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- EMDB-70469: BG505 MD39.3 SOSIP.664 in complex with 3BC315, BG18 and VRC01 Fabs -

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Basic information

Entry
Database: EMDB / ID: EMD-70469
TitleBG505 MD39.3 SOSIP.664 in complex with 3BC315, BG18 and VRC01 Fabs
Map datasharpened map
Sample
  • Complex: BG505 MD39.3 SOSIP.664 in complex with 3BC315, BG18 and VRC01 Fabs
    • Protein or peptide: BG18 Fab heavy chain
    • Protein or peptide: BG18 Fab light chain
    • Protein or peptide: VRC01 Fab heavy chain
    • Protein or peptide: VRC01 Fab light chain
    • Protein or peptide: 3BC315 Fab heavy chain
    • Protein or peptide: 3BC315 Fab light chain
    • Protein or peptide: Envelope glycoprotein gp160
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsMPER / HIV-1 / gp41 / broadly neutralizing antibody / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
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: 3.1 Å
AuthorsOzorowski G / Phulera S / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
CitationJournal: bioRxiv / Year: 2025
Title: Virus glycoprotein nanodisc platform for vaccine design.
Authors: Kimmo Rantalainen / Alessia Liguori / Gabriel Ozorowski / Claudia Flynn / Jon M Steichen / Olivia Swanson / Patrick J Madden / Sabyasachi Baboo / Swastik Phulera / Anant Gharpure / Danny Lu ...Authors: Kimmo Rantalainen / Alessia Liguori / Gabriel Ozorowski / Claudia Flynn / Jon M Steichen / Olivia Swanson / Patrick J Madden / Sabyasachi Baboo / Swastik Phulera / Anant Gharpure / Danny Lu / Oleksandr Kalyuzhniy / Patrick Skog / Sierra Terada / Monolina Shil / Jolene K Diedrich / Erik Georgeson / Ryan Tingle / Saman Eskandarzadeh / Wen-Hsin Lee / Nushin Alavi / Diana Goodwin / Michael Kubitz / Sonya Amirzehni / Sunny Himansu / Devin Sok / Jeong Hyun Lee / John R Yates / James C Paulson / Shane Crotty / Torben Schiffner / Andrew B Ward / William R Schief
Abstract: Transmembrane glycoproteins of enveloped viruses are the targets of neutralizing antibodies and essential vaccine antigens. mRNA-LNP technology allows in situ production of transmembrane ...Transmembrane glycoproteins of enveloped viruses are the targets of neutralizing antibodies and essential vaccine antigens. mRNA-LNP technology allows in situ production of transmembrane glycoproteins upon immunization, but biophysical characterization of transmembrane antigens and in vitro analysis of post-immunization antibody responses typically rely on soluble proteins. Here, we present a methodological platform for assembling transmembrane glycoprotein vaccine candidates into lipid nanodiscs. We demonstrate the utility of the nanodiscs in HIV membrane proximal external region (MPER)-targeting vaccine development by binding assays using surface plasmon resonance (SPR), ex vivo B cell sorting with fluorescence-activated cell sorting (FACS), and by determining the structure of a prototypical HIV MPER-targeting immunogen nanodisc in complex with three broadly neutralizing antibodies (bnAbs), including the MPER bnAb 10E8, to 3.5 Å by cryogenic electron microscopy (cryo-EM), providing a template for structure-based immunogen design for MPER. Overall, the platform offers a tool for accelerating the development of next-generation viral vaccines.
History
DepositionApr 30, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70469.png

Downloads & links

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Map

FileDownload / File: emd_70469.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 400 pix.
= 413.56 Å		1.03 Å/pix.
x 400 pix.
= 413.56 Å		1.03 Å/pix.
x 400 pix.
= 413.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0339 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.9169398 - 1.5333265
Average (Standard dev.)-0.00019510875 (±0.027871469)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 413.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70469_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_70469_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_70469_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BG505 MD39.3 SOSIP.664 in complex with 3BC315, BG18 and VRC01 Fabs

EntireName: BG505 MD39.3 SOSIP.664 in complex with 3BC315, BG18 and VRC01 Fabs
Components
  • Complex: BG505 MD39.3 SOSIP.664 in complex with 3BC315, BG18 and VRC01 Fabs
    • Protein or peptide: BG18 Fab heavy chain
    • Protein or peptide: BG18 Fab light chain
    • Protein or peptide: VRC01 Fab heavy chain
    • Protein or peptide: VRC01 Fab light chain
    • Protein or peptide: 3BC315 Fab heavy chain
    • Protein or peptide: 3BC315 Fab light chain
    • Protein or peptide: Envelope glycoprotein gp160
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BG505 MD39.3 SOSIP.664 in complex with 3BC315, BG18 and VRC01 Fabs

SupramoleculeName: BG505 MD39.3 SOSIP.664 in complex with 3BC315, BG18 and VRC01 Fabs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: BG18 Fab heavy chain

