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- EMDB-21112: VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Str... -

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Basic information

Entry
Database: EMDB / ID: EMD-21112
TitleVRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure
Map dataVRC03 and 10-1074 Bound BG505 F14/Vt8 HIV-1 SOSIP Envelope Trimer
Sample
  • Complex: Complex between VRC03, 10-1074, and BG505 F14 HIV-1 SOSIP Env Trimer
    • Complex: BG505 F14/Vt8 HIV-1 SOSIP Env Trimer
      • Protein or peptide: Envelope glycoprotein gp120
      • Protein or peptide: envelope glycoprotein gp41
    • Complex: VRC03
      • Protein or peptide: 10-1074 Fab Heavy Chain
      • Protein or peptide: VRC03 Fab Light Chain
    • Complex: 10-1074
      • Protein or peptide: 10-1074 Fab Light Chain
      • Protein or peptide: VRC03 Fab Heavy Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsTrimer / Complex / Immunogen / HIV-1 / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


immunoglobulin complex / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...immunoglobulin complex / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Envelope glycoprotein Gp160 / : / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain ...: / Envelope glycoprotein Gp160 / : / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin gamma-1 heavy chain / Envelope glycoprotein gp160 / Envelope glycoprotein gp160 / Ig-like domain-containing protein / IGK@ protein / IGL@ protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsHenderson R / Acharya P / Bartesaghi A / Zhou Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI145687-01 United States
CitationJournal: Nat Commun / Year: 2020
Title: Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements.
Authors: Rory Henderson / Maolin Lu / Ye Zhou / Zekun Mu / Robert Parks / Qifeng Han / Allen L Hsu / Elizabeth Carter / Scott C Blanchard / R J Edwards / Kevin Wiehe / Kevin O Saunders / Mario J ...Authors: Rory Henderson / Maolin Lu / Ye Zhou / Zekun Mu / Robert Parks / Qifeng Han / Allen L Hsu / Elizabeth Carter / Scott C Blanchard / R J Edwards / Kevin Wiehe / Kevin O Saunders / Mario J Borgnia / Alberto Bartesaghi / Walther Mothes / Barton F Haynes / Priyamvada Acharya / S Munir Alam /
Abstract: The trimeric HIV-1 Envelope protein (Env) mediates viral-host cell fusion via a network of conformational transitions, with allosteric elements in each protomer orchestrating host receptor-induced ...The trimeric HIV-1 Envelope protein (Env) mediates viral-host cell fusion via a network of conformational transitions, with allosteric elements in each protomer orchestrating host receptor-induced exposure of the co-receptor binding site and fusion elements. To understand the molecular details of this allostery, here, we introduce Env mutations aimed to prevent CD4-induced rearrangements in the HIV-1 BG505 Env trimer. Binding analysis and single-molecule Förster Resonance Energy Transfer confirm that these mutations prevent CD4-induced transitions of the HIV-1 Env. Structural analysis by single-particle cryo-electron microscopy performed on the BG505 SOSIP mutant Env proteins shows rearrangements in the gp120 topological layer contacts with gp41. Displacement of a conserved tryptophan (W571) from its typical pocket in these Env mutants renders the Env insensitive to CD4 binding. These results reveal the critical function of W571 as a conformational switch in Env allostery and receptor-mediated viral entry and provide insights on Env conformation that are relevant for vaccine design.
History
DepositionDec 12, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseFeb 5, 2020-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 10.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6v8z
  • Surface level: 10.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21112.png

Downloads & links

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Map

FileDownload / File: emd_21112.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVRC03 and 10-1074 Bound BG505 F14/Vt8 HIV-1 SOSIP Envelope Trimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 230 pix.
= 249.118 Å		1.08 Å/pix.
x 230 pix.
= 249.118 Å		1.08 Å/pix.
x 230 pix.
= 249.118 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08312 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 10.5 / Movie #1: 10.5
Minimum - Maximum-20.185516 - 37.497204000000004
Average (Standard dev.)0.16872019 (±1.8629501)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions230230230
Spacing230230230
CellA=B=C: 249.1176 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.08312173913041.08312173913041.0831217391304
M x/y/z230230230
origin x/y/z0.0000.0000.000
length x/y/z249.118249.118249.118
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS230230230
D min/max/mean-20.18637.4970.169

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Supplemental data

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Sample components

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Entire : Complex between VRC03, 10-1074, and BG505 F14 HIV-1 SOSIP Env Trimer

EntireName: Complex between VRC03, 10-1074, and BG505 F14 HIV-1 SOSIP Env Trimer
Components
  • Complex: Complex between VRC03, 10-1074, and BG505 F14 HIV-1 SOSIP Env Trimer
    • Complex: BG505 F14/Vt8 HIV-1 SOSIP Env Trimer
      • Protein or peptide: Envelope glycoprotein gp120
      • Protein or peptide: envelope glycoprotein gp41
    • Complex: VRC03
      • Protein or peptide: 10-1074 Fab Heavy Chain
      • Protein or peptide: VRC03 Fab Light Chain
    • Complex: 10-1074
      • Protein or peptide: 10-1074 Fab Light Chain
      • Protein or peptide: VRC03 Fab Heavy Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex between VRC03, 10-1074, and BG505 F14 HIV-1 SOSIP Env Trimer

SupramoleculeName: Complex between VRC03, 10-1074, and BG505 F14 HIV-1 SOSIP Env Trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: BG505 F14/Vt8 HIV-1 SOSIP Env Trimer

SupramoleculeName: BG505 F14/Vt8 HIV-1 SOSIP Env Trimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #3: VRC03

SupramoleculeName: VRC03 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3, #6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: 10-1074

SupramoleculeName: 10-1074 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 52.955289 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ENLWVTVYYG VPVWKDAETT LFCASDAKAY ETEKHNIWAT HACVPTDPNP QEIHLENVTE EFNMWKNNMV EQMHTDIISL WDQSLKPCV KLTPLCVTLQ CTNVTNAITD DMRGELKNCS FNMTTELRDK KQKVYSLFYR LDVVQINENQ GNRSNNSNKE Y RLINCNTS ...String:
ENLWVTVYYG VPVWKDAETT LFCASDAKAY ETEKHNIWAT HACVPTDPNP QEIHLENVTE EFNMWKNNMV EQMHTDIISL WDQSLKPCV KLTPLCVTLQ CTNVTNAITD DMRGELKNCS FNMTTELRDK KQKVYSLFYR LDVVQINENQ GNRSNNSNKE Y RLINCNTS AITMVCPKLS FEPIPIHYCA PAGFAILKCK DKKFNGTGPC PSVSTVQCTH GIKPVLSTQL LLNGSLAEEE VM IRSENIT NNAKNILVQF NTPVQINCTR PLNLTRKSIR IGPGQAFYAM GDIIGDIRQA HCNVSKATWN ETLGKVVKQL RKH FGNNTI IRFANSSGGD LEVTTHSFNC GGEFFYCNTS GLFNSTWISN TSVQGSNSTG SNDSITLPCR IKMIINMWQR IGQA MYAPP IQGVIRCVSN ITGLILTRDG GSTNSTTETF RPGGGDMRDN WRSELYKYKV VKIEPLGVAP TRCKRRV

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: envelope glycoprotein gp41

MacromoleculeName: envelope glycoprotein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 16.677932 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VFLGFLGAAG STMGAASMTL TVQARNLLSG IVQQQSNLLR APEAQQHLLK LTVWGIKQLQ ARVLAVERYL RDQQLLGIWG CSGKLICCT NVPWNSSWSN RNLSEIWDNM TWLQWDKEIS NYTQIIYGLL EESQNQQEKN EQDLLALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: 10-1074 Fab Heavy Chain

MacromoleculeName: 10-1074 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.316314 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSETLSV TCSVSGDSMN NYYWTWIRQS PGKGLEWIGY ISDRESATYN PSLNSRVVIS RDTSKNQLSL KLNSVTPAD TAVYYCATAR RGQRIYGVVS FGEFFYYYSM DVWGKGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
QVQLQESGPG LVKPSETLSV TCSVSGDSMN NYYWTWIRQS PGKGLEWIGY ISDRESATYN PSLNSRVVIS RDTSKNQLSL KLNSVTPAD TAVYYCATAR RGQRIYGVVS FGEFFYYYSM DVWGKGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSC

UniProtKB: Ig-like domain-containing protein

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Macromolecule #4: 10-1074 Fab Light Chain

MacromoleculeName: 10-1074 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.84343 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VRPLSVALGE TARISCGRQA LGSRAVQWYQ HRPGQAPILL IYNNQDRPSG IPERFSGTPD INFGTRATLT ISGVEAGDEA DYYCHMWDS RSGFSWSFGG ATRLTVLGQP KAAPSVTLFP PSSEELQANK ATLVCLISDF YPGAVTVAWK ADSSPVKAGV E TTTPSKQS ...String:
VRPLSVALGE TARISCGRQA LGSRAVQWYQ HRPGQAPILL IYNNQDRPSG IPERFSGTPD INFGTRATLT ISGVEAGDEA DYYCHMWDS RSGFSWSFGG ATRLTVLGQP KAAPSVTLFP PSSEELQANK ATLVCLISDF YPGAVTVAWK ADSSPVKAGV E TTTPSKQS NNKYAASSYL SLTPEQWKSH RSYSCQVTHE GSTVEKTVAP TEC

UniProtKB: IGL@ protein

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Macromolecule #5: VRC03 Fab Heavy Chain

MacromoleculeName: VRC03 Fab Heavy Chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.104303 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAV IKTPGSSVKI SCRASGYNFR DYSIHWVRLI PDKGFEWIGW IKPLWGAVSY ARQLQGRVSM TRQLSQDPDD PDWGVAYME FSGLTPADTA EYFCVRRGSC DYCGDFPWQY WCQGTVVVVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT ...String:
QVQLVQSGAV IKTPGSSVKI SCRASGYNFR DYSIHWVRLI PDKGFEWIGW IKPLWGAVSY ARQLQGRVSM TRQLSQDPDD PDWGVAYME FSGLTPADTA EYFCVRRGSC DYCGDFPWQY WCQGTVVVVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPK

UniProtKB: Immunoglobulin gamma-1 heavy chain

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Macromolecule #6: VRC03 Fab Light Chain

MacromoleculeName: VRC03 Fab Light Chain / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.043652 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGI LSLSPGETAT LFCKASQGGN AMTWYQKRRG QVPRLLIYDT SRRASGVPDR FVGSGSGTDF FLTINKLDRE DFAVYYCQQ FEFFGLGSEL EVHRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL QSGNSQESVT E QDSKDSTY ...String:
EIVLTQSPGI LSLSPGETAT LFCKASQGGN AMTWYQKRRG QVPRLLIYDT SRRASGVPDR FVGSGSGTDF FLTINKLDRE DFAVYYCQQ FEFFGLGSEL EVHRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL QSGNSQESVT E QDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE

UniProtKB: IGK@ protein

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Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 21 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84378
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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