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- EMDB-71678: HIV-1 bnAb 9-71 in complex with BG505 MD39 SOSIP and RM19R -

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Basic information

Entry
Database: EMDB / ID: EMD-71678
TitleHIV-1 bnAb 9-71 in complex with BG505 MD39 SOSIP and RM19R
Map dataSharpened map.
Sample
  • Complex: HIV-1 bnAb 9-71 in complex with BG505 MD39 SOSIP and RM19R
    • Protein or peptide: RM19R light chain Fv
    • Protein or peptide: RM19R heavy chain Fv
    • Protein or peptide: 9-71 heavy chain Fv
    • Protein or peptide: 9-71 light chain Fv
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Envelope glycoprotein gp41 - BG505 MD39
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / SOSIP / human / broadly neutralizing antibody / VIRAL PROTEIN
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
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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBader DLV / 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: To Be Published
Title: Structural and immunogenetic signatures guide CD4-mimetic HIV vaccine development
Authors: Bader DLV / Flynn CT
History
DepositionJul 11, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71678.png

Downloads & links

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Map

FileDownload / File: emd_71678.map.gz / Format: CCP4 / Size: 103 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.)
1.05 Å/pix.
x 300 pix.
= 313.5 Å		1.05 Å/pix.
x 300 pix.
= 313.5 Å		1.05 Å/pix.
x 300 pix.
= 313.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.3
Minimum - Maximum-0.7860292 - 1.5447904
Average (Standard dev.)0.0074013774 (±0.050750624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 313.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71678_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A.

Fileemd_71678_half_map_1.map
AnnotationHalf map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B.

Fileemd_71678_half_map_2.map
AnnotationHalf 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 bnAb 9-71 in complex with BG505 MD39 SOSIP and RM19R

EntireName: HIV-1 bnAb 9-71 in complex with BG505 MD39 SOSIP and RM19R
Components
  • Complex: HIV-1 bnAb 9-71 in complex with BG505 MD39 SOSIP and RM19R
    • Protein or peptide: RM19R light chain Fv
    • Protein or peptide: RM19R heavy chain Fv
    • Protein or peptide: 9-71 heavy chain Fv
    • Protein or peptide: 9-71 light chain Fv
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Envelope glycoprotein gp41 - BG505 MD39
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 bnAb 9-71 in complex with BG505 MD39 SOSIP and RM19R

SupramoleculeName: HIV-1 bnAb 9-71 in complex with BG505 MD39 SOSIP and RM19R
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: RM19R light chain Fv

MacromoleculeName: RM19R light chain Fv / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.808134 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AIRMTQSPAI LSLSPGERAT LSCRASQSVD SRLAWYQQKP GQSPRLLIYD VSSRATGIPD RFSGSGSGTE FTLTISSLEP EDVAVYFCH QENDWPWTFG QGTKVEIK

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Macromolecule #2: RM19R heavy chain Fv

MacromoleculeName: RM19R heavy chain Fv / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 13.268667 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGPG LVRPSETLSL TCAVSGDSIS TNNGWSWIRQ TPGKGLEWIG YINGRSGSTR YNPSLQSRVT ISTDTSGNQF SLKVNSVTA ADTAKYYCAF FWSTYYKRFD VWGPGVRVTV SS

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Macromolecule #3: 9-71 heavy chain Fv

MacromoleculeName: 9-71 heavy chain Fv / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.060739 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QLAQSGGGVK KPGASVKISC VTPESTFTKY WLHWVRQAPG QGFEWLGVVS PHGGRPMFAN KFRDRLTLTR DIHTTTHYME LRGLTSDDT AIYYCARDSF GETFRHSGDQ PYQMDVWGGG TNIVVSS

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Macromolecule #4: 9-71 light chain Fv

MacromoleculeName: 9-71 light chain Fv / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.826159 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EPVLTQSPGT LSLSPGERAT LSCRASQGFS VDHLAWFQKR PGRPPRLLIF ETSRRANGSP DRFSGSASGA EYTLTISNVE PEDFAVYYC QSYGSITPLI FGGGTRVDVK

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Macromolecule #5: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 57.141047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GAENLWVTVY YGVPVWKDAE TTLFCASDAK AYETEKHNVW ATHACVPTDP NPQEIHLEN VTEEFNMWKN NMVEQMHEDI ISLWDQSLKP CVKLTPLCVT LQCTNVTNNI TDDMRGELKN CSFNMTTELR D KKQKVYSL ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GAENLWVTVY YGVPVWKDAE TTLFCASDAK AYETEKHNVW ATHACVPTDP NPQEIHLEN VTEEFNMWKN NMVEQMHEDI ISLWDQSLKP CVKLTPLCVT LQCTNVTNNI TDDMRGELKN CSFNMTTELR D KKQKVYSL FYRLDVVQIN ENQGNRSNNS NKEYRLINCN TSAITQACPK VSFEPIPIHY CAPAGFAILK CKDKKFNGTG PC PSVSTVQ CTHGIKPVVS TQLLLNGSLA EEEVIIRSEN ITNNAKNILV QLNTPVQINC TRPNNNTVKS IRIGPGQAFY YTG DIIGDI RQAHCNVSKA TWNETLGKVV KQLRKHFGNN TIIRFAQSSG GDLEVTTHSF NCGGEFFYCN TSGLFNSTWI SNTS VQGSN STGSNDSITL PCRIKQIINM WQRIGQAMYA PPIQGVIRCV SNITGLILTR DGGSTNSTTE TFRPGGGDMR DNWRS ELYK YKVVKIEPLG VAPTRCKRRV VGRRRRRR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #6: Envelope glycoprotein gp41 - BG505 MD39

MacromoleculeName: Envelope glycoprotein gp41 - BG505 MD39 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 18.250541 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVSLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEP QQHLLKDTHW GIKQLQARVL AVEHYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALDGTKHHH H HH

UniProtKB: Envelope glycoprotein gp160

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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: 30 / 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

Concentration5.88 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 KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 5300 / Average exposure time: 7.02 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
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: 958003 / Details: 1052718
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio (cryoSPARC)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v.4.7.0) / Number images used: 230472
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v.4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v.4.7.0)
FSC plot (resolution estimation)

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