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- EMDB-34190: Structure of X18 UFO protomer in complex with F6 Fab VHVL domain -
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Open data
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Basic information
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Title | Structure of X18 UFO protomer in complex with F6 Fab VHVL domain | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | 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 | ![]() | 43.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.9 KB 16.9 KB | Display Display | ![]() |
Images | ![]() | 37.5 KB | ||
Masks | ![]() | 83.7 MB | ![]() | |
Others | ![]() ![]() | 77.8 MB 77.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gp5MC ![]() 8gpgC ![]() 8gpiC ![]() 8gpjC ![]() 8gpkC M: atomic model generated by this map C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | map | ||||||||||||||||||||
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
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-Half map: half A
File | emd_34190_half_map_1.map | ||||||||||||
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Annotation | half_A | ||||||||||||
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-Half map: half B
File | emd_34190_half_map_2.map | ||||||||||||
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Annotation | half_B | ||||||||||||
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Density Histograms |
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Sample components
-Entire : X18 UFO protomer in complex with F6 VHVL domain
Entire | Name: X18 UFO protomer in complex with F6 VHVL domain |
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Components |
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-Supramolecule #1: X18 UFO protomer in complex with F6 VHVL domain
Supramolecule | Name: X18 UFO protomer in complex with F6 VHVL domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: F6 Fab VH domain
Macromolecule | Name: F6 Fab VH domain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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 VL domain
Macromolecule | Name: F6 Fab VL domain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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: X18 UFO Env protomer
Macromolecule | Name: X18 UFO Env protomer / type: protein_or_peptide / ID: 3 / Number of copies: 1 / 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: 6 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | ![]() |
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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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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film 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 model | Type of model: OTHER |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1052397 |