6VRW: Envelope glycoprotein gp120

Cryo-EM structure of stabilized HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2. Determined by electron microscopy at 3.71 Å resolution. Released 11 Mar 2020.

Method
Electron microscopy
Resolution
3.71 Å
Organism
Human immunodeficiency virus 1
Chains
6
Atoms
14,568
Mol. weight
232.31 kDa
Ligands
NAG
Released
11 Mar 2020

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

Secondary structure: helices and β-sheets

6VRW contains 50 α-helices and 138 β-strands across 6 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, D and G: 10 helices, 43 β-strands

ElementResiduesLengthSheet
β-strand35-40614
β-strand45-47315
β-strand53-56416
β-strand67117
β-strand75-76216
α-helix77-782
β-strand83-85315
β-strand91-93318
α-helix102-11514
β-strand121119
β-strand130-131220
β-strand154-162920
β-strand169-177920
α-helix178-1803
β-strand181-183321
β-strand191-193321
β-strand202-203219
β-strand209117
β-strand215122
β-strand216-218316
α-helix219-2202
β-strand221115
β-strand223-228615
β-strand237-239318
β-strand242-245415
β-strand247116
β-strand251122
β-strand256123
β-strand261124
α-helix263-2653
β-strand272-273225
β-strand284-286325
α-helix2911
β-strand292-298724
β-strand301-3121020
β-strand315-3231020
β-strand330-333424
α-helix336-35015
β-strand360-361225
β-strand374-378523
β-strand381-385523
β-strand414-417424
β-strand418-421423
β-strand423-424219
α-helix426-4283
β-strand434-435219
α-helix436-4383
β-strand443-449724
β-strand452-456525
β-strand467-470425
α-helix476-4794
β-strand486-491615
β-strand494-499614
Chain B: 6 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix517-5215
β-strand529113
α-helix571-59424
β-strand605-60951
α-helix619-6246
β-strand627113
α-helix628-6347
α-helix639-65315
α-helix654-6596
Chains C and E: 7 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix517-5215
β-strand529126
α-helix530-5334
α-helix571-59424
β-strand605-609514
α-helix619-6246
β-strand627126
α-helix628-6347
α-helix639-65315
α-helix654-6596

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Envelope glycoprotein gp120A, D, Gprotein471Human immunodeficiency virus 1A0A0N9FF17
Envelope glycoprotein gp41B, C, Eprotein154Human immunodeficiency virus 1
Sequence of entity 1 (A, D, G), FASTA
>6VRW_1 Envelope glycoprotein gp120 (chains A, D, G)
GLWVTVYYGVPVWREAKTTLFCASDAKSYEKEVHNVWATHACVPTDPNPQELVLENVTEN
FNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLNCSDAKVNATYKGTREEIKNCSF
NATTELRDKKRREYALFYRLDIVPLSGEGNNNSEYRLINCNTSVITQICPKVTFDPIPIH
YCAPAGYAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSEN
LTDNVKTIIVHLNESVEITCTRPNNMTRKSVRIGPGQTFYALGDIIGDIRQPHCNISEIK
WEKTLQRVSEKLREHFNKTIIFNQSSGGDLEITTHSFNCGGEFFYCNTSDLFFNKTFNET
YSTGSNSTNSTITLPCRIKQIINMWQEVGRAMYAPPIAGNITCKSNITGLLLTRDGGGNN
STKETFRPGGGNMRDNWRSELYKYKVVEVKPLGIAPTECNRTVVQRRRRRR
Sequence of entity 2 (B, C, E), FASTA
>6VRW_2 Envelope glycoprotein gp41 (chains B, C, E)
AVVGLGAVFLGFLGAAGSTMGAASNTLTVQARQLLSGIVQQQSNLLRAPEAQQHMLQLGV
WGFKQLQARVLAIERYLEVQQLLGMWGCSGKLICCTNVPWNSSWSNKTYNEIWDNMTWMQ
WDREIGNYTDTIYKLLEVSQFQQEINEKDNLTLD

Ligands and cofactors

IDNameFormulaCopies
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O639

Primary citation

Structure of Super-Potent Antibody CAP256-VRC26.25 in Complex with HIV-1 Envelope Reveals a Combined Mode of Trimer-Apex Recognition. Gorman, J., Chuang, G.Y., Lai, Y.T. et al. Cell Rep (2020) 31:107488-107488. DOI 10.1016/j.celrep.2020.03.052 · PubMed

Other PDB entries of the same protein (UniProt A0A0N9FF17), best resolution first:

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