MacromoleculeName: BG18 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.043186 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLRESGPG LVKPSETLSL SCTVSNDSRP SDHSWTWVRQ SPGKALEWIG DIHYNGATTY NPSLRSRVRI ELDQSIPRFS LKMTSMTAA DTGMYYCARN AIRIYGVVAL GEWFHYGMDV WGQGTAVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT ...String:
QVQLRESGPG LVKPSETLSL SCTVSNDSRP SDHSWTWVRQ SPGKALEWIG DIHYNGATTY NPSLRSRVRI ELDQSIPRFS LKMTSMTAA DTGMYYCARN AIRIYGVVAL GEWFHYGMDV WGQGTAVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSC

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Macromolecule #2: BG18 Fab light chain

MacromoleculeName: BG18 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.937352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SSELTQPPSV SVSPGQTARI TCSGAPLTSR FTYWYRQKPG QAPVLIISRS SQRSSGWSGR FSASWSGTTV TLTIRGVQAD DEADYYCQS SDTSDSYKMF GGGTKLTVLG QPKAAPSVTL FPPSSEELQA NKATLVCLIS DFYPGAVTVA WKADSSPVKA G VETTTPSK ...String:
SSELTQPPSV SVSPGQTARI TCSGAPLTSR FTYWYRQKPG QAPVLIISRS SQRSSGWSGR FSASWSGTTV TLTIRGVQAD DEADYYCQS SDTSDSYKMF GGGTKLTVLG QPKAAPSVTL FPPSSEELQA NKATLVCLIS DFYPGAVTVA WKADSSPVKA G VETTTPSK QSNNKYAASS YLSLTPEQWK SHRSYSCQVT HEGSTVEKTV APTECS

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Macromolecule #3: VRC01 Fab heavy chain

MacromoleculeName: VRC01 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.367631 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGGQ MKKPGESMRI SCRASGYEFI DCTLNWIRLA PGKRPEWMGW LKPRGGAVNY ARPLQGRVTM TRDVYSDTAF LELRSLTVD DTAVYFCTRG KNCDYNWDFE HWGRGTPVIV SSPSTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
QVQLVQSGGQ MKKPGESMRI SCRASGYEFI DCTLNWIRLA PGKRPEWMGW LKPRGGAVNY ARPLQGRVTM TRDVYSDTAF LELRSLTVD DTAVYFCTRG KNCDYNWDFE HWGRGTPVIV SSPSTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK AEPKSC

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Macromolecule #4: VRC01 Fab light chain

MacromoleculeName: VRC01 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.172686 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGETAI ISCRTSQYGS LAWYQQRPGQ APRLVIYSGS TRAAGIPDRF SGSRWGPDYN LTISNLESGD FGVYYCQQY EFFGQGTKVQ VDIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA LQSGNSQESV T EQDSKDST ...String:
EIVLTQSPGT LSLSPGETAI ISCRTSQYGS LAWYQQRPGQ APRLVIYSGS TRAAGIPDRF SGSRWGPDYN LTISNLESGD FGVYYCQQY EFFGQGTKVQ VDIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA LQSGNSQESV T EQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLR SPVTKSFNRG EC

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Macromolecule #5: 3BC315 Fab heavy chain

MacromoleculeName: 3BC315 Fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.99924 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE MKDPGASVKV SCRASGYKFT DYYMHWVRQA PGQGLEWVGW VNTNGGFTKY GAKFQGRVTV TRDTSTNTVF LELSRLTFG DTAMYFCARP MRPVSHGIDY SGLFVFQFWG RGTMVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String:
QVQLVQSGAE MKDPGASVKV SCRASGYKFT DYYMHWVRQA PGQGLEWVGW VNTNGGFTKY GAKFQGRVTV TRDTSTNTVF LELSRLTFG DTAMYFCARP MRPVSHGIDY SGLFVFQFWG RGTMVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCD

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Macromolecule #6: 3BC315 Fab light chain

MacromoleculeName: 3BC315 Fab light chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.009605 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSALTQPASV SASPGQSITI SCSGTRSDVG GYDFVSWYQQ HPGKVPKLII YEVTKRPSGI PQRFSGSKSG NTASLTISGL QADDEADYY CCSYANYDKL ILGGGTKLTV LGQPKANPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADGSPV K AGVETTKP ...String:
QSALTQPASV SASPGQSITI SCSGTRSDVG GYDFVSWYQQ HPGKVPKLII YEVTKRPSGI PQRFSGSKSG NTASLTISGL QADDEADYY CCSYANYDKL ILGGGTKLTV LGQPKANPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADGSPV K AGVETTKP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #7: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 71.434477 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT SAITQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CQNVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV IIRSENI TNNAKNILVQ LNTSVQINCT RPNNNTVKSI RIGPGQAFYY TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFAQSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ AMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG SHSGS GGSG SGGHAAVGIG AVSLGFLGAA GSTMGAASMT LTVQARNLLS GIVQQQSNLL RAPEPQQHLL KDTHWGIKQL QARVLA VEH YLRDQQLLGI WGCSGKLICC TNVPWNSSWS NRNLSEIWDN MTWLQWDKEI SNYTQIIYGL LEESQNQQEK NEQDLLA LD

UniProtKB: Envelope glycoprotein gp160, Envelope glycoprotein gp160

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Macromolecule #18: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 18 / Number of copies: 39 / 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

Concentration10 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / 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: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab initio reconstruction from cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 243503
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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