+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34193 | |||||||||
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Title | HIV-1 Env X18 UFO in complex with 8ANC195 Fab | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Antibody / HIV-1 / Env protein / Complex / VIRAL PROTEIN | |||||||||
Biological species | Homo sapiens (human) / Human immunodeficiency virus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Niu J / Xu YW / Yang B | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34193.map.gz | 74.5 MB | EMDB map data format | |
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Header (meta data) | emd-34193-v30.xml emd-34193.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
Images | emd_34193.png | 34.8 KB | ||
Masks | emd_34193_msk_1.map | 83.7 MB | Mask map | |
Others | emd_34193_half_map_1.map.gz emd_34193_half_map_2.map.gz | 65.4 MB 65.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34193 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34193 | HTTPS FTP |
-Validation report
Summary document | emd_34193_validation.pdf.gz | 751.7 KB | Display | EMDB validaton report |
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Full document | emd_34193_full_validation.pdf.gz | 751.3 KB | Display | |
Data in XML | emd_34193_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | emd_34193_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34193 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34193 | HTTPS FTP |
-Related structure data
Related structure data | 8gpiMC 8gp5C 8gpgC 8gpjC 8gpkC C: citing same article (ref.) M: atomic model generated by this map |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34193.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34193_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34193_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34193_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HIV-1 Env X18 UFO in complex with 8ANC195 Fab
Entire | Name: HIV-1 Env X18 UFO in complex with 8ANC195 Fab |
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Components |
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-Supramolecule #1: HIV-1 Env X18 UFO in complex with 8ANC195 Fab
Supramolecule | Name: HIV-1 Env X18 UFO in complex with 8ANC195 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #2: 8ANC195 Fab
Supramolecule | Name: 8ANC195 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: HIV-1 Env X18 UFO
Supramolecule | Name: HIV-1 Env X18 UFO / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
-Macromolecule #1: 8ANC195 Fab heavy chain
Macromolecule | Name: 8ANC195 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.923986 KDa |
Recombinant expression | Organism: Trichopalpus nigribasis (fry) |
Sequence | String: 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 |
-Macromolecule #2: 8ANC195 Fab light chain
Macromolecule | Name: 8ANC195 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.401984 KDa |
Recombinant expression | Organism: Trichopalpus nigribasis (fry) |
Sequence | String: 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 |
-Macromolecule #3: X18 UFO gp41
Macromolecule | Name: X18 UFO gp41 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 69.513727 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: 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 |
-Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 29 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 / Details: 25 mM HEPES pH 7.5, 300 mM NaCl |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 205630 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |