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- EMDB-73109: RVz20_wk72_08 Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-73109
TitleRVz20_wk72_08 Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab
Map datasharpened map
Sample
  • Complex: RVz20_wk72_08 Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab
    • Protein or peptide: RVz20_wk72_08 Fab heavy chain
    • Protein or peptide: RVz20_wk72_08 light chain
    • Protein or peptide: RM20A3 Fab heavy chain
    • Protein or peptide: RM20A3 light chain
    • Protein or peptide: BG505 MD39 SOSIP gp120
    • Protein or peptide: BG505 MD39 SOSIP gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / Env / NHP / V3 glycan / BG18 / germline targeting / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / 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 ...symbiont-mediated perturbation of host defense response / 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 / membrane / identical protein binding
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 speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSewall LM / Ozorowski G / 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: Nature / Year: 2026
Title: Vaccination elicits HIV broadly neutralizing antibodies in primates
Authors: Steichen JM / Madden PJ / Flynn CT / Phulera S / Shil M / Kalyuzhniy O / Liguori A / Kifude C / Sewall LM / Cottrell CA / Ma KM / Baboo S / Diedrich JK / McKenney K / deCamp AC / Carnathan ...Authors: Steichen JM / Madden PJ / Flynn CT / Phulera S / Shil M / Kalyuzhniy O / Liguori A / Kifude C / Sewall LM / Cottrell CA / Ma KM / Baboo S / Diedrich JK / McKenney K / deCamp AC / Carnathan DG / Phung I / Ramezani-Rad P / Marina-Zarate E / Freeman B / Xie Z / Lee JH / Sincomb T / Phelps N / Lu D / Goodwin D / Tingle R / Adachi Y / Alavi N / Tran J / Tran AS / Nascimento A / Sovie C / Bader DLV / Voic H / Zhou X / Pixton G / Walsh A / Melo MB / Schiffner T / Batista FD / Burton DR / Irvine DJ / Paulson JC / Yates JR / Ozorowski G / Ward AB / Silvestri G / Crotty S / Schief WR
History
DepositionOct 10, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73109.png

Downloads & links

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Map

FileReleased
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: 0.25
Minimum - Maximum-1.5734575 - 2.191132
Average (Standard dev.)-0.00038682655 (±0.039973103)
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_73109_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_73109_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_73109_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 : RVz20_wk72_08 Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab

EntireName: RVz20_wk72_08 Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab
Components
  • Complex: RVz20_wk72_08 Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab
    • Protein or peptide: RVz20_wk72_08 Fab heavy chain
    • Protein or peptide: RVz20_wk72_08 light chain
    • Protein or peptide: RM20A3 Fab heavy chain
    • Protein or peptide: RM20A3 light chain
    • Protein or peptide: BG505 MD39 SOSIP gp120
    • Protein or peptide: BG505 MD39 SOSIP gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: RVz20_wk72_08 Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab

SupramoleculeName: RVz20_wk72_08 Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #5-#6, #1-#4
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: RM20A3 Fab heavy chain

MacromoleculeName: RM20A3 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.194145 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVETGGG LVQPGGSLKL SCRASGYTFS SFAMSWVRQA PGKGLEWVSL INDRGGLTFY VDSVKGRFTI SRDNSKNTLS LQMHSLRDG DTAVYYCATG GMSSALQSSK YYFDFWGQGA LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
EVQLVETGGG LVQPGGSLKL SCRASGYTFS SFAMSWVRQA PGKGLEWVSL INDRGGLTFY VDSVKGRFTI SRDNSKNTLS LQMHSLRDG DTAVYYCATG GMSSALQSSK YYFDFWGQGA LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVEPKSC D

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Macromolecule #2: RM20A3 light chain

