5M0R: Integrase

Cryo-EM reconstruction of the maedi-visna virus (MVV) strand transfer complex. Determined by electron microscopy at 8.2 Å resolution. Released 18 Jan 2017.

Method: Electron microscopy
Resolution: 8.2 Å
Organisms: Maedi visna virus (strain KV1772), Visna lentivirus (strain 1514), synthetic construct
Chains: 22
Atoms: 34,774
Mol. weight: 575.74 kDa
Released: 18 Jan 2017

Explore 5M0R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M0R contains 202 α-helices and 246 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.

Chain A: 18 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	19-25	7
α-helix	31-39	9
α-helix	42-45	4
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	121-124	4
α-helix	126-134	9
β-strand	138-141	4	1
α-helix	142-143	2
α-helix	151-167	17
α-helix	168-170	3
α-helix	174-183	10
α-helix	184-188	5
β-strand	191	1	2
β-strand	195	1	2
α-helix	197-207	11
α-helix	210-215	6
α-helix	216-218	3
β-strand	223-225	3	3
β-strand	229-230	2	4
β-strand	233-234	2	4
β-strand	240-242	3	3
β-strand	245-246	2	5
β-strand	250	1	6
β-strand	251-252	2	5
β-strand	253-255	3	7
β-strand	260-262	3	7
β-strand	265	1	6
α-helix	266-268	3
α-helix	269-271	3
α-helix	273-275	3

Chain B: 13 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	19-26	8
α-helix	30-39	10
β-strand	62-64	3	8
β-strand	67-69	3	8
β-strand	74-80	7	8
β-strand	86-91	6	8
α-helix	96-108	13
β-strand	114-116	3	8
β-strand	117	1	9
α-helix	121-124	4
α-helix	126-135	10
β-strand	138	1	8
β-strand	141	1	9
α-helix	147-167	21
α-helix	168-170	3
α-helix	174-183	10
α-helix	184-188	5
β-strand	191	1	10
β-strand	195	1	10
α-helix	197-211	15
α-helix	212-216	5
β-strand	223-226	4	11
β-strand	229-230	2	12
β-strand	233-234	2	12
β-strand	238-242	5	11
β-strand	250-255	6	13
β-strand	260-265	6	13
α-helix	266-268	3
β-strand	269-272	4	11

Chain C: 14 helices, 12 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	62-69	8	14
β-strand	74-80	7	14
β-strand	86-91	6	14
α-helix	96-109	14
β-strand	114-117	4	14
α-helix	121-124	4
α-helix	126-134	9
β-strand	138-141	4	14
α-helix	147-167	21
α-helix	168-170	3
α-helix	174-183	10
α-helix	184-188	5
α-helix	197-219	23
β-strand	223-226	4	15
β-strand	229-230	2	16
β-strand	233-234	2	16
α-helix	235-237	3
β-strand	238-242	5	15
β-strand	250-255	6	17
β-strand	260-265	6	17
α-helix	266-268	3
β-strand	269-272	4	15

Chain D: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	62-69	8	18
β-strand	74-80	7	18
β-strand	86-91	6	18
α-helix	96-109	14
β-strand	114-117	4	18
α-helix	121-124	4
α-helix	126-135	10
β-strand	138-141	4	18
α-helix	147-167	21
α-helix	168-170	3
α-helix	174-183	10
α-helix	184-188	5
β-strand	191	1	19
β-strand	195	1	19
α-helix	197-218	22
β-strand	223-224	2	20
β-strand	225	1	21
β-strand	226	1	20
β-strand	238-242	5	20
β-strand	245-246	2	22
β-strand	250-255	6	22
β-strand	260-265	6	22
α-helix	266-268	3
β-strand	270	1	21

