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- EMDB-41459: Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with ant... -
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Open data
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Basic information
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Title | Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with antibody GPZ6-b.01 targeting the fusion peptide | |||||||||
![]() | Cryo-EM map of HIV-1 BG505 DS-SOSIP in complex with antibody GPZ6-b.01 | |||||||||
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![]() | HIV-1 Envelope / antibody / GPZ6-b.01 / SHIV / BG505 DS-SOSIP / neutralization / immunization / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | ![]() positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.52 Å | |||||||||
![]() | Zhou T / Morano NC / Roark RS / Kwong PD / Xu J | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with antibody GPZ6-b.01 targeting the fusion peptide Authors: Wang H | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 442.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22 KB 22 KB | Display Display | ![]() |
Images | ![]() | 95.2 KB | ||
Masks | ![]() | 909.2 MB | ![]() | |
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() ![]() ![]() | 859.1 MB 842.5 MB 842.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 774.9 KB | Display | ![]() |
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Full document | ![]() | 774.5 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8topMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Cryo-EM map of HIV-1 BG505 DS-SOSIP in complex with antibody GPZ6-b.01 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 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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Projections & Slices |
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Density Histograms |
-Additional map: Sharpened cryo-EM map of HIV-1 BG505 DS-SOSIP in...
File | emd_41459_additional_1.map | ||||||||||||
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Annotation | Sharpened cryo-EM map of HIV-1 BG505 DS-SOSIP in complex with antibody GPZ6-b.01 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryo-EM half map of HIV-1 BG505 DS-SOSIP in...
File | emd_41459_half_map_1.map | ||||||||||||
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Annotation | cryo-EM half map of HIV-1 BG505 DS-SOSIP in complex with antibody GPZ6-b.01 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryo-EM half map of HIV-1 BG505 DS-SOSIP in...
File | emd_41459_half_map_2.map | ||||||||||||
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Annotation | cryo-EM half map of HIV-1 BG505 DS-SOSIP in complex with antibody GPZ6-b.01 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Complex between HIV-1 Env BG505 DS-SOSIP and antibody GPZ6-b.01
Entire | Name: Complex between HIV-1 Env BG505 DS-SOSIP and antibody GPZ6-b.01 |
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Components |
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-Supramolecule #1: Complex between HIV-1 Env BG505 DS-SOSIP and antibody GPZ6-b.01
Supramolecule | Name: Complex between HIV-1 Env BG505 DS-SOSIP and antibody GPZ6-b.01 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 720 KDa |
-Macromolecule #1: HIV-1 BG505 DS-SOSIP gp120
Macromolecule | Name: HIV-1 BG505 DS-SOSIP gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 54.086324 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT SACTQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNILVQ FNTPVQINCT RPNNNTRKSI RIGPGQAFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ CMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG RRRRR R UniProtKB: Envelope glycoprotein gp160 |
-Macromolecule #2: HIV-1 BG505 DS-SOSIP glycoprotein gp41
Macromolecule | Name: HIV-1 BG505 DS-SOSIP glycoprotein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 17.146482 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD UniProtKB: Envelope glycoprotein gp160 |
-Macromolecule #3: Heavy chain of antibody GPZ6-b.01
Macromolecule | Name: Heavy chain of antibody GPZ6-b.01 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 25.294381 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QVQLQESGPG LVKPSETLSL TCAVYGSSIS GGYFYWHWIR QAPGKGLEWI GDVYFSGTTG YNPSLKRRVR ISADTSKNQF SLNLRSVTA ADTAVYFCAR DPRGGGWVPN RFDVWGAGVL VTVSSASTKG PSVFPLAPSS RSTSESTAAL GCLVKDYFPE P VTVSWNSG ...String: QVQLQESGPG LVKPSETLSL TCAVYGSSIS GGYFYWHWIR QAPGKGLEWI GDVYFSGTTG YNPSLKRRVR ISADTSKNQF SLNLRSVTA ADTAVYFCAR DPRGGGWVPN RFDVWGAGVL VTVSSASTKG PSVFPLAPSS RSTSESTAAL GCLVKDYFPE P VTVSWNSG SLTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYVCN VNHKPSNTKV DKRVEIKTCG GLEVLFQGP |
-Macromolecule #4: Light chain of antibody GPZ6-b.01
Macromolecule | Name: Light chain of antibody GPZ6-b.01 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.162631 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCRASQDIS SFLNWYQQKP GKAPKLLISS VNRLESGVPS RFSGSGSGTE FTLTVSSLQP EDFATYSCQ QCGSVPYTFG QGTTLEIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS ...String: DIQMTQSPSS LSASVGDRVT ITCRASQDIS SFLNWYQQKP GKAPKLLISS VNRLESGVPS RFSGSGSGTE FTLTVSSLQP EDFATYSCQ QCGSVPYTFG QGTTLEIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS KDNTYSLSST LTLSSTEYQS HKVYACEVTH QGLSSPVTKS FNRGEC |
-Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 82 / 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 | 3 mg/mL |
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Buffer | pH: 7.4 / Component - Concentration: 137.0 mM / Component - Name: PBS Details: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, and 1.8 mM KH2PO4 |
Vitrification | Cryogen name: ETHANE |
Details | Purified complex by FPLC and concentrated to final concentration. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 100.0 K |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 58.06 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 103000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 82.9 |
Output model | ![]() PDB-8top: |