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- EMDB-70022: BG505 SOSIP in complex with 007 bNAb IgG1 - trimer-dimer class -

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Basic information

Entry
Database: EMDB / ID: EMD-70022
TitleBG505 SOSIP in complex with 007 bNAb IgG1 - trimer-dimer class
Map dataSharpened EM map
Sample
  • Complex: HIV-1 BG505 SOSIP trimer bound by three 007 bNAb IgG1 molecules
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: 007 IgG1 Heavy Chain
    • Protein or peptide: 007 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsantibody / envelope / SOSIP / VIRAL PROTEIN-IMMUNE SYSTEM 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
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsDeLaitsch AT / Bjorkman PJ
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-002143 United States
CitationJournal: bioRxiv / Year: 2025
Title: Identification of a broad and potent V3 glycan site bNAb targeting an N332 glycan-independent epitope.
Authors: Lutz Gieselmann / Andrew T DeLaitsch / Malena Rohde / Caelan Radford / Johanna Worczinski / Anna Momot / Elvin Ahmadov / Judith A Burger / Colin Havenar-Daughton / Sharvari Deshpande / ...Authors: Lutz Gieselmann / Andrew T DeLaitsch / Malena Rohde / Caelan Radford / Johanna Worczinski / Anna Momot / Elvin Ahmadov / Judith A Burger / Colin Havenar-Daughton / Sharvari Deshpande / Federico Giovannoni / Davide Corti / Christoph Kreer / Meryem Seda Ercanoglu / Philipp Schommers / Ivelin S Georgiev / Anthony P West / Jacqueline Knüfer / Ricarda Stumpf / Arne Kroidl / Christof Geldmacher / Lucas Maganga / Wiston William / Nyanda E Ntinginya / Michael Hoelscher / Zhengrong Yang / Qing Wei / Matthew Renfrow / Todd J Green / Jan Novak / Marit J van Gils / Harry B Gristick / Henning Gruell / Jesse D Bloom / Michael S Seaman / Pamela J Bjorkman / Florian Klein /
Abstract: Broadly neutralizing antibodies (bNAbs) against HIV-1 can suppress viremia and inform vaccine development. Here, we characterized 007, a V3 glycan site bNAb exhibiting high levels of antiviral ...Broadly neutralizing antibodies (bNAbs) against HIV-1 can suppress viremia and inform vaccine development. Here, we characterized 007, a V3 glycan site bNAb exhibiting high levels of antiviral activity against multiclade pseudovirus panels (GeoMean IC = 0.012 μg/mL, breadth = 69%, 217 virus strains) by targeting a N332 glycan-independent V3 epitope, a site of Env vulnerability to which only weakly neutralizing antibodies had previously been identified. Functional analyses demonstrated distinct binding and neutralization profiles compared to classical V3 glycan site bNAbs. A 007 Fab-Env cryo-EM structure revealed contacts with the V3 GD/NIR motif and interactions with N156 and N301 glycans. In contrast to classical V3 bNAbs, 007 binding to Env does not depend on the N332 glycan, rendering it resistant to common escape mutations. Structures of 007 IgG-Env trimer complexes showed two Env trimers crosslinked by three bivalent IgGs, and bivalent 007 IgG was up to ~300-fold more potent than monovalent 007 IgG heterodimer, suggesting a role for avidity in potent neutralization. Finally, in HIV-1-infected humanized mice, 007 caused transient decline of viremia and overcame classical V3 escape mutations, highlighting 007's potential for HIV-1 prevention, therapy, functional cure, and vaccine design.
History
DepositionApr 4, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70022.png

Downloads & links

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Map

FileDownload / File: emd_70022.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.44 Å/pix.
x 360 pix.
= 518.4 Å		1.44 Å/pix.
x 360 pix.
= 518.4 Å		1.44 Å/pix.
x 360 pix.
= 518.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.552949 - 1.1524975
Average (Standard dev.)0.0007661096 (±0.026422873)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 518.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened EM map

Fileemd_70022_additional_1.map
AnnotationUnsharpened EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map A

Fileemd_70022_half_map_1.map
AnnotationEM half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map B

Fileemd_70022_half_map_2.map
AnnotationEM half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV-1 BG505 SOSIP trimer bound by three 007 bNAb IgG1 molecules

