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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | HIV-1 Env X18 UFO in complex with F6 Fab | |||||||||
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![]() | Antibody / HIV-1 / Env protein / Complex / VIRAL PROTEIN | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
![]() | Niu J / Xu YW / Yang B | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 43.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18 KB 18 KB | Display Display | ![]() |
Images | ![]() | 42.9 KB | ||
Others | ![]() ![]() | 77.8 MB 77.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 997 KB | Display | ![]() |
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Full document | ![]() | 996.6 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gpgMC ![]() 8gp5C ![]() 8gpiC ![]() 8gpjC ![]() 8gpkC C: citing same article ( M: atomic model generated by this map |
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Links
EMDB pages | ![]() ![]() |
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Map
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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
-Half map: #1
File | emd_34192_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34192_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : HIV-1 Env X18 UFO in complex with F6 Fab
Entire | Name: HIV-1 Env X18 UFO in complex with F6 Fab |
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Components |
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-Supramolecule #1: HIV-1 Env X18 UFO in complex with F6 Fab
Supramolecule | Name: HIV-1 Env X18 UFO in complex with F6 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() |
-Supramolecule #2: F6 Fab
Supramolecule | Name: F6 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
-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: ![]() ![]() |
-Macromolecule #1: F6 Fab heavy chain
Macromolecule | Name: F6 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.333791 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: F6 Fab light chain
Macromolecule | Name: F6 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.109902 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #3: HIV-1 Env X18 UFO
Macromolecule | Name: HIV-1 Env X18 UFO / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 69.513727 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 21 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 8 mg/mL |
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Buffer | pH: 7.5 / Details: 25 mM HEPES pH 7.5, 300 mM NaCl |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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 |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 350799 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |