8EU8: CH848 10.17DT DS-SOSIP-2P Env

Cryo-EM structure of CH848 10.17DT DS-SOSIP-2P Env. Determined by electron microscopy at 3.73 Å resolution. Released 4 Jan 2023.

Method: Electron microscopy
Resolution: 3.73 Å
Organism: Human immunodeficiency virus 1
Chains: 3
Atoms: 14,181
Mol. weight: 246.7 kDa
Ligands: NAG
Released: 4 Jan 2023

Explore 8EU8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EU8 contains 77 α-helices and 117 β-strands across 3 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 B: 25 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	2
α-helix	52	1
β-strand	53-56	4	3
α-helix	69-71	3
β-strand	75-76	2	3
β-strand	84-85	2	2
β-strand	91-94	4	4
α-helix	95-97	3
α-helix	99-114	16
α-helix	120	1
β-strand	121	1	5
α-helix	123-125	3
β-strand	129-136	8	6
β-strand	139-160	14	6
β-strand	167-175	9	6
α-helix	176-178	3
β-strand	179-181	3	6
β-strand	190-193	4	6
α-helix	194-197	4
β-strand	202-203	2	5
α-helix	204-205	2
β-strand	215-218	4	3
α-helix	219-220	2
β-strand	223-228	6	2
β-strand	236-239	4	4
β-strand	242-245	4	2
β-strand	247	1	3
α-helix	250	1
β-strand	251	1	3
α-helix	252	1
β-strand	259-261	3	6
α-helix	263-266	4
β-strand	271-273	3	6
β-strand	284-308	25	6
β-strand	316-322	8	6
β-strand	330-334	5	6
α-helix	335-350	16
β-strand	357-361	4	6
α-helix	369-372	4
β-strand	374-379	6	7
β-strand	381-385	5	7
β-strand	393-395	3	6
β-strand	413-417	5	6
β-strand	418-421	4	7
β-strand	423-425	3	5
α-helix	432	1
β-strand	433-435	3	5
α-helix	437-440	4
β-strand	441-456	16	6
β-strand	465-470	6	6
α-helix	476-482	7
β-strand	486-491	6	2
β-strand	494-499	6	1
β-strand	529	1	8
α-helix	530-533	4
α-helix	537-542	6
α-helix	570-595	26
β-strand	603-609	7	1
α-helix	619-623	5
β-strand	627	1	8
α-helix	628-635	8
α-helix	636-638	3
α-helix	639-660	22

Chain C: 27 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	17
β-strand	45-47	3	18
α-helix	52	1
β-strand	53-56	4	19
α-helix	68	1
α-helix	69-73	5
β-strand	75-76	2	19
β-strand	84-85	2	18
β-strand	91-94	4	20
α-helix	95-97	3
α-helix	99-114	16
α-helix	120	1
β-strand	121	1	21
α-helix	123-125	3
β-strand	129-136	8	22
β-strand	139-160	14	22
β-strand	167-175	9	22
α-helix	176-178	3
β-strand	179-181	3	22
β-strand	190-193	4	22
α-helix	194-197	4
β-strand	202-203	2	21
α-helix	204-205	2
α-helix	213-214	2
β-strand	215-218	4	19
α-helix	219-220	2
β-strand	223-228	6	18
β-strand	236-239	4	20
β-strand	242-245	4	18
β-strand	247	1	19
α-helix	250	1
β-strand	251	1	19
α-helix	252	1
β-strand	259-261	3	22
α-helix	263-266	4
β-strand	271-273	3	22
β-strand	284-308	25	22
β-strand	316-322	8	22
β-strand	330-334	5	22
α-helix	335-350	16
β-strand	357-361	4	22
α-helix	369-372	4
β-strand	374-379	6	23
β-strand	381-385	5	23
β-strand	393-395	3	22
β-strand	413-417	5	22
β-strand	418-421	4	23
β-strand	423-425	3	21
α-helix	432	1
β-strand	433-435	3	21
α-helix	437-440	4
β-strand	441-456	16	22
β-strand	465-470	6	22
α-helix	476-482	7
β-strand	486-491	6	18
β-strand	494-499	6	17
β-strand	529	1	24
α-helix	530-533	4
α-helix	537-542	6
α-helix	570-595	26
β-strand	603-609	7	17
α-helix	619-623	5
β-strand	627	1	24
α-helix	628-635	8
α-helix	636-638	3
α-helix	639-660	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CH848 10.17DT SOSIP Envelope glycoprotein gp160	A, B, C	protein	698	Human immunodeficiency virus 1	A0A1W6IPB2

Sequence of entity 1 (A, B, C), FASTA

>8EU8_1 CH848 10.17DT SOSIP Envelope glycoprotein gp160 (chains A, B, C)
MPMGSLQPLATLYLLGMLVASVLAAENLWVTVYYGVPVWKEAKTTLFCASDARAYEKEVH
NVWATHACVPTDPSPQELVLGNVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLC
VTLICSDATVKTGTVEEMKNCSFNTTTEIRDKEKKEYALFYKPDIVPLSETNNTSEYRLI
NCNTSACTQACPKVTFEPIPIHYCAPAGYAILKCNDETFNGTGPCSNVSTVQCTHGIRPV
VSTQLLLNGSLAEKEIVIRSENLTNNAKIIIVHLHTPVEIVCTRPNNNTRKSVRIGPGQT
FYATGDIIGDIKQAHCNISEEKWNDTLQKVGIELQKHFPNKTIKYNQSAGGDMEITTHSF
NCGGEFFYCNTSNLFNGTYNGTYISTNSSANSTSTITLQCRIKQIINMWQGVGRCMYAPP
IAGNITCRSNITGLLLTRDGGTNSNETETFRPAGGDMRDNWRSELYKYKVVKIEPLGVAP
TRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLL
RAPEAQQHLLKPPVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSN
RNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALDGSLEVLFQGPGH
HHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	27

Primary citation

Structure-Based Stabilization of SOSIP Env Enhances Recombinant Ectodomain Durability and Yield. Wrapp, D., Mu, Z., Thakur, B. et al. J Virol (2023) 97:e0167322-e0167322. DOI 10.1128/jvi.01673-22 · 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
6UM7 3.5 Å, Cryo-EM structure of vaccine-elicited HIV-1 neutralizing antibody DH270.mu1 in complex…
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
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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