EntireName: HIV-1 BG505 SOSIP trimer bound by three 007 bNAb IgG1 molecules
Components
  • Complex: HIV-1 BG505 SOSIP trimer bound by three 007 bNAb IgG1 molecules
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: 007 IgG1 Heavy Chain
    • Protein or peptide: 007 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 BG505 SOSIP trimer bound by three 007 bNAb IgG1 molecules

SupramoleculeName: HIV-1 BG505 SOSIP trimer bound by three 007 bNAb IgG1 molecules
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
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: 6 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.3925 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHTDIISLW DQSLKPCVK LTPLCVTLQC TNVTNNITDD MRGELKNCSF NMTTELRDKK QKVYSLFYRL DVVQINENQG NRSNNSNKEY R LINCNTSA ...String:
NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHTDIISLW DQSLKPCVK LTPLCVTLQC TNVTNNITDD MRGELKNCSF NMTTELRDKK QKVYSLFYRL DVVQINENQG NRSNNSNKEY R LINCNTSA ITQACPKVSF EPIPIHYCAP AGFAILKCKD KKFNGTGPCP SVSTVQCTHG IKPVVSTQLL LNGSLAEEEV MI RSENITN NAKNILVQFN TPVQINCTRP NNNTRKSIRI GPGQAFYATG DIIGDIRQAH CNVSKATWNE TLGKVVKQLR KHF GNNTII RFANSSGGDL EVTTHSFNCG GEFFYCNTSG LFNSTWISNT SVQGSNSTGS NDSITLPCRI KQIINMWQRI GQAM YAPPI QGVIRCVSNI TGLILTRDGG STNSTTETFR PGGGDMRDNW RSELYKYKVV KIEPLGVAPT RCKRRVVGRR R

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: 6 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.618064 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
RRRAVGIGAV FLGFLGAAGS TMGAASMTLT VQARNLLSGI VQQQSNLLRA PEAQQHLLKL TVWGIKQLQA RVLAVERYLR DQQLLGIWG CSGKLICCTN VPWNSSWSNR NLSEIWDNMT WLQWDKEISN YTQIIYGLLE ESQNQQEKNE QDLLALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: 007 IgG1 Heavy Chain

MacromoleculeName: 007 IgG1 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.497047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QARLQQWEGR PLKPAETLSL TCGVHGVGLG GSGWGWIRQP PGQGLQWIGE IDHDGSHKHN PALRSRLSMS LDTSRNQVSL RLTSVTAAD TAIYYCVRVY REKFLIGEFL TDYRFMDMWG TGTTVIVSPA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String:
QARLQQWEGR PLKPAETLSL TCGVHGVGLG GSGWGWIRQP PGQGLQWIGE IDHDGSHKHN PALRSRLSMS LDTSRNQVSL RLTSVTAAD TAIYYCVRVY REKFLIGEFL TDYRFMDMWG TGTTVIVSPA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KSCDKTHTCP PC PAPELLG GPSVFLFPPK PKDTLMISRT PEVTCVVVDV SHEDPEVKFN WYVDGVEVHN AKTKPREEQY NSTYRVVSVL TVL HQDWLN GKEYKCKVSN KALPAPIEKT ISKAKGQPRE PQVYTLPPSR EEMTKNQVSL TCLVKGFYPS DIAVEWESNG QPEN NYKTT PPVLDSDGSF FLYSKLTVDK SRWQQGNVFS CSVMHEALHN HYTQKSLSLS PGK

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Macromolecule #4: 007 Light Chain

MacromoleculeName: 007 Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.50027 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AIQLTQAPLT VSASIGDTIT LTCRASQDIS IWLSWYRQMP GKAPELLIYA ASTLRGGVPS RFSGARSGTD FSLKIKNLQP EDFATYYCF QSDSYPRAFG QGTKVEITRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
AIQLTQAPLT VSASIGDTIT LTCRASQDIS IWLSWYRQMP GKAPELLIYA ASTLRGGVPS RFSGARSGTD FSLKIKNLQP EDFATYYCF QSDSYPRAFG QGTKVEITRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 48 / 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

Concentration2.6 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris
150.0 mMSodium ChlorideNaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2290 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model generated in cryoSPARC
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 49254
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6udj

source_name: PDB, initial_model_type: experimental model

5bzd

source_name: PDB, initial_model_type: experimental model

7ps3

source_name: PDB, initial_model_type: experimental model

8uki

source_name: PDB, initial_model_type: experimental model
Detailschains individually rigid body fit into density
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9o2u:
BG505 SOSIP in complex with 007 bNAb IgG1 - trimer-dimer class

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