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- EMDB-23411: Cryo-EM map of BG505 DS-SOSIP in complex with glycan276-dependent... -

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Basic information

Entry
Database: EMDB / ID: EMD-23411
TitleCryo-EM map of BG505 DS-SOSIP in complex with glycan276-dependent broadly neutralizing antibody VRC40.01 Fab
Map dataCryo-EM structure of BG505 DS-SOSIP in complex with VRC40.01 Fab
Sample
  • Complex: Trimer HIV-1 Env in complex with VRC40.01 Fab
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: VRC40.01 Fab Heavy chain
    • Protein or peptide: VRC40.01 Fab Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsBG505 DS-SOSIP / glycan276-dependent / glycan276 / broadly neutralizing antibody / VRC40.01 Fab / HIV- 1 Env / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / 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 ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / 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 / identical protein binding / 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
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsManne K / Acharya P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI145687 United States
CitationJournal: Cell Rep / Year: 2021
Title: Structural basis of glycan276-dependent recognition by HIV-1 broadly neutralizing antibodies.
Authors: Christopher A Cottrell / Kartik Manne / Rui Kong / Shuishu Wang / Tongqing Zhou / Gwo-Yu Chuang / Robert J Edwards / Rory Henderson / Katarzyna Janowska / Megan Kopp / Bob C Lin / Mark K ...Authors: Christopher A Cottrell / Kartik Manne / Rui Kong / Shuishu Wang / Tongqing Zhou / Gwo-Yu Chuang / Robert J Edwards / Rory Henderson / Katarzyna Janowska / Megan Kopp / Bob C Lin / Mark K Louder / Adam S Olia / Reda Rawi / Chen-Hsiang Shen / Justin D Taft / Jonathan L Torres / Nelson R Wu / Baoshan Zhang / Nicole A Doria-Rose / Myron S Cohen / Barton F Haynes / Lawrence Shapiro / Andrew B Ward / Priyamvada Acharya / John R Mascola / Peter D Kwong /
Abstract: Recognition of N-linked glycan at residue N276 (glycan276) at the periphery of the CD4-binding site (CD4bs) on the HIV-envelope trimer is a formidable challenge for many CD4bs-directed antibodies. To ...Recognition of N-linked glycan at residue N276 (glycan276) at the periphery of the CD4-binding site (CD4bs) on the HIV-envelope trimer is a formidable challenge for many CD4bs-directed antibodies. To understand how this glycan can be recognized, here we isolate two lineages of glycan276-dependent CD4bs antibodies. Antibody CH540-VRC40.01 (named for donor-lineage.clone) neutralizes 81% of a panel of 208 diverse strains, while antibody CH314-VRC33.01 neutralizes 45%. Cryo-electron microscopy (cryo-EM) structures of these two antibodies and 179NC75, a previously identified glycan276-dependent CD4bs antibody, in complex with HIV-envelope trimer reveal substantially different modes of glycan276 recognition. Despite these differences, binding of glycan276-dependent antibodies maintains a glycan276 conformation similar to that observed in the absence of glycan276-binding antibodies. By contrast, glycan276-independent CD4bs antibodies, such as VRC01, displace glycan276 upon binding. These results provide a foundation for understanding antibody recognition of glycan276 and suggest its presence may be crucial for priming immunogens seeking to initiate broad CD4bs recognition.
History
DepositionFeb 3, 2021-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.35
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.35
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7ll1
  • Surface level: 1.35
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23411.png

Downloads & links

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Map

FileDownload / File: emd_23411.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of BG505 DS-SOSIP in complex with VRC40.01 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.35 / Movie #1: 1.35
Minimum - Maximum-0.8915951 - 3.5678554
Average (Standard dev.)0.003947007 (±0.13451476)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ416416416
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.8923.5680.004

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Supplemental data

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Half map: Cryo-EM half map B structure of BG505 DS-SOSIP...

Fileemd_23411_half_map_1.map
AnnotationCryo-EM half map B structure of BG505 DS-SOSIP in complex with VRC40.01 Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half map A structure of BG505 DS-SOSIP...

Fileemd_23411_half_map_2.map
AnnotationCryo-EM half map A structure of BG505 DS-SOSIP in complex with VRC40.01 Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimer HIV-1 Env in complex with VRC40.01 Fab

EntireName: Trimer HIV-1 Env in complex with VRC40.01 Fab
Components
  • Complex: Trimer HIV-1 Env in complex with VRC40.01 Fab
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: VRC40.01 Fab Heavy chain
    • Protein or peptide: VRC40.01 Fab Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Trimer HIV-1 Env in complex with VRC40.01 Fab

SupramoleculeName: Trimer HIV-1 Env in complex with VRC40.01 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human immunodeficiency virus 1

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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: 52.986969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT SACTQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNILVQ FNTPVQINCT RPNNNTRKSI RIGPGQAFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ CMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRV

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: 17.162525 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAIEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: VRC40.01 Fab Heavy chain

MacromoleculeName: VRC40.01 Fab Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.553941 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLIQSGPQ FKTPGASVTV SCKASGYIFT DYLIHWVRLV PGKGLEWLGR INTNAGLMYL SHKFEGRLIL RRVVDWRTPS LGTVNMELR NVRSDDSAIY FCGRVVDGFN AAGPLEFWGQ GSPVIVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
QVQLIQSGPQ FKTPGASVTV SCKASGYIFT DYLIHWVRLV PGKGLEWLGR INTNAGLMYL SHKFEGRLIL RRVVDWRTPS LGTVNMELR NVRSDDSAIY FCGRVVDGFN AAGPLEFWGQ GSPVIVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK S

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Macromolecule #4: VRC40.01 Fab Light chain

MacromoleculeName: VRC40.01 Fab Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.616271 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVVMTQSPAT LSLSPGETAA VSCRASQYVD RSISWYQLKT GRAPRLLVYA ASSRSIGVPD RFSGSGSGRD FTLTIRGVQS DDFALYYCQ QDYYWPVTFG QGTRLDMKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
QVVMTQSPAT LSLSPGETAA VSCRASQYVD RSISWYQLKT GRAPRLLVYA ASSRSIGVPD RFSGSGSGRD FTLTIRGVQS DDFALYYCQ QDYYWPVTFG QGTRLDMKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 9 / 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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA EM GP / Details: Blot for 2.5 S before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 93.15 K / Max: 93.15 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7l79

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 489824
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial model
PDB IDChain

7l79

source_name: PDB, initial_model_type: experimental model

6cdi

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-7ll1:
Cryo-EM structure of BG505 DS-SOSIP in complex with glycan276-dependent broadly neutralizing antibody VRC40.01 Fab

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