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- EMDB-41459: Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with ant... -

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Basic information

Entry
Database: EMDB / ID: EMD-41459
TitleCryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with antibody GPZ6-b.01 targeting the fusion peptide
Map dataCryo-EM map of HIV-1 BG505 DS-SOSIP in complex with antibody GPZ6-b.01
Sample
  • Complex: Complex between HIV-1 Env BG505 DS-SOSIP and antibody GPZ6-b.01
    • Protein or peptide: HIV-1 BG505 DS-SOSIP gp120
    • Protein or peptide: HIV-1 BG505 DS-SOSIP glycoprotein gp41
    • Protein or peptide: Heavy chain of antibody GPZ6-b.01
    • Protein or peptide: Light chain of antibody GPZ6-b.01
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 Envelope / antibody / GPZ6-b.01 / SHIV / BG505 DS-SOSIP / neutralization / immunization / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / 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
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsZhou T / Morano NC / Roark RS / Kwong PD / Xu J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with antibody GPZ6-b.01 targeting the fusion peptide
Authors: Wang H
History
DepositionAug 3, 2023-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41459.png

Downloads & links

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Map

FileDownload / File: emd_41459.map.gz / Format: CCP4 / Size: 909.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of HIV-1 BG505 DS-SOSIP in complex with antibody GPZ6-b.01
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 620 pix.
= 514.6 Å		0.83 Å/pix.
x 620 pix.
= 514.6 Å		0.83 Å/pix.
x 620 pix.
= 514.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.299
Minimum - Maximum-0.09399398 - 0.70934707
Average (Standard dev.)0.00024001274 (±0.026643993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions620620620
Spacing620620620
CellA=B=C: 514.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41459_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened cryo-EM map of HIV-1 BG505 DS-SOSIP in...

Fileemd_41459_additional_1.map
AnnotationSharpened cryo-EM map of HIV-1 BG505 DS-SOSIP in complex with antibody GPZ6-b.01
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryo-EM half map of HIV-1 BG505 DS-SOSIP in...

Fileemd_41459_half_map_1.map
Annotationcryo-EM half map of HIV-1 BG505 DS-SOSIP in complex with antibody GPZ6-b.01
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryo-EM half map of HIV-1 BG505 DS-SOSIP in...

Fileemd_41459_half_map_2.map
Annotationcryo-EM half map of HIV-1 BG505 DS-SOSIP in complex with antibody GPZ6-b.01
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex between HIV-1 Env BG505 DS-SOSIP and antibody GPZ6-b.01

EntireName: Complex between HIV-1 Env BG505 DS-SOSIP and antibody GPZ6-b.01
Components
  • Complex: Complex between HIV-1 Env BG505 DS-SOSIP and antibody GPZ6-b.01
    • Protein or peptide: HIV-1 BG505 DS-SOSIP gp120
    • Protein or peptide: HIV-1 BG505 DS-SOSIP glycoprotein gp41
    • Protein or peptide: Heavy chain of antibody GPZ6-b.01
    • Protein or peptide: Light chain of antibody GPZ6-b.01
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex between HIV-1 Env BG505 DS-SOSIP and antibody GPZ6-b.01

SupramoleculeName: Complex between HIV-1 Env BG505 DS-SOSIP and antibody GPZ6-b.01
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 720 KDa

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Macromolecule #1: HIV-1 BG505 DS-SOSIP gp120

MacromoleculeName: HIV-1 BG505 DS-SOSIP gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.086324 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 PTRCKRRVVG RRRRR R

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: HIV-1 BG505 DS-SOSIP glycoprotein gp41

MacromoleculeName: HIV-1 BG505 DS-SOSIP glycoprotein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.146482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: Heavy chain of antibody GPZ6-b.01

MacromoleculeName: Heavy chain of antibody GPZ6-b.01 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 25.294381 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSETLSL TCAVYGSSIS GGYFYWHWIR QAPGKGLEWI GDVYFSGTTG YNPSLKRRVR ISADTSKNQF SLNLRSVTA ADTAVYFCAR DPRGGGWVPN RFDVWGAGVL VTVSSASTKG PSVFPLAPSS RSTSESTAAL GCLVKDYFPE P VTVSWNSG ...String:
QVQLQESGPG LVKPSETLSL TCAVYGSSIS GGYFYWHWIR QAPGKGLEWI GDVYFSGTTG YNPSLKRRVR ISADTSKNQF SLNLRSVTA ADTAVYFCAR DPRGGGWVPN RFDVWGAGVL VTVSSASTKG PSVFPLAPSS RSTSESTAAL GCLVKDYFPE P VTVSWNSG SLTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYVCN VNHKPSNTKV DKRVEIKTCG GLEVLFQGP

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Macromolecule #4: Light chain of antibody GPZ6-b.01

MacromoleculeName: Light chain of antibody GPZ6-b.01 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.162631 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQDIS SFLNWYQQKP GKAPKLLISS VNRLESGVPS RFSGSGSGTE FTLTVSSLQP EDFATYSCQ QCGSVPYTFG QGTTLEIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQDIS SFLNWYQQKP GKAPKLLISS VNRLESGVPS RFSGSGSGTE FTLTVSSLQP EDFATYSCQ QCGSVPYTFG QGTTLEIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS KDNTYSLSST LTLSSTEYQS 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: 82 / 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

Concentration3 mg/mL
BufferpH: 7.4 / Component - Concentration: 137.0 mM / Component - Name: PBS
Details: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, and 1.8 mM KH2PO4
VitrificationCryogen name: ETHANE
DetailsPurified complex by FPLC and concentrated to final concentration.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 100.0 K
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 58.06 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 103000
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

Particle selectionNumber selected: 566072 / Details: Blob pick in cryoSparc
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5i8h

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 199205
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial modelPDB ID:

7lpn


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 82.9
Output model

PDB-8top:
Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with antibody GPZ6-b.01 targeting the fusion peptide

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