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- EMDB-24071: Cryo-EM structure of broadly neutralizing V2-apex-targeting antib... -

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Basic information

Entry
Database: EMDB / ID: EMD-24071
TitleCryo-EM structure of broadly neutralizing V2-apex-targeting antibody J038 in complex with HIV-1 Env
Map data
Sample
  • Complex: A complex of HIV-1 Env with antibodies 3BNC117 and J038
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: 3BNC117 antibody heavy chain
    • Protein or peptide: 3BNC117 antibody light chain
    • Protein or peptide: J038 antibody heavy chain
    • Protein or peptide: J038 antibody light chain
    • Protein or peptide: Envelope glycoprotein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PHOSPHATE IONPhosphate
Function / homology
Function and homology information


: / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 ...: / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 / 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
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhou T / Gao F
CitationJournal: Adv Sci (Weinh) / Year: 2022
Title: Development of Neutralization Breadth against Diverse HIV-1 by Increasing Ab-Ag Interface on V2.
Authors: Nan Gao / Yanxin Gai / Lina Meng / Chu Wang / Wei Wang / Xiaojun Li / Tiejun Gu / Mark K Louder / Nicole A Doria-Rose / Kevin Wiehe / Alexandra F Nazzari / Adam S Olia / Jason Gorman / Reda ...Authors: Nan Gao / Yanxin Gai / Lina Meng / Chu Wang / Wei Wang / Xiaojun Li / Tiejun Gu / Mark K Louder / Nicole A Doria-Rose / Kevin Wiehe / Alexandra F Nazzari / Adam S Olia / Jason Gorman / Reda Rawi / Wenmin Wu / Clayton Smith / Htet Khant / Natalia de Val / Bin Yu / Junhong Luo / Haitao Niu / Yaroslav Tsybovsky / Huaxin Liao / Thomas B Kepler / Peter D Kwong / John R Mascola / Chuan Qin / Tongqing Zhou / Xianghui Yu / Feng Gao /
Abstract: Understanding maturation pathways of broadly neutralizing antibodies (bnAbs) against HIV-1 can be highly informative for HIV-1 vaccine development. A lineage of J038 bnAbs is now obtained from a long- ...Understanding maturation pathways of broadly neutralizing antibodies (bnAbs) against HIV-1 can be highly informative for HIV-1 vaccine development. A lineage of J038 bnAbs is now obtained from a long-term SHIV-infected macaque. J038 neutralizes 54% of global circulating HIV-1 strains. Its binding induces a unique "up" conformation for one of the V2 loops in the trimeric envelope glycoprotein and is heavily dependent on glycan, which provides nearly half of the binding surface. Their unmutated common ancestor neutralizes the autologous virus. Continuous maturation enhances neutralization potency and breadth of J038 lineage antibodies via expanding antibody-Env contact areas surrounding the core region contacted by germline-encoded residues. Developmental details and recognition features of J038 lineage antibodies revealed here provide a new pathway for elicitation and maturation of V2-targeting bnAbs.
History
DepositionMay 19, 2021-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateJun 22, 2022-
Current statusJun 22, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24071.png

Downloads & links

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Map

FileDownload / File: emd_24071.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.09069457 - 0.16946732
Average (Standard dev.)0.0002584932 (±0.003550362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 348.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_24071_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_24071_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A complex of HIV-1 Env with antibodies 3BNC117 and J038

EntireName: A complex of HIV-1 Env with antibodies 3BNC117 and J038
Components
  • Complex: A complex of HIV-1 Env with antibodies 3BNC117 and J038
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: 3BNC117 antibody heavy chain
    • Protein or peptide: 3BNC117 antibody light chain
    • Protein or peptide: J038 antibody heavy chain
    • Protein or peptide: J038 antibody light chain
    • Protein or peptide: Envelope glycoprotein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PHOSPHATE IONPhosphate

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Supramolecule #1: A complex of HIV-1 Env with antibodies 3BNC117 and J038

