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Yorodumi- EMDB-41461: Cryo-EM structure of BG505 Env mutant A517E in complex with antib... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41461 | |||||||||
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Title | Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab | |||||||||
Map data | ||||||||||
Sample |
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Keywords | complex / viral antigen / antibody / VIRAL PROTEIN / VIRAL PROTEIN-ANTIVIRAL PROTEIN / IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information 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 | Human immunodeficiency virus 1 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
Authors | Wang S / Kwong PD | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab Authors: Wang S / Kwong PD | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41461.map.gz | 172.2 MB | EMDB map data format | |
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Header (meta data) | emd-41461-v30.xml emd-41461.xml | 20 KB 20 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41461_fsc.xml | 14.7 KB | Display | FSC data file |
Images | emd_41461.png | 73.7 KB | ||
Filedesc metadata | emd-41461.cif.gz | 6.9 KB | ||
Others | emd_41461_half_map_1.map.gz emd_41461_half_map_2.map.gz | 318.2 MB 318.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41461 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41461 | HTTPS FTP |
-Validation report
Summary document | emd_41461_validation.pdf.gz | 725.5 KB | Display | EMDB validaton report |
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Full document | emd_41461_full_validation.pdf.gz | 725.1 KB | Display | |
Data in XML | emd_41461_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | emd_41461_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41461 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41461 | HTTPS FTP |
-Related structure data
Related structure data | 8toxMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41461.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
-Half map: #2
File | emd_41461_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41461_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HIV-1 Env trimer complexed with antibody Fab
Entire | Name: HIV-1 Env trimer complexed with antibody Fab |
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Components |
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-Supramolecule #1: HIV-1 Env trimer complexed with antibody Fab
Supramolecule | Name: HIV-1 Env trimer complexed with antibody Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 Details: gp41 and gp120 expressed as a single polypeptide, post translationally cleaved; antibody expressed and purified separately; purified Env trimer and Fab were mixed to make complex |
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Source (natural) | Organism: Human immunodeficiency virus 1 / Strain: BG505 |
-Supramolecule #2: antibody Fab
Supramolecule | Name: antibody Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Envelope glycoprotein gp41
Macromolecule | Name: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 / Strain: BG505 |
Molecular weight | Theoretical: 17.134404 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AVGIGEVFLG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QSNLLRAPEA QQHLLKLGVW GFKQLQARVL AVERYLEVQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEIGNYTQ IIYGLLEESQ FQQEINEQDL LALD UniProtKB: Envelope glycoprotein gp160 |
-Macromolecule #2: Envelope glycoprotein gp120
Macromolecule | Name: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 / Strain: BG505 |
Molecular weight | Theoretical: 53.262453 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 SACTQICPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CKNVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNIIVQ FNTPVQINCT RPNNMTRKSI RIGPGQAFYA LGDIIGDIRQ PHCTVSKATW NETLGKVVKQ LRK HFGNNT IIFFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RVGQ CMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG UniProtKB: Envelope glycoprotein gp160 |
-Macromolecule #3: antibody ACS202 Fab heavy chain
Macromolecule | Name: antibody ACS202 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 25.295486 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVESGGG VVQPGGSLRL SCAASGFAFK DFGMHWVRQA PGKGLEWVAV IGGGHGQHQS YSESVKGRFA ITRDNEKNKL YLHMDRLRT EDTAVYYCAK DRLGRPWNIG GRLVYYYYGM DVWGQGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String: QVQLVESGGG VVQPGGSLRL SCAASGFAFK DFGMHWVRQA PGKGLEWVAV IGGGHGQHQS YSESVKGRFA ITRDNEKNKL YLHMDRLRT EDTAVYYCAK DRLGRPWNIG GRLVYYYYGM DVWGQGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCD |
-Macromolecule #4: antibody ACS202 Fab light chain
Macromolecule | Name: antibody ACS202 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.470197 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AIRMTQSPSS LSASVGDRVT ITCQASQDIK KSLNWYRQKP GKAPELLIHD ASILQTGVPS AFTASGSGTH FSFVINKLQP EDVGTYFCQ EYENLQFTFG PGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: AIRMTQSPSS LSASVGDRVT ITCQASQDIK KSLNWYRQKP GKAPELLIHD ASILQTGVPS AFTASGSGTH FSFVINKLQP EDVGTYFCQ EYENLQFTFG PGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC |
-Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 12 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #10: water
Macromolecule | Name: water / type: ligand / ID: 10 / Number of copies: 369 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.4 / Details: PBS with 0.1 mM DTT |
Grid | Model: Quantifoil R2/2 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 54.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8tox: |