-helix	174-183	10
α-helix	184-188	5
β-strand	191	1	7
β-strand	195	1	7
α-helix	197-214	18

Chains c and i: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	348-362	15
α-helix	365-367	3
α-helix	370-382	13
α-helix	387-392	6
α-helix	394-403	10
α-helix	410-425	16

Chain C: 12 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	62-70	9	8
β-strand	73-80	8	8
β-strand	86-91	6	8
α-helix	96-106	11
β-strand	114-117	4	8
α-helix	126-135	10
β-strand	138-141	4	8
α-helix	147-165	19
α-helix	174-182	9
α-helix	183-188	6
β-strand	191	1	9
β-strand	195	1	9
α-helix	197-209	13
α-helix	211-218	8
β-strand	223-226	4	10
β-strand	230	1	11
β-strand	233	1	11
β-strand	238-242	5	10
β-strand	245	1	12
β-strand	250-254	5	12
β-strand	261-265	5	12
α-helix	266-268	3
β-strand	270-271	2	10

Chains d and j: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	348-362	15
α-helix	365-367	3
α-helix	371-382	12
α-helix	387-392	6
α-helix	394-403	10
α-helix	410-423	14

Chains D and L: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	62-70	9	13
β-strand	73-80	8	13
β-strand	86-91	6	13
α-helix	96-109	14
β-strand	114-117	4	13
α-helix	126-135	10
β-strand	138-140	3	13
α-helix	147-167	21
α-helix	174-183	10
α-helix	184-188	5
α-helix	197-210	14
α-helix	216-219	4
β-strand	223-226	4	14
β-strand	230	1	15
β-strand	233	1	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
α-helix	273-275	3

7 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
Gag-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	a, b, c, d, e, g, h, i, j, k	protein	530	Homo sapiens	O75475 (AlphaFold model)
DNA EV392	T, U	DNA	32	synthetic construct
DNA EV306	W, Y	DNA	29	synthetic construct
DNA EV391	X, Z	DNA	65	synthetic construct

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

>9S28_1 Gag-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 (a, b, c, d, e, g, h, i, j, k), FASTA

>9S28_2 PC4 and SFRS1-interacting protein (chains a, b, c, d, e, g, h, i, j, k)
MTRDFKPGDLIFAKMKGYPHWPARVDEVPDGAVKPPTNKLPIFFFGTHETAFLGPKDIFP
YSENKEKYGKPNKRKGFNEGLWEIDNNPKVKFSSQQAATKQSNASSDVEVEEKETSVSKE
DTDHEEKASNEDVTKAVDITTPKAARRGRKRKAEKQVETEEAGVVTTATASVNLKVSPKR
GRPAATEVKIPKPRGRPKMVKQPCPSESDIITEEDKSKKKGQEEKQPKKQPKKDEEGQKE
EDKPRKEPDKKEGKKEVESKRKNLAKTGVTSTSDSEEEGDDQEGEKKRKGGRNFQTAHRR
NMLKGQHEKEAADRKRKQEEQMETEQQNKDEGKKPEVKKVEKKRETSMDSRLQRIHAEIK
NSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLY
NKFKNMFLVGEGDSVITQVLNKSLAEQRQHEEANKTKDQGKKGPNKKLEKEQTGSKTLNG
GSDAQDGNQPQHNGESNEDSKDNHEASTKKKPSSEERETEISLKDSTLDN

Sequence of entity 3 (T, U), FASTA

>9S28_3 DNA EV392 (chains T, U)
CCCGTATCCGCTTAAGTGACTTGATTAGGGTG

Sequence of entity 4 (W, Y), FASTA

>9S28_4 DNA EV306 (chains W, Y)
GCTGCGAGATCCGCTCCGGTGTTGCACGG

Sequence of entity 5 (X, Z), FASTA

>9S28_5 DNA EV391 (chains X, Z)
CCGTGCAACACCGGAGCGGATCTCGCAGTCGACCACCCTAATCAAGTCACTTAAGCGGAT
ACGGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	14

Primary citation

Core nucleosomes are refractory to lentiviral DNA integration. Hope, J., Punch, E., Cook, N.J. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-76698-8 · 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
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
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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