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- EMDB-8693: BG505 SOSIP.664 in complex with broadly neutralizing antibodies B... -

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Basic information

Entry
Database: EMDB / ID: EMD-8693
TitleBG505 SOSIP.664 in complex with broadly neutralizing antibodies BG1 and 8ANC195
Map datacryo-EM map of BG505 SOSIP.664 in complex with broadly neutralizing antibodies BG1 and 8ANC195
Sample
  • Complex: BG505 SOSIP-BG1-8ANC195 complex
    • Complex: BG505 SOSIP
      • Protein or peptide: Envelope glycoprotein gp160
      • Protein or peptide: Envelope glycoprotein gp160
    • Complex: BG1
      • Protein or peptide: BG1 Fab light chain
      • Protein or peptide: BG1 Fab heavy chain
    • Complex: 8ANC195
      • Protein or peptide: 8ANC195 G52K5 Fab heavy chain
      • Protein or peptide: 8ANC195 G52K5 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / immunoglobulin mediated immune response / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / host cell endosome membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / clathrin-dependent endocytosis of virus by host cell / blood microparticle / adaptive immune response / Potential therapeutics for SARS / viral protein processing / immune response / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / extracellular space / extracellular exosome / extracellular region / identical protein binding / metal ion binding / plasma 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain ...: / Envelope glycoprotein Gp160 / : / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin kappa constant / Envelope glycoprotein gp160 / Ig-like domain-containing protein / IgG H chain
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsWang H / Bjorkman PJ
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50 19 GM082545-06 United States
Bill & Melinda Gates FoundationCollaboration for AIDS Vaccine Discovery Grant 593 1040753 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI100148 United States
CitationJournal: Elife / Year: 2017
Title: Asymmetric recognition of HIV-1 Envelope trimer by V1V2 loop-targeting antibodies.
Authors: Haoqing Wang / Harry B Gristick / Louise Scharf / Anthony P West / Rachel P Galimidi / Michael S Seaman / Natalia T Freund / Michel C Nussenzweig / Pamela J Bjorkman /
Abstract: The HIV-1 envelope (Env) glycoprotein binds to host cell receptors to mediate membrane fusion. The prefusion Env trimer is stabilized by V1V2 loops that interact at the trimer apex. Broadly ...The HIV-1 envelope (Env) glycoprotein binds to host cell receptors to mediate membrane fusion. The prefusion Env trimer is stabilized by V1V2 loops that interact at the trimer apex. Broadly neutralizing antibodies (bNAbs) against V1V2 loops, exemplified by PG9, bind asymmetrically as a single Fab to the apex of the symmetric Env trimer using a protruding CDRH3 to penetrate the Env glycan shield. Here we characterized a distinct mode of V1V2 epitope recognition by the new bNAb BG1 in which two Fabs bind asymmetrically per Env trimer using a compact CDRH3. Comparisons between cryo-EM structures of Env trimer complexed with BG1 (6.2 Å resolution) and PG9 (11.5 Å resolution) revealed a new V1V2-targeting strategy by BG1. Analyses of the EM structures provided information relevant to vaccine design including molecular details for different modes of asymmetric recognition of Env trimer and a binding model for BG1 recognition of V1V2 involving glycan flexibility.
History
DepositionApr 17, 2017-
Header (metadata) releaseJun 21, 2017-
Map releaseJun 21, 2017-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0342
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0342
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5viy
  • Surface level: 0.0342
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8693.png

Downloads & links

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Map

FileDownload / File: emd_8693.map.gz / Format: CCP4 / Size: 51.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map of BG505 SOSIP.664 in complex with broadly neutralizing antibodies BG1 and 8ANC195
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 238 pix.
= 321.3 Å		1.35 Å/pix.
x 238 pix.
= 321.3 Å		1.35 Å/pix.
x 238 pix.
= 321.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0342 / Movie #1: 0.0342
Minimum - Maximum-0.014185969 - 0.084809035
Average (Standard dev.)0.0009000785 (±0.005458961)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions238238238
Spacing238238238
CellA=B=C: 321.30002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z238238238
origin x/y/z0.0000.0000.000
length x/y/z321.300321.300321.300
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS238238238
D min/max/mean-0.0140.0850.001

