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- EMDB-73108: RQd20_wk56_28 Fab in complex with V703-0537_L14 SOSIP and 3BNC117 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-73108
TitleRQd20_wk56_28 Fab in complex with V703-0537_L14 SOSIP and 3BNC117 Fab
Map datasharpened map
Sample
  • Complex: RQd20_wk56_28 Fab in complex with V703-0537_L14 SOSIP and 3BNC117 Fab
    • Protein or peptide: 3BNC117 Fab heavy chain
    • Protein or peptide: 3BNC117 light chain
    • Protein or peptide: RQd20_wk56_28 Fab heavy chain
    • Protein or peptide: RQd20_wk56_28 light chain
    • Protein or peptide: V703-0537_L14 SOSIP
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / Env / NHP / V3 glycan / BG18 / germline targeting / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human) / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPhulera S / 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_73108.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: 0.15
Minimum - Maximum-0.544 - 0.98403054
Average (Standard dev.)-0.000091027 (±0.019347105)
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_73108_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_73108_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_73108_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 : RQd20_wk56_28 Fab in complex with V703-0537_L14 SOSIP and 3BNC117 Fab

EntireName: RQd20_wk56_28 Fab in complex with V703-0537_L14 SOSIP and 3BNC117 Fab
Components
  • Complex: RQd20_wk56_28 Fab in complex with V703-0537_L14 SOSIP and 3BNC117 Fab
    • Protein or peptide: 3BNC117 Fab heavy chain
    • Protein or peptide: 3BNC117 light chain
    • Protein or peptide: RQd20_wk56_28 Fab heavy chain
    • Protein or peptide: RQd20_wk56_28 light chain
    • Protein or peptide: V703-0537_L14 SOSIP
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: RQd20_wk56_28 Fab in complex with V703-0537_L14 SOSIP and 3BNC117 Fab

SupramoleculeName: RQd20_wk56_28 Fab in complex with V703-0537_L14 SOSIP and 3BNC117 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: 3BNC117 Fab heavy chain

MacromoleculeName: 3BNC117 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.656484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLLQSGAA VTKPGASVRV SCEASGYNIR DYFIHWWRQA PGQGLQWVGW INPKTGQPNN PRQFQGRVSL TRHASWDFDT YSFYMDLKA LRSDDTAVYF CARQRSDYWD FDVWGSGTQV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
QVQLLQSGAA VTKPGASVRV SCEASGYNIR DYFIHWWRQA PGQGLQWVGW INPKTGQPNN PRQFQGRVSL TRHASWDFDT YSFYMDLKA LRSDDTAVYF CARQRSDYWD FDVWGSGTQV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSC

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Macromolecule #2: 3BNC117 light chain

MacromoleculeName: 3BNC117 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.022658 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDTVT ITCQANGYLN WYQQRRGKAP KLLIYDGSKL ERGVPSRFSG RRWGQEYNLT INNLQPEDIA TYFCQVYEF VVPGTRLDLK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD S KDSTYSLS ...String:
DIQMTQSPSS LSASVGDTVT ITCQANGYLN WYQQRRGKAP KLLIYDGSKL ERGVPSRFSG RRWGQEYNLT INNLQPEDIA TYFCQVYEF VVPGTRLDLK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD S KDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #3: RQd20_wk56_28 Fab heavy chain

MacromoleculeName: RQd20_wk56_28 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.55765 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVHLQESGPG LVKPGETLSL TCGLSGAAIR DWWWTWVRQA PGKGLEWIGE IYGRDGSTHY NPSLKSRVTI SRDASKNHFS LRVTSVTAA DTAVYFCARV GPIYGVVFLG EFYHGFESWG QGVVVAVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String:
QVHLQESGPG LVKPGETLSL TCGLSGAAIR DWWWTWVRQA PGKGLEWIGE IYGRDGSTHY NPSLKSRVTI SRDASKNHFS LRVTSVTAA DTAVYFCARV GPIYGVVFLG EFYHGFESWG QGVVVAVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSC

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Macromolecule #4: RQd20_wk56_28 light chain

MacromoleculeName: RQd20_wk56_28 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 22.838182 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SFELTQPPSV SAASGQTAKI TCGGDNIGSL SVHWYQQSPP QAPVVLIYRD YRRPSGIPER FSGSHSGNTA TLTINRVEAG DEADYYCQV WDSNNYIFGT GTRLTVLGQP KAAPSVTLFP PSSEELQANK ATLVCLISDF YPGAVTVAWK ADSSPVKAGV E TTTPSKQS ...String:
SFELTQPPSV SAASGQTAKI TCGGDNIGSL SVHWYQQSPP QAPVVLIYRD YRRPSGIPER FSGSHSGNTA TLTINRVEAG DEADYYCQV WDSNNYIFGT GTRLTVLGQP KAAPSVTLFP PSSEELQANK ATLVCLISDF YPGAVTVAWK ADSSPVKAGV E TTTPSKQS NNKYAASSYL SLTPEQWKSH RSYSCQVTHE GSTVEKTVAP TECS

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Macromolecule #5: V703-0537_L14 SOSIP

MacromoleculeName: V703-0537_L14 SOSIP / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 72.726281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ETGAEDLWVT VYYGVPVWRD AITTLFCASD AKAYEKEVHN VWATHACVPT DPNPQEMVLE NVTENFNMWK NNMVDQMHED IISLWDQSL KPCVQLTPLC VTLNCTDVVG NNTATRRNNT ATRRNNTATI NDTDTGIKNC SFNITTEVRD KKKKVHALFY R LDIVPIDG ...String:
ETGAEDLWVT VYYGVPVWRD AITTLFCASD AKAYEKEVHN VWATHACVPT DPNPQEMVLE NVTENFNMWK NNMVDQMHED IISLWDQSL KPCVQLTPLC VTLNCTDVVG NNTATRRNNT ATRRNNTATI NDTDTGIKNC SFNITTEVRD KKKKVHALFY R LDIVPIDG KNSNSTEYIL INCNTSVITQ ICPKVSFDPI PIHYCAPAGY AILKCNNKTF NGTGPCNNVS TIQCTHGIKP VV STQLLLN GSLAEEDIII SSENMTDNTK TIIVHFNESV GIECTRPNNN TVESIRIGPG QTFYVTGEII GDIRQAHCNI SKG NWSKTL QRVKEKLKKY YHNKTIKFEP SSGGDLEITT HSFNCRGEFF YCYTSGLFNE SIVNGTNGTI TLPCRIKQIV NMWQ KVGRA MYAPPIAGNI TCSSNITGLL LTRDGGRGTN GTETFRPAGG NMKDNWRSEL YKYKVVEIKP LGIAPTKCRR RVVGS HSGS GGSGSGGHAA VLGTAILGFL GAAGSTMGAA SNALFVQTRQ LLSGFVQQQS NLPKAPKAQQ QLLQLGVWGI KQLQTR VLA IERYLEVQQF LGLWGCSGKA ICCTAVPWNT TWSNKSEQEI WNNMTWMQWD REVGNYTDTI YKLLFVAQFQ QEINEVD LL ALNGTKHHHH HH

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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: 42 / 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

Concentration2.8 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: 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 36490
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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