SupramoleculeName: A complex of HIV-1 Env with antibodies 3BNC117 and J038
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.23475 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDADT TLFCASDAKA HETEAHNIWA THACVPTDPN PQEIYMENVT ENFNMWKNNM VEQMQEDIIS LWDQSLKPC VKLTPLCVTL SCTNVTLTNV NYTNNFPNIG NITDEVRNCS FNVTTEIRDK KQKVYALFYK LDIVQMENKN S YRLINCNT ...String:
AENLWVTVYY GVPVWKDADT TLFCASDAKA HETEAHNIWA THACVPTDPN PQEIYMENVT ENFNMWKNNM VEQMQEDIIS LWDQSLKPC VKLTPLCVTL SCTNVTLTNV NYTNNFPNIG NITDEVRNCS FNVTTEIRDK KQKVYALFYK LDIVQMENKN S YRLINCNT SVCKQACPKI SFDPIPIHYC TPAGYAILKC NEKNFNGTGP CKNVSSVQCT HGIKPVVSTQ LLLNGSLAEG EI IIRSENL TNNAKTIIVH LNKSVEINCT RPSNNTRTSV TIGPGQVFYR TGDIIGDIRK AYCEINGTKW NETLKQVVGK LKE HFPNKT ISFQPPSGGD LEITMHHFNC RGEFFYCNTT QLFNSTWINS TTIKEYNDTI IYLPCKIKQI INMWQGVGQC MYAP PIRGK INCVSNITGI LLTRDGGDAN ATNDTETFRP GGGNIKDNWR SELYKYKVVQ IEPLGIAPTK CKRRVVERRR RRR

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Macromolecule #2: 3BNC117 antibody heavy chain

MacromoleculeName: 3BNC117 antibody heavy chain / type: protein_or_peptide / ID: 2 / 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 #3: 3BNC117 antibody light chain

MacromoleculeName: 3BNC117 antibody light chain / type: protein_or_peptide / ID: 3 / 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 #4: J038 antibody heavy chain

MacromoleculeName: J038 antibody heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.413338 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QLHLQESGPG LVRPSETLSL TCDVSGGAFN DAYCSWIRRF PGGGLEWIGR ISGRDGYVES NPALTGRVTM SIDATWKKIV LRLTSMTAS DTATYFCAGE TPEDDFGYYQ PYFKTWGQGL GVTVSSASTK GPSVFPLAPC SRSTSESTAA LGCLVKDYFP E PVTVSWNS ...String:
QLHLQESGPG LVRPSETLSL TCDVSGGAFN DAYCSWIRRF PGGGLEWIGR ISGRDGYVES NPALTGRVTM SIDATWKKIV LRLTSMTAS DTATYFCAGE TPEDDFGYYQ PYFKTWGQGL GVTVSSASTK GPSVFPLAPC SRSTSESTAA LGCLVKDYFP E PVTVSWNS GSLTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYVC NVNHKPSNTK VDKRVEIKTC

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Macromolecule #5: J038 antibody light chain

MacromoleculeName: J038 antibody light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.187713 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQLIQSPSS VSASLGDRVT ITCRSTQGIG SDLAWYQATP GTAPKLLIYN SFALHKGVPS RFSGSGSGTE FSLTITGLQP EDFATYYCQ HYRRLPLTFG GGTNIEVKRA VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGVLKTGNS Q ESVTEQDS ...String:
DIQLIQSPSS VSASLGDRVT ITCRSTQGIG SDLAWYQATP GTAPKLLIYN SFALHKGVPS RFSGSGSGTE FSLTITGLQP EDFATYYCQ HYRRLPLTFG GGTNIEVKRA VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGVLKTGNS Q ESVTEQDS KDNTYSLSST LTLSNTDYQS HNVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #6: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.2185 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAMIFG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QSNLPRAPEA QQHLLQLTVW GIKQLQARVL AVERYLEVQK FLGLWGCSG KIICCTAVPW NSTWSNKSFE QIWNNMTWIE WEREISNYTS QIYDILTESQ FQQDINEVDL LELD

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Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 38 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #13: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 13 / Number of copies: 3 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION / Phosphate

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 18000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.10)
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.08)
Final 3D classificationSoftware - Name: RELION (ver. 3.08)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.08)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.08) / Number images used: 312379
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7mxd:
Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J038 in complex with HIV-1 Env

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