6CDI: Cryo-EM structure

Cryo-EM structure at 3.6 A resolution of vaccine-elicited antibody vFP16.02 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122. Determined by electron microscopy at 3.6 Å resolution. Released 16 May 2018.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 24
Atoms: 32,763
Mol. weight: 575.99 kDa
Ligands: NAG
Released: 16 May 2018

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

Secondary structure: helices and β-sheets

6CDI contains 76 α-helices and 375 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 and C: 11 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	37
β-strand	45-47	3	38
β-strand	53	1	39
β-strand	55-56	2	40
α-helix	58-62	5
β-strand	75-76	2	40
α-helix	77-78	2
β-strand	84-85	2	38
β-strand	91-94	4	41
α-helix	102-114	13
β-strand	121	1	42
α-helix	123-125	3
β-strand	129	1	43
β-strand	130-133	4	44
β-strand	154-162	9	44
β-strand	169-177	9	44
β-strand	181-183	3	43
β-strand	191-193	3	43
α-helix	194-197	4
β-strand	202-203	2	42
α-helix	204-205	2
β-strand	215	1	40
β-strand	218	1	39
β-strand	223-228	6	38
β-strand	236-239	4	41
β-strand	242-245	4	38
β-strand	247	1	39
β-strand	251	1	40
β-strand	261	1	45
α-helix	264-266	3
β-strand	271-273	3	45
β-strand	284-298	15	45
β-strand	302-308	7	46
β-strand	316-322	8	46
β-strand	330-334	5	45
α-helix	335-349	15
β-strand	358	1	47
β-strand	359-361	3	45
α-helix	369-372	4
β-strand	374-377	4	48
β-strand	382-385	4	48
β-strand	393-395	3	45
β-strand	413-417	5	45
β-strand	423-424	2	42
β-strand	434-435	2	42
α-helix	436-438	3
β-strand	443-456	14	45
β-strand	458	1	49
β-strand	465	1	47
β-strand	468-470	3	45
α-helix	476-480	5
β-strand	486-491	6	38
β-strand	495-499	5	37

Chains 3, h and H: 0 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	62
β-strand	10-11	2	63
β-strand	17-18	2	64
β-strand	22-23	2	65
β-strand	25	1	62
β-strand	34-40	7	66
β-strand	44-51	8	66
β-strand	57-59	3	66
β-strand	71-72	2	65
β-strand	77-78	2	65
β-strand	82-82A	2	64
β-strand	88-90	3	63
β-strand	91-92	2	66
β-strand	93	1	67
β-strand	103	1	67
β-strand	107-110	4	63

Chains 4, l and L: 1 helix, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	68
β-strand	10-12	3	69
β-strand	19	1	70
β-strand	22-24	3	68
β-strand	33	1	71
β-strand	35-36	2	72
β-strand	46-48	3	72
β-strand	54	1	72
β-strand	63-67	5	68
β-strand	70-74	5	68
β-strand	75	1	70
β-strand	84-86	3	69
β-strand	87	1	72
β-strand	89-90	2	71
α-helix	96	1
β-strand	97-98	2	71
β-strand	102-105	4	69

Chains 5, m and M: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	54
β-strand	11-12	2	55
β-strand	19-22	4	54
β-strand	34-39	6	53
β-strand	46-51	6	53
β-strand	59	1	53
β-strand	67-72	6	54
β-strand	77-82	6	54
α-helix	84-86	3
β-strand	89-93	5	53
β-strand	95-96	2	56
β-strand	99-100A	3	57
β-strand	100J-100L	3	57
β-strand	100O-100P	2	56
β-strand	105-106	2	53
β-strand	108-109	2	55

Chains 6, n and N: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	3	50
β-strand	19-23	5	51
α-helix	25-27	3
β-strand	31	1	52
β-strand	34-38	5	50
β-strand	44-48	5	50
β-strand	62-64	3	51
β-strand	71-75	5	51
β-strand	85-89	5	50
β-strand	92	1	52
β-strand	97	1	53
β-strand	102-105	4	50

Chains 7, r and R: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	58
β-strand	10-13	4	59
β-strand	19-25	7	58
β-strand	33-37	5	59
β-strand	44-48	5	59
β-strand	52-53	2	59
β-strand	61-66	6	58
β-strand	69-74	6	58
α-helix	79-81	3
β-strand	84-89	6	59
β-strand	92-93	2	59
β-strand	97-101	5	59

