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- EMDB-34192: HIV-1 Env X18 UFO in complex with F6 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-34192
TitleHIV-1 Env X18 UFO in complex with F6 Fab
Map data
Sample
  • Complex: HIV-1 Env X18 UFO in complex with F6 Fab
    • Complex: F6 Fab
      • Protein or peptide: F6 Fab heavy chain
      • Protein or peptide: F6 Fab light chain
    • Complex: HIV-1 Env X18 UFO
      • Protein or peptide: HIV-1 Env X18 UFO
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAntibody / HIV-1 / Env protein / Complex / VIRAL PROTEIN
Biological specieshuman (human) / Homo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 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-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34192.png

Downloads & links

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Map

FileDownload / File: emd_34192.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 280 pix.
= 296.8 Å		1.06 Å/pix.
x 280 pix.
= 296.8 Å		1.06 Å/pix.
x 280 pix.
= 296.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.60245806 - 0.9197249
Average (Standard dev.)0.0009008441 (±0.02380401)
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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Half map: #1

Fileemd_34192_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_34192_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 : HIV-1 Env X18 UFO in complex with F6 Fab

EntireName: HIV-1 Env X18 UFO in complex with F6 Fab
Components
  • Complex: HIV-1 Env X18 UFO in complex with F6 Fab
    • Complex: F6 Fab
      • Protein or peptide: F6 Fab heavy chain
      • Protein or peptide: F6 Fab light chain
    • Complex: HIV-1 Env X18 UFO
      • Protein or peptide: HIV-1 Env X18 UFO
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 Env X18 UFO in complex with F6 Fab

SupramoleculeName: HIV-1 Env X18 UFO in complex with F6 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: human (human)

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Supramolecule #2: F6 Fab

SupramoleculeName: F6 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: F6 Fab heavy chain

MacromoleculeName: F6 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.333791 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLQQWGTG LLKPSETLSL TCAVYGVSLR GYYWTWIRQS PKKGLEWIGE IDEIGRTKYS QSLRSRATLS IDTSKKQFSL RLTSVTAAD MATYYCARWR LMMVDEVTRH GMDVWSQGTM VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
QVQLQQWGTG LLKPSETLSL TCAVYGVSLR GYYWTWIRQS PKKGLEWIGE IDEIGRTKYS QSLRSRATLS IDTSKKQFSL RLTSVTAAD MATYYCARWR LMMVDEVTRH GMDVWSQGTM VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSCD KTHT

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Macromolecule #2: F6 Fab light chain

MacromoleculeName: F6 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.109902 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIVMTQSPLS LSVAPGEAAS ISCRSTQSLL NRNGDNYLEW YLRRPGRSPQ LLIYLGSERA LGVPDRFSGS GSGRDFTLKI SRVEAQDVG TYYCLQTRQG AFTFGQGTKL EIKRTVAAPS VFIFPPSDSQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
DIVMTQSPLS LSVAPGEAAS ISCRSTQSLL NRNGDNYLEW YLRRPGRSPQ LLIYLGSERA LGVPDRFSGS GSGRDFTLKI SRVEAQDVG TYYCLQTRQG AFTFGQGTKL EIKRTVAAPS VFIFPPSDSQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE CG

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Macromolecule #3: HIV-1 Env X18 UFO

MacromoleculeName: HIV-1 Env X18 UFO / type: protein_or_peptide / ID: 3 / Number of copies: 3 / 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 #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 21 / 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

Concentration8 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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 22500
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 350799
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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