Chain E: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	4-15	12
α-helix	19-26	8
α-helix	30-39	10
β-strand	62-69	8	23
β-strand	74-80	7	23
β-strand	86-91	6	23
α-helix	96-109	14
β-strand	114-116	3	23
α-helix	121-124	4
α-helix	126-134	9
β-strand	138	1	23
α-helix	147-167	21
α-helix	168-170	3
α-helix	174-182	9
α-helix	183-188	6
β-strand	191	1	24
β-strand	195	1	24
α-helix	197-218	22
β-strand	223-226	4	25
β-strand	229-230	2	26
β-strand	233-234	2	26
α-helix	235-237	3
β-strand	238-242	5	25
β-strand	245-246	2	27
β-strand	250	1	28
β-strand	251-252	2	27
β-strand	253-255	3	29
β-strand	260-262	3	29
β-strand	265	1	28
α-helix	266-268	3
β-strand	269-271	3	25

Chain F: 14 helices, 21 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	30
β-strand	74-80	7	30
β-strand	86-91	6	30
α-helix	96-109	14
β-strand	114	1	31
β-strand	115-116	2	30
β-strand	117	1	32
α-helix	121-124	4
α-helix	126-134	9
β-strand	138	1	31
β-strand	141	1	32
α-helix	147-167	21
α-helix	168-170	3
α-helix	174-182	9
α-helix	183-188	6
β-strand	191	1	33
β-strand	195	1	33
α-helix	197-217	21
β-strand	223-226	4	34
β-strand	229-230	2	35
β-strand	233-234	2	35
α-helix	235-237	3
β-strand	238-242	5	34
β-strand	245	1	36
β-strand	250	1	37
β-strand	252	1	36
β-strand	253-255	3	38
β-strand	260-262	3	38
β-strand	265	1	37
α-helix	266-268	3
β-strand	271-272	2	34

Chain G: 12 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	39
β-strand	74-80	7	39
β-strand	86-91	6	39
α-helix	96-109	14
β-strand	114-117	4	39
α-helix	121-124	4
α-helix	126-134	9
β-strand	138-141	4	39
α-helix	147-167	21
α-helix	168-170	3
α-helix	174-183	10
α-helix	184-188	5
β-strand	191	1	40
β-strand	195	1	40
α-helix	197-218	22

Chain H: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	62-69	8	41
β-strand	74-80	7	41
β-strand	86-87	2	41
β-strand	90-91	2	41
α-helix	96-109	14
β-strand	114-117	4	41
α-helix	121-124	4
α-helix	126-135	10
β-strand	138-141	4	41
α-helix	147-167	21
α-helix	168-170	3
α-helix	174-182	9
α-helix	183-188	6
β-strand	191	1	42
β-strand	195	1	42
α-helix	197-206	10
α-helix	210-218	9
β-strand	223-226	4	43
β-strand	229-230	2	44
β-strand	233-234	2	44
β-strand	238-242	5	43
β-strand	245-246	2	45
β-strand	250-255	6	45
β-strand	260-265	6	45
β-strand	269-271	3	43
α-helix	272-275	4

8 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	Maedi visna virus (strain KV1772)	P35956
vDNA, non-transfered strand	Q, S	DNA	21	Visna lentivirus (strain 1514)
vDNA-tDNA, transferred strand, joined to a model tDNA	R, T	DNA	50	Visna lentivirus (strain 1514)
tDNA	U, V	DNA	23	synthetic construct

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

>5M0R_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

>5M0R_2 vDNA, non-transfered strand (chains Q, S)
GCTGCGAGATCCGCTCCGGTG

Sequence of entity 3 (R, T), FASTA

>5M0R_3 vDNA-tDNA, transferred strand, joined to a model tDNA (chains R, T)
AACACCGGAGCGGATCTCGCAGTCGACCACCCTAATCAAGTTTTTTGGGG

Sequence of entity 4 (U, V), FASTA

>5M0R_4 tDNA (chains U, V)
CCCCAAAAAACTTGATTAGGGTG

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
7ZPP 4.5 Å, Cryo-EM structure of the MVV CSC intasome at 4.5A resolution

Browse structure collections

About this viewer

MolViewer shows 5M0R directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.