6MPG: Cryo-EM structure

Cryo-EM structure at 3.2 A resolution of HIV-1 fusion peptide-directed antibody, A12V163-b.01, elicited by vaccination of Rhesus macaques, in complex with stabilized HIV-1 Env BG505 DS-SOSIP, which was also bound to antibodies VRC03 and PGT122. Determined by electron microscopy at 3.2 Å resolution. Released 24 Jul 2019.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Macaca mulatta, Human immunodeficiency virus 1, Homo sapiens
Chains: 24
Atoms: 32,085
Mol. weight: 502.65 kDa
Ligands: NAG
Released: 24 Jul 2019

Explore 6MPG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MPG contains 78 α-helices and 348 β-strands across 24 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 2, C and V: 10 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	33
β-strand	45-47	3	34
β-strand	53	1	35
β-strand	55-57	3	36
α-helix	58-62	5
β-strand	75-77	3	36
β-strand	83-85	3	34
β-strand	91-94	4	37
α-helix	101-114	14
β-strand	121	1	38
β-strand	129-133	5	39
β-strand	154-162	9	39
β-strand	169-177	9	39
β-strand	181-183	3	39
β-strand	190-193	4	39
α-helix	194-197	4
β-strand	202-203	2	38
α-helix	204-205	2
β-strand	215	1	40
β-strand	218	1	35
β-strand	223-228	6	34
β-strand	236-239	4	37
β-strand	242-245	4	34
β-strand	247	1	35
α-helix	248-250	3
β-strand	251	1	40
β-strand	261	1	41
α-helix	264-266	3
β-strand	271-273	3	41
β-strand	284-298	15	41
β-strand	301-312	10	42
β-strand	315-323	10	42
β-strand	330-334	5	41
α-helix	335-349	15
β-strand	358-361	4	41
α-helix	369-371	3
β-strand	374-377	4	43
β-strand	382-385	4	43
β-strand	393-395	3	41
β-strand	413-417	5	41
β-strand	418-421	4	43
β-strand	423-424	2	38
α-helix	426-428	3
β-strand	434-435	2	38
β-strand	443-456	14	41
β-strand	458	1	44
β-strand	465-470	6	41
α-helix	476-480	5
β-strand	487-491	5	34
β-strand	495-499	5	33

Chains 3, W and X: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	45
β-strand	11-12	2	46
β-strand	17-25	9	45
β-strand	32	1	47
β-strand	34-39	6	48
β-strand	45-51	7	48
β-strand	57-59	3	48
β-strand	67-72	6	45
β-strand	77-83	7	45
α-helix	87-89	3
β-strand	91-97	7	48
β-strand	106-107	2	48
β-strand	111-113	3	48
β-strand	114-115	2	46

Chains 4, B and Y: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	49
β-strand	10-13	4	50
β-strand	20-25	6	49
β-strand	30-31	2	51
β-strand	36-37	2	51
β-strand	39-44	6	50
β-strand	51-55	5	50
β-strand	59-60	2	50
α-helix	61	1
β-strand	68-71	4	49
β-strand	76-81	6	49
β-strand	91-96	6	50
β-strand	104	1	50
β-strand	108-112	5	50

Chains 5, m and M: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	52
β-strand	11-12	2	53
β-strand	18-23	6	52
β-strand	34-39	6	54
β-strand	46-51	6	54
β-strand	57-59	3	54
β-strand	67-72	6	52
β-strand	77-82	6	52
α-helix	84-86	3
β-strand	88-93	6	54
β-strand	95-97	3	55
β-strand	100-100A	2	56
α-helix	100E-100G	3
β-strand	100J-100K	2	56
β-strand	100N-100P	3	55
β-strand	105-107	3	54
β-strand	108-109	2	53

Chains 6, n and N: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	19	1	57
α-helix	26-27	2
β-strand	35-38	4	58
β-strand	45-48	4	58
β-strand	63-64	2	59
β-strand	73-74	2	59
β-strand	75	1	57
α-helix	80-82	3
β-strand	85-87	3	58
β-strand	97	1	54
α-helix	98-100	3
β-strand	102-103	2	58

Chains 7, r and R: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	60
β-strand	11-13	3	61
β-strand	19-25	7	60
β-strand	33-37	5	62
β-strand	44-48	5	62
β-strand	52-53	2	62
β-strand	61-66	6	60
β-strand	69-74	6	60
α-helix	79-81	3
β-strand	84-89	6	62
β-strand	92-93	2	62
β-strand	97-98	2	62
β-strand	99-101	3	61

Chains 8, q and Q: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	63
β-strand	10-11	2	64
β-strand	17-25	9	63
β-strand	34-40	7	64
β-strand	44-52	9	64
β-strand	56-59	4	64
β-strand	60	1	44
α-helix	61-63	3
β-strand	67-72	6	63
β-strand	76F-82A	9	63
α-helix	84-86	3
β-strand	88-95	8	64
β-strand	100F-103	4	64
β-strand	107-110	4	64

