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- EMDB-34193: HIV-1 Env X18 UFO in complex with 8ANC195 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-34193
TitleHIV-1 Env X18 UFO in complex with 8ANC195 Fab
Map data
Sample
  • Complex: HIV-1 Env X18 UFO in complex with 8ANC195 Fab
    • Complex: 8ANC195 Fab
      • Protein or peptide: 8ANC195 Fab heavy chain
      • Protein or peptide: 8ANC195 Fab light chain
    • Complex: HIV-1 Env X18 UFO
      • Protein or peptide: X18 UFO gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAntibody / HIV-1 / Env protein / Complex / VIRAL PROTEIN
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsNiu J / Xu YW / Yang B
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: Structures and immune recognition of Env trimers from two Asia prevalent HIV-1 CRFs.
Authors: Jun Niu / Qi Wang / Wenwen Zhao / Bing Meng / Youwei Xu / Xianfang Zhang / Yi Feng / Qilian Qi / Yanling Hao / Xuan Zhang / Ying Liu / Jiangchao Xiang / Yiming Shao / Bei Yang /
Abstract: Structure-guided immunofocusing HIV-1 vaccine design entails a comprehensive understanding of Envs from diverse HIV-1 subtypes, including circulating recombinant forms (CRFs). Here, we present the ...Structure-guided immunofocusing HIV-1 vaccine design entails a comprehensive understanding of Envs from diverse HIV-1 subtypes, including circulating recombinant forms (CRFs). Here, we present the cryo-EM structures of Envs from two Asia prevalent CRFs (CRF01_AE and CRF07_BC) at 3.0 and 3.5 Å. We compare the structures and glycosylation patterns of Envs from different subtypes and perform cross-clade statistical analyses to reveal the unique features of CRF01_AE V1 region, which are associated with the resistance to certain bNAbs. We also solve a 4.1 Å cryo-EM structure of CRF01_AE Env in complex with F6, the first bNAb from CRF01_AE-infected individuals. F6 recognizes a gp120-gp41 spanning epitope to allosterically destabilize the Env trimer apex and weaken inter-protomer packing, which in turn hinders the receptor binding and induces Env trimer disassembly, demonstrating a dual mechanism of neutralization. These findings broaden our understanding of CRF Envs and shed lights on immunofocusing HIV-1 vaccine design.
History
DepositionAug 26, 2022-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34193.png

Downloads & links

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Map

FileDownload / File: emd_34193.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.001712281 - 1.6277044
Average (Standard dev.)0.0017948856 (±0.029813578)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 296.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34193_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #1

Fileemd_34193_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_34193_half_map_2.map
Projections & Slices
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Sample components

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Entire : HIV-1 Env X18 UFO in complex with 8ANC195 Fab

EntireName: HIV-1 Env X18 UFO in complex with 8ANC195 Fab
Components
  • Complex: HIV-1 Env X18 UFO in complex with 8ANC195 Fab
    • Complex: 8ANC195 Fab
      • Protein or peptide: 8ANC195 Fab heavy chain
      • Protein or peptide: 8ANC195 Fab light chain
    • Complex: HIV-1 Env X18 UFO
      • Protein or peptide: X18 UFO gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 Env X18 UFO in complex with 8ANC195 Fab

SupramoleculeName: HIV-1 Env X18 UFO in complex with 8ANC195 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: 8ANC195 Fab

SupramoleculeName: 8ANC195 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: HIV-1 Env X18 UFO

SupramoleculeName: HIV-1 Env X18 UFO / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: 8ANC195 Fab heavy chain

MacromoleculeName: 8ANC195 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.923986 KDa
Recombinant expressionOrganism: Trichopalpus nigribasis (fry)
SequenceString: QIHLVQSGTE VKKPGSSVTV SCKAYGVNTF GLYAVNWVRQ APGQSLEYIG QIWRWKSSAS HHFRGRVLIS AVDLTGSSPP ISSLEIKDL TSDDTAVYFC TTTSTYDKWS GLHHDGVMAF SSWGQGTLIS VSAASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
QIHLVQSGTE VKKPGSSVTV SCKAYGVNTF GLYAVNWVRQ APGQSLEYIG QIWRWKSSAS HHFRGRVLIS AVDLTGSSPP ISSLEIKDL TSDDTAVYFC TTTSTYDKWS GLHHDGVMAF SSWGQGTLIS VSAASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSC

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Macromolecule #2: 8ANC195 Fab light chain

MacromoleculeName: 8ANC195 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.401984 KDa
Recombinant expressionOrganism: Trichopalpus nigribasis (fry)
SequenceString: DIQMTQSPST LSASIGDTVR ISCRASQSIT GNWVAWYQQR PGKAPRLLIY RGAALLGGVP SRFSGSAAGT DFTLTIGNLQ AEDFGTFYC QQYDTYPGTF GQGTKVEVKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPST LSASIGDTVR ISCRASQSIT GNWVAWYQQR PGKAPRLLIY RGAALLGGVP SRFSGSAAGT DFTLTIGNLQ AEDFGTFYC QQYDTYPGTF GQGTKVEVKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #3: X18 UFO gp41

MacromoleculeName: X18 UFO gp41 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 69.513727 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: NLWVTVYYGV PVWRDADTTL FCASDAKAHV PEAHNVWATH ACVPTDPNPQ EIPLENVTEN FNMWKNNMVE QMQEDVISLW DQSLKPCVK LTPLCVTLNC TKANLTHNTT NDKNGTGNIT DEVKIGNITD EVKNCTFNMT TEIRDKQQKV HALFYALDIV Q MKENGSEY ...String:
NLWVTVYYGV PVWRDADTTL FCASDAKAHV PEAHNVWATH ACVPTDPNPQ EIPLENVTEN FNMWKNNMVE QMQEDVISLW DQSLKPCVK LTPLCVTLNC TKANLTHNTT NDKNGTGNIT DEVKIGNITD EVKNCTFNMT TEIRDKQQKV HALFYALDIV Q MKENGSEY RLISCNTSVI KQACPKISFD PIPIHYCAPA GYAILKCNDK KFNGTGPCKN VSTVQCTHGI KPVVSTQLLL NG SLAEEEI IIRSENLTNN AKNIIVHLNK SVSISCTRPS NNTRTSIRIG PGQMFYRTGD IIGDIRKAYC ELNGTEWNET LNK VTEKLK EHFNKTIVFQ PPSGGDLETT MHHFNCRGEF FYCNTTKLFN TKNGTREEFN GTIILPCRIK QIVNMWQGVG QAMY APPIS GIINCTSNIT GIILTRDGGN GNTTDETFRP GGGNIKDNWR SELYKYKVVQ IEPLGIAPTR CKRRVVDGGG GSGGG GSAV GIGAMIFGFL GAAGSTMGAA SITLTVQARQ LLSGNPDWLP DMTVWGIKQL QARVLAVERY LKDQKFLGLW GCSGKI ICC TNVPWNSTWS NKSYEEIWNN MTWIEWEKEI SNYTNRIYDL LTESQNQQER NEKDLLELD

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 29 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5 / Details: 25 mM HEPES pH 7.5, 300 mM NaCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 22500
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 205630

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