Chains 8, q and Q: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	60
α-helix	7-9	3
β-strand	10-11	2	61
β-strand	17-25	9	60
β-strand	34-40	7	61
β-strand	44-52	9	61
β-strand	56-59	4	61
β-strand	60	1	49
α-helix	61-63	3
β-strand	67-68	2	60
β-strand	71-72	2	60
β-strand	76G-82A	8	60
α-helix	84-86	3
β-strand	88-95	8	61
β-strand	100F-103	4	61
β-strand	107-110	4	61

Chains A, c and D: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	515-519	5
α-helix	530-533	4
α-helix	538-542	5
α-helix	571-594	24
β-strand	603-609	7	37
α-helix	619-622	4
α-helix	628-635	8
α-helix	641-663	23

1 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
Glycoprotein gp41	A, D, c	protein	153	Human immunodeficiency virus 1	Q2N0S7
Glycoprotein 120	2, C, d	protein	473	Human immunodeficiency virus 1	Q2N0S5
PGT122 Light Chain	6, N, n	protein	107	Homo sapiens
PGT122 Heavy Chain	5, M, m	protein	132	Homo sapiens
VRC03 light chain	7, R, r	protein	102	Homo sapiens
VRC03 Heavy Chain	8, Q, q	protein	227	Homo sapiens
vFP16.02 Heavy Chain	3, H, h	protein	211	Homo sapiens
vFP16.02 Light Chain	4, L, l	protein	216	Homo sapiens

Sequence of entity 1 (A, D, c), FASTA

>6CDI_1 Glycoprotein gp41 (chains A, D, c)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAIEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 2 (2, C, d), FASTA

>6CDI_2 Glycoprotein 120 (chains 2, C, d)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV

Sequence of entity 3 (6, N, n), FASTA

>6CDI_3 PGT122 Light Chain (chains 6, N, n)
APTFVSVAPGQTARITCGEESLGSRSVIWYQQRPGQAPSLIIYNNNDRPSGIPDRFSGSP
GSTFGTTATLTITSVEAGDEADYYCHIWDSRRPTNWVFGEGTTLIVL

Sequence of entity 4 (5, M, m), FASTA

>6CDI_4 PGT122 Heavy Chain (chains 5, M, m)
QVHLQESGPGLVKPSETLSLTCNVSGTLVRDNYWSWIRQPLGKQPEWIGYVHDSGDTNYN
PSLKSRVHLSLDKSKNLVSLRLTGVTAADSAIYYCATTKHGRRIYGVVAFKEWFTYFYMD
VWGKGTSVTVSS

Sequence of entity 5 (7, R, r), FASTA

>6CDI_5 VRC03 light chain (chains 7, R, r)
EIVLTQSPGILSLSPGETATLFCKASQGGNAMTWYQKRRGQVPRLLIYDTSRRASGVPDR
FVGSGSGTDFFLTINKLDREDFAVYYCQQFEFFGLGSELEVH

Sequence of entity 6 (8, Q, q), FASTA

>6CDI_6 VRC03 Heavy Chain (chains 8, Q, q)
QVQLVQSGAVIKTPGSSVKISCRASGYNFRDYSIHWVRLIPDKGFEWIGWIKPLWGAVSY
ARQLQGRVSMTRQLSQDPDDPDWGVAYMEFSGLTPADTAEYFCVRRGSCDYCGDFPWQYW
GQGTVVVVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 7 (3, H, h), FASTA

>6CDI_7 vFP16.02 Heavy Chain (chains 3, H, h)
QVQLLQSGAELVRPGASVTLSCKASGYAFSDYEIHWVKQTPVRGLDWIGAFDPKSGASAS
NQKVKGRAILTADKSSSTAYMELRSLTSEDSAVYYCTRLRYFGYFDVWGTGTTVTVSPAS
TKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVV
TVPSSSLGTQTYICNVNHKPSNTKVDKKAEP

Sequence of entity 8 (4, L, l), FASTA

>6CDI_8 vFP16.02 Light Chain (chains 4, L, l)
DVLMTQTPLSLPVSLGGQASISCRSSQSVVYSDGDTYLEWYLQKPGQSPKLLIYKVSRRF
SGVPDRFSGSGSGTDFTLKISRVETEDLGVYYCFQGSHVPYTFGGGTKLEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1. Xu, K., Acharya, P., Kong, R. et al. Nat Med (2018) 24:857-867. DOI 10.1038/s41591-018-0042-6 · 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
6MPG 3.2 Å, Cryo-EM structure at 3.2 A resolution of HIV-1 fusion peptide-directed antibody,…
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
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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