Chains A, D and U: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	515	1	47
α-helix	538-542	5
α-helix	571-594	24
β-strand	603-609	7	33
α-helix	612-615	4
α-helix	620-623	4
α-helix	628-634	7
α-helix	642-663	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
A12V163-b.01 Light Chain	4, B, Y	protein	113	Macaca mulatta
Envelope glycoprotein gp41	A, D, U	protein	153	Human immunodeficiency virus 1	Q2N0S7
Envelope glycoprotein gp120	2, C, V	protein	473	Human immunodeficiency virus 1	Q2N0S6
A12V163-b.01 Heavy Chain	3, W, X	protein	117	Macaca mulatta
PGT122 Heavy chain	5, M, m	protein	132	Homo sapiens
PGT122 Light chain	6, N, n	protein	107	Homo sapiens
VRC03 heavy chain	8, Q, q	protein	227	Homo sapiens
VRC03 Light chain	7, R, r	protein	102	Homo sapiens

Sequence of entity 1 (4, B, Y), FASTA

>6MPG_1 A12V163-b.01 Light Chain (chains 4, B, Y)
DIVMTQSPDSLAVSLGERVTLNCKSSQSLLASSNNKNYLAWYYQKPGQAPKLLIYWASTR
ESGVPNRFSGSGSGSDFTLTISGLQAEDVAVYYCQQYYTTPLTFGGGTKVEIK

Sequence of entity 2 (A, D, U), FASTA

>6MPG_2 Envelope glycoprotein gp41 (chains A, D, U)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAIEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 3 (2, C, V), FASTA

>6MPG_3 Envelope glycoprotein gp120 (chains 2, C, V)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV

Sequence of entity 4 (3, W, X), FASTA

>6MPG_4 A12V163-b.01 Heavy Chain (chains 3, W, X)
EVQLVESGGGLAKPGGSLRLSCAASGFTFSDYYMDWVRQAPGKGLEWVSRISNSGITWYT
DSVRGRFTIFRDNAKNTLYLQMNSLRAEDTAVYYCTKESAAAIGHYWGQGVLVTVSS

Sequence of entity 5 (5, M, m), FASTA

>6MPG_5 PGT122 Heavy chain (chains 5, M, m)
QVHLQESGPGLVKPSETLSLTCNVSGTLVRDNYWSWIRQPLGKQPEWIGYVHDSGDTNYN
PSLKSRVHLSLDKSKNLVSLRLTGVTAADSAIYYCATTKHGRRIYGVVAFKEWFTYFYMD
VWGKGTSVTVSS

Sequence of entity 6 (6, N, n), FASTA

>6MPG_6 PGT122 Light chain (chains 6, N, n)
APTFVSVAPGQTARITCGEESLGSRSVIWYQQRPGQAPSLIIYNNNDRPSGIPDRFSGSP
GSTFGTTATLTITSVEAGDEADYYCHIWDSRRPTNWVFGEGTTLIVL

Sequence of entity 7 (8, Q, q), FASTA

>6MPG_7 VRC03 heavy chain (chains 8, Q, q)
QVQLVQSGAVIKTPGSSVKISCRASGYNFRDYSIHWVRLIPDKGFEWIGWIKPLWGAVSY
ARQLQGRVSMTRQLSQDPDDPDWGVAYMEFSGLTPADTAEYFCVRRGSCDYCGDFPWQYW
GQGTVVVVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 8 (7, R, r), FASTA

>6MPG_8 VRC03 Light chain (chains 7, R, r)
EIVLTQSPGILSLSPGETATLFCKASQGGNAMTWYQKRRGQVPRLLIYDTSRRASGVPDR
FVGSGSGTDFFLTINKLDREDFAVYYCQQFEFFGLGSELEVH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12

Primary citation

Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization. Kong, R., Duan, H., Sheng, Z. et al. Cell (2019) 178:567-584.e19. DOI 10.1016/j.cell.2019.06.030 · PubMed

Other PDB entries of the same protein (UniProt Q2N0S7), best resolution first:

5I8C 1.54 Å, Crystal Structure of HIV-1 Clade A BG505 Fusion Peptide (residue 512-520) in Complex…
6WX2 2.39 Å, Vaccine-elicited mouse FP-targeting neutralizing antibody vFP16.02 with F60P mutation on…
8FR6 2.5 Å, Antibody vFP53.02 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
8G4T 2.81 Å, Vaccine-elicited human antibody 2C09 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
6V8Z 2.9 Å, VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure
8G4M 2.95 Å, Vaccine-elicited human antibody 2C06 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
6UM7 3.5 Å, Cryo-EM structure of vaccine-elicited HIV-1 neutralizing antibody DH270.mu1 in complex…
9PNN 3.5 Å, Cryo-EM structure of J601-A6 Fab in complex with HIV-1 BG505 DS-SOSIP Env trimer
6CM3 3.54 Å, BG505 SOSIP in complex with sCD4, 17b, 8ANC195
6CDI 3.6 Å, Cryo-EM structure at 3.6 A resolution of vaccine-elicited antibody vFP16.02 in complex…
8DOW 3.69 Å, Cryo-EM structure of HIV-1 Env(CH848 10.17 DS.SOSIP_DT) in complex with DH1030.1 Fab
7LL1 3.73 Å, Cryo-EM structure of BG505 DS-SOSIP in complex with glycan276-dependent broadly…

Browse structure collections

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