6UM7: Envelope glycoprotein gp120

Cryo-EM structure of vaccine-elicited HIV-1 neutralizing antibody DH270.mu1 in complex with CH848 10.17DT Env. Determined by electron microscopy at 3.5 Å resolution. Released 18 Dec 2019.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 12
Atoms: 20,334
Mol. weight: 380.78 kDa
Ligands: NAG
Released: 18 Dec 2019

Explore 6UM7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6UM7 contains 117 α-helices and 192 β-strands across 12 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 1, D and H: 12 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	514-515	2
α-helix	516-520	5
α-helix	524-527	4
α-helix	530-535	6
α-helix	539-542	4
α-helix	571-596	26
β-strand	603-609	7	31
α-helix	610-611	2
α-helix	612-614	3
α-helix	619-620	2
α-helix	621-625	5
α-helix	628-634	7
α-helix	639-663	25

Chains A, E and I: 18 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	1
β-strand	45-47	3	2
β-strand	53	1	3
β-strand	56	1	4
α-helix	63-67	5
β-strand	68	1	5
α-helix	75	1
β-strand	76	1	4
α-helix	79-82	4
β-strand	85	1	2
β-strand	91-94	4	6
α-helix	95-97	3
α-helix	100-115	16
β-strand	121	1	7
α-helix	123-125	3
β-strand	129-132	4	8
α-helix	139-150	4
β-strand	152-160	9	8
β-strand	167-175	9	8
α-helix	176-178	3
β-strand	179-181	3	8
α-helix	182	1
β-strand	190-193	4	8
α-helix	194-197	4
β-strand	202	1	7
β-strand	209	1	5
β-strand	215	1	9
β-strand	218	1	3
α-helix	219-220	2
β-strand	223-228	6	2
β-strand	236-239	4	6
β-strand	242-245	4	2
β-strand	247	1	3
α-helix	248-250	3
β-strand	251	1	9
β-strand	260-261	2	10
β-strand	271-273	3	10
β-strand	284-298	15	10
β-strand	302-308	7	8
β-strand	316-322	8	8
β-strand	329-334	6	10
α-helix	335-349	15
β-strand	357-361	4	10
α-helix	369-372	4
β-strand	374-376	3	10
α-helix	378-380	3
β-strand	382-385	4	10
α-helix	390-392	3
β-strand	394-395	2	10
β-strand	413-421	9	10
β-strand	423-426	4	7
β-strand	429-435	7	7
α-helix	436-438	3
β-strand	443-457	15	10
β-strand	465-470	6	10
α-helix	475-483	9
β-strand	486-491	6	2
β-strand	495-498	4	1

Chains B, F and J: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	32
β-strand	10-12	3	33
β-strand	18-25	8	32
α-helix	29-31	3
β-strand	32-39	8	33
β-strand	45-51	7	33
β-strand	58	1	33
α-helix	60-61	2
β-strand	68-73	6	32
α-helix	74-76	3
β-strand	78-83	6	32
α-helix	88-90	3
β-strand	92-101	10	33
β-strand	116-117	2	33
β-strand	121-125	5	33

Chains C, G and K: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	5	1	34
β-strand	9-10	2	35
β-strand	18-23	6	34
α-helix	26-29	4
β-strand	35-40	6	35
α-helix	45-46	2
β-strand	47-50	4	35
β-strand	51	1	36
β-strand	55	1	36
α-helix	56-57	2
β-strand	64-69	6	34
β-strand	72-77	6	34
α-helix	82-84	3
β-strand	87-95	9	35
β-strand	98-101	4	35
β-strand	105-107	3	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp120	A, E, I	protein	463	Human immunodeficiency virus 1	A0A1W6IPB2
Envelope glycoprotein gp41	1, D, H	protein	161	Human immunodeficiency virus 1	Q2N0S7
DH270.mu1 Fab Heavy Chain	B, F, J	protein	251	Homo sapiens
DH270.mu1 Fab Light chain	C, G, K	protein	235	Homo sapiens

Sequence of entity 1 (A, E, I), FASTA

>6UM7_1 Envelope glycoprotein gp120 (chains A, E, I)
AENLWVTVYYGVPVWKEAKTTLFCASDARAYEKEVHNVWATHACVPTDPSPQELVLGNVT
ENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLICSDATVKTGTVEEMKNCSFN
TTTEIRDKEKKEYALFYKPDIVPLSETNNTSEYRLINCNTSACTQACPKVTFEPIPIHYC
APAGYAILKCNDETFNGTGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEKEIVIRSENLT
NNAKIIIVHLHTPVEIVCTRPNNNTRKSVRIGPGQTFYATGDIIGDIKQAHCNISEEKWN
DTLQKVGIELQKHFPNKTIKYNQSAGGDMEITTHSFNCGGEFFYCNTSNLFNGTYNGTYI
STNSSANSTSTITLQCRIKQIINMWQGVGRCMYAPPIAGNITCRSNITGLLLTRDGGTNS
NETETFRPAGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV

Sequence of entity 2 (1, D, H), FASTA

>6UM7_2 Envelope glycoprotein gp41 (chains 1, D, H)
VGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQ
HLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIW
DNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 3 (B, F, J), FASTA

>6UM7_3 DH270.mu1 Fab Heavy Chain (chains B, F, J)
MGWSCIILFLVATATGVHSQVQLVQSGAEVKKPGASVKVSCKASGYTFTDYYIHWVRQAP
GQGLEWMGWINPNSGRTNSAQKFQDRVTMTRDTSITTASMELSRLTSDDTAVYYCARGGW
ISLYYDSSGYPNFNYWGQGSRVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFP
EPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKV
DKKVEPKSCDK

Sequence of entity 4 (C, G, K), FASTA

>6UM7_4 DH270.mu1 Fab Light chain (chains C, G, K)
MGWSCIILFLVATATGSWAQSALTQPASVSGSPGQSITISCTGTSYDVGTYNLVSWYQQH
PGKAPKLMIYEVSKRPSGVSFRFSGSKSGNTASLTISGLQAEDAADYYCCSYAGSATVIF
GGGSKMTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKA
GVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	24

Primary citation

Targeted selection of HIV-specific antibody mutations by engineering B cell maturation. Saunders, K.O., Wiehe, K., Tian, M. et al. Science (2019) 366. DOI 10.1126/science.aay7199 · PubMed

Other PDB entries of the same protein (UniProt A0A1W6IPB2), best resolution first:

8SAU 3.3 Å, CryoEM structure of DH270.4-CH848.10.17
8SAW 3.3 Å, CryoEM structure of DH270.UCA.G57R-CH848.10.17DT
8SAY 3.4 Å, CryoEM structure of DH270.3-CH848.10.17
8SB2 3.5 Å, CryoEM structure of DH270.I2-CH848.10.17
8DTO 3.57 Å, Vaccine elicited Antibody MU89 bound to CH848.D949.10.17_N133D_N138T.DS.SOSIP.664 HIV-1…
8SB4 3.6 Å, CryoEM structure of DH270.1-CH848.10.17
8VGV 3.6 Å, DH270.6 Fab bound to the HIV-1 CH848 DE3 SOSIP
9AUH 3.6 Å, Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3
8DOW 3.69 Å, Cryo-EM structure of HIV-1 Env(CH848 10.17 DS.SOSIP_DT) in complex with DH1030.1 Fab
8EU8 3.73 Å, Cryo-EM structure of CH848 10.17DT DS-SOSIP-2P Env
9AUG 3.8 Å, Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3.G57R
9AUI 3.8 Å, Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA4

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