MacromoleculeName: RM20A3 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 22.82715 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ALTQPPSVSG SPGQSVTISC TGTSSDIGSY NYVSWYQQHP GKAPKLMIYD VTQRPSGVSD RFSGSKSGNT ASLTISGLQA DDEADYYCS AYAGRQTFYI FGGGTRLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK A GVETTTPS ...String:
ALTQPPSVSG SPGQSVTISC TGTSSDIGSY NYVSWYQQHP GKAPKLMIYD VTQRPSGVSD RFSGSKSGNT ASLTISGLQA DDEADYYCS AYAGRQTFYI FGGGTRLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK A GVETTTPS KQSNNKYAAS SYLSLTPEQW KSHRSYSCQV THEGSTVEKT VAPTECS

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Macromolecule #3: BG505 MD39 SOSIP gp120

MacromoleculeName: BG505 MD39 SOSIP gp120 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 57.652625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKRGLCCVLL LCGAVFVSPS QEIHARFRRG ARAENLWVTV YYGVPVWKDA ETTLFCASDA KAYETEKHNV WATHACVPTD PNPQEIHLE NVTEEFNMWK NNMVEQMHED IISLWDQSLK PCVKLTPLCV TLQCTNVTNN ITDDMRGELK NCSFNMTTEL R DKKQKVYS ...String:
MKRGLCCVLL LCGAVFVSPS QEIHARFRRG ARAENLWVTV YYGVPVWKDA ETTLFCASDA KAYETEKHNV WATHACVPTD PNPQEIHLE NVTEEFNMWK NNMVEQMHED IISLWDQSLK PCVKLTPLCV TLQCTNVTNN ITDDMRGELK NCSFNMTTEL R DKKQKVYS LFYRLDVVQI NENQGNRSNN SNKEYRLINC NTSAITQACP KVSFEPIPIH YCAPAGFAIL KCKDKKFNGT GP CPSVSTV QCTHGIKPVV STQLLLNGSL AEEEVIIRSE NITNNAKNIL VQLNTPVQIN CTRPNNNTVK SIRIGPGQAF YYT GDIIGD IRQAHCNVSK ATWNETLGKV VKQLRKHFGN NTIIRFAQSS GGDLEVTTHS FNCGGEFFYC NTSGLFNSTW ISNT SVQGS NSTGSNDSIT LPCRIKQIIN MWQRIGQAMY APPIQGVIRC VSNITGLILT RDGGSTNSTT ETFRPGGGDM RDNWR SELY KYKVVKIEPL GVAPTRCKRR VVGRRRRRR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #4: BG505 MD39 SOSIP gp41

MacromoleculeName: BG505 MD39 SOSIP gp41 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.134324 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVSLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEP QQHLLKDTHW GIKQLQARVL AVEHYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #5: RVz20_wk72_08 Fab heavy chain

MacromoleculeName: RVz20_wk72_08 Fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.545498 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVHLQESGPG LVKPSETLSL TCDVSGASLE SHWWAWIRQS PGKGLEWIGE VNGYNGDFHC KPSLTSRVIF SKDASKNQFS LDLKSVTAA DTAVYYCARN RWEDVIVFTS RGNLLDSWGQ GVVVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
QVHLQESGPG LVKPSETLSL TCDVSGASLE SHWWAWIRQS PGKGLEWIGE VNGYNGDFHC KPSLTSRVIF SKDASKNQFS LDLKSVTAA DTAVYYCARN RWEDVIVFTS RGNLLDSWGQ GVVVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SC

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Macromolecule #6: RVz20_wk72_08 light chain

MacromoleculeName: RVz20_wk72_08 light chain / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.324746 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVVFTQPHSV SGSPGQTVTI SCIRSSGSIG SEYVQWYQHR PGYAPSAVIF KNNQRWSGVP DRFSGSVDTS SNSASLVISG LKSEDEADY YCLSHVDTYN MLFGGGTRLT VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT ...String:
EVVFTQPHSV SGSPGQTVTI SCIRSSGSIG SEYVQWYQHR PGYAPSAVIF KNNQRWSGVP DRFSGSVDTS SNSASLVISG LKSEDEADY YCLSHVDTYN MLFGGGTRLT VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPTECS

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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: 36 / 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

Concentration15 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY
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: 1.8 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: cryoSPARC ab initio
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 252448
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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