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- EMDB-24128: Cryo-EM structure of broadly neutralizing V2-apex-targeting antib... -

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Basic information

Entry
Database: EMDB / ID: EMD-24128
TitleCryo-EM structure of broadly neutralizing V2-apex-targeting antibody J033 in complex with HIV-1 Env
Map dataJ33 full map
Sample
  • Complex: A complex of HIV-1 Env with antibodies 3BNC117 and J033
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: 3BNC117 antibody heavy chain
    • Protein or peptide: 3BNC117 antibody light chain
    • Protein or peptide: J033 antibody heavy chain
    • Protein or peptide: J033 antibody light chain
    • Protein or peptide: Envelope glycoprotein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PHOSPHATE ION
  • Ligand: alpha-D-mannopyranose
KeywordsHIV-1 / SIV-1 / V2-apex / envelope glycoprotein / neutralizing antibody / glycan-dependent / IMMUNE SYSTEM-VIRAL PROTEIN 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
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: 4.2 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 28, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24128.png

Downloads & links

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Map

FileDownload / File: emd_24128.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationJ33 full map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 480 pix.
= 489.6 Å		1.02 Å/pix.
x 480 pix.
= 489.6 Å		1.02 Å/pix.
x 480 pix.
= 489.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0019
Minimum - Maximum-0.018479833 - 0.040118016
Average (Standard dev.)0.000048871298 (±0.00069005357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 489.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: J33 half map

Fileemd_24128_half_map_1.map
AnnotationJ33 half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: J33 half map

Fileemd_24128_half_map_2.map
AnnotationJ33 half 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 J033

EntireName: A complex of HIV-1 Env with antibodies 3BNC117 and J033
Components
  • Complex: A complex of HIV-1 Env with antibodies 3BNC117 and J033
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: 3BNC117 antibody heavy chain
    • Protein or peptide: 3BNC117 antibody light chain
    • Protein or peptide: J033 antibody heavy chain
    • Protein or peptide: J033 antibody light chain
    • Protein or peptide: Envelope glycoprotein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PHOSPHATE ION
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: A complex of HIV-1 Env with antibodies 3BNC117 and J033

SupramoleculeName: A complex of HIV-1 Env with antibodies 3BNC117 and J033
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: 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

UniProtKB: Envelope glycoprotein gp160

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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: J033 antibody heavy chain

MacromoleculeName: J033 antibody heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.47341 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QIHLQESGPG LVRPSETLSL TCDVSGGAFN DAYCSWIRRL PGGSLEWIGR ISGRDGYVES NPSLTGRVTM SIDATWKKIV LRLTSVTAS DTATYFCAGE TPEDDFGYYQ PYFKSWGQGL LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
QIHLQESGPG LVRPSETLSL TCDVSGGAFN DAYCSWIRRL PGGSLEWIGR ISGRDGYVES NPSLTGRVTM SIDATWKKIV LRLTSVTAS DTATYFCAGE TPEDDFGYYQ PYFKSWGQGL LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVEPKSC DK

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Macromolecule #5: J033 antibody light chain

MacromoleculeName: J033 antibody light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.267928 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQLIQSPSS VSASVGDRVT ITCRSTQAIG TDLAWYQATP GTAPKLLIYH SFARHEGVPS RFSAGGSGSE FSLTITGLQP EDFATFFCQ HYKRLPLTFG GGTKVEVKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQLIQSPSS VSASVGDRVT ITCRSTQAIG TDLAWYQATP GTAPKLLIYH SFARHEGVPS RFSAGGSGSE FSLTITGLQP EDFATFFCQ HYKRLPLTFG GGTKVEVKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH 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: 19.174828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAMIFG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QSNLPRAPEA QQHLLQLTVW GIKQLQARVL AVERYLEVQK FLGLWGCSG KIICCTAVPW NSTWSNKSFE QIWNNMTWIE WEREISNYTS QIYDILTESQ FQQDINEVDL LELDGSAPTK A KRRVVQRE KR

UniProtKB: Envelope glycoprotein gp160

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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: 40 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #16: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 16 / Number of copies: 3 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #17: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 17 / Number of copies: 2 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.10) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.08) / Number images used: 383584
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.08)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.08)
Final 3D classificationSoftware - Name: RELION (ver. 3.08)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7n28:
Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J033 in complex with HIV-1 Env

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