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Supplemental data

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Sample components

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Entire : BG505 SOSIP-BG1-8ANC195 complex

EntireName: BG505 SOSIP-BG1-8ANC195 complex
Components
  • Complex: BG505 SOSIP-BG1-8ANC195 complex
    • Complex: BG505 SOSIP
      • Protein or peptide: Envelope glycoprotein gp160
      • Protein or peptide: Envelope glycoprotein gp160
    • Complex: BG1
      • Protein or peptide: BG1 Fab light chain
      • Protein or peptide: BG1 Fab heavy chain
    • Complex: 8ANC195
      • Protein or peptide: 8ANC195 G52K5 Fab heavy chain
      • Protein or peptide: 8ANC195 G52K5 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BG505 SOSIP-BG1-8ANC195 complex

SupramoleculeName: BG505 SOSIP-BG1-8ANC195 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: BG505 SOSIP

SupramoleculeName: BG505 SOSIP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: BG1

SupramoleculeName: BG1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #4: 8ANC195

SupramoleculeName: 8ANC195 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.146482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

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Macromolecule #2: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.064277 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT SAITQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNILVQ FNTPVQINCT RPNNNTRKSI RIGPGQAFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ AMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG RRRRR R

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Macromolecule #3: BG1 Fab light chain

MacromoleculeName: BG1 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.527102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIHMTQSPVS LSASVGDRVT ITCRASHFIA NYVNWYQQKP GKAPTLLIFE SSTLQRGVPS RFSAYGDGTE FTLSINTLQP EDFASYICQ QSHSPPVTFG AGTRVDQKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIHMTQSPVS LSASVGDRVT ITCRASHFIA NYVNWYQQKP GKAPTLLIFE SSTLQRGVPS RFSAYGDGTE FTLSINTLQP EDFASYICQ QSHSPPVTFG AGTRVDQKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #4: BG1 Fab heavy chain

MacromoleculeName: BG1 Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.931861 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AEQLVESGGG LVPPGRSLRL SCSASGFYFP DYAMAWVRQA PGQGLQWVGF MRGWAYGGSA QFAAFAVGKF AISRDDGRNV VYLDVKNPT FEDTGVYFCA REQRNKDYRY GQEGFGYSYG MDVWGRGTTV VVSTASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE ...String:
AEQLVESGGG LVPPGRSLRL SCSASGFYFP DYAMAWVRQA PGQGLQWVGF MRGWAYGGSA QFAAFAVGKF AISRDDGRNV VYLDVKNPT FEDTGVYFCA REQRNKDYRY GQEGFGYSYG MDVWGRGTTV VVSTASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KRVEP

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Macromolecule #5: 8ANC195 G52K5 Fab heavy chain

MacromoleculeName: 8ANC195 G52K5 Fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.788809 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QIHLVQSGTE VKKPGSSVTV SCKAYGVNTF GLYAVNWVRQ APGQSLEYIG QIWRWKSSAS HHFRGRVLIS AVDLTGSSPP ISSLEIKNL TSDDTAVYFC TTTSTYDRWS GLHHDGVMAF SSWGQGTLIS VSAASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
QIHLVQSGTE VKKPGSSVTV SCKAYGVNTF GLYAVNWVRQ APGQSLEYIG QIWRWKSSAS HHFRGRVLIS AVDLTGSSPP ISSLEIKNL TSDDTAVYFC TTTSTYDRWS GLHHDGVMAF SSWGQGTLIS VSAASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPK

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Macromolecule #6: 8ANC195 G52K5 Fab light chain

MacromoleculeName: 8ANC195 G52K5 Fab light chain / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.460047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPST LSASTGDTVR ISCRASQSIT GNWVAWYQQR PGKAPRLLIY RGAALLGGVP SRFRGSAAGT DFTLTIGNLQ AEDFGTFYC QQYDTYPGTF GQGTKVEVKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPST LSASTGDTVR ISCRASQSIT GNWVAWYQQR PGKAPRLLIY RGAALLGGVP SRFRGSAAGT DFTLTIGNLQ AEDFGTFYC QQYDTYPGTF GQGTKVEVKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #15: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 15 / Number of copies: 13 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 66000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-5viy:
BG505 SOSIP.664 in complex with broadly neutralizing antibodies BG1 and 8ANC195

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