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Yorodumi- EMDB-22104: Cryo-EM reconstruction of HIV-1 Env BG505 SOSIP.664 in complex wi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22104 | ||||||||||||
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Title | Cryo-EM reconstruction of HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 11B fragment antigen binding | ||||||||||||
Map data | Sharpened map | ||||||||||||
Sample |
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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 / Oryctolagus cuniculus (rabbit) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.38 Å | ||||||||||||
Authors | Ozorowski G / Cottrell CA / Ward AB | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: To Be Published Title: Limited breadth of anti-HIV Env glycan hole antibodies is further hindered by strain-specific peptide interactions Authors: Ozorowski G / Cottrell CA / de Val N / Scaringi N / Polveroni TM / Ward AB | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22104.map.gz | 85.9 MB | EMDB map data format | |
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Header (meta data) | emd-22104-v30.xml emd-22104.xml | 24.1 KB 24.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22104_fsc.xml | 10.4 KB | Display | FSC data file |
Images | emd_22104.png | 233.9 KB | ||
Masks | emd_22104_msk_1.map | 91.1 MB | Mask map | |
Others | emd_22104_half_map_1.map.gz emd_22104_half_map_2.map.gz | 84.5 MB 84.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22104 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22104 | HTTPS FTP |
-Validation report
Summary document | emd_22104_validation.pdf.gz | 802.9 KB | Display | EMDB validaton report |
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Full document | emd_22104_full_validation.pdf.gz | 802.4 KB | Display | |
Data in XML | emd_22104_validation.xml.gz | 18 KB | Display | |
Data in CIF | emd_22104_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22104 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22104 | HTTPS FTP |
-Related structure data
Related structure data | 6x98MC 6x96C 6x97C 7ra7C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22104.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_22104_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_22104_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_22104_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antib...
Entire | Name: HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 11B fragment antigen binding |
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Components |
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-Supramolecule #1: HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antib...
Supramolecule | Name: HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 11B fragment antigen binding type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Molecular weight | Theoretical: 570 KDa |
-Supramolecule #2: HIV-1 Env BG505 SOSIP.664
Supramolecule | Name: HIV-1 Env BG505 SOSIP.664 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293F |
-Supramolecule #3: rabbit monoclonal antibody 11B fragment antigen
Supramolecule | Name: rabbit monoclonal antibody 11B fragment antigen / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 Details: Fab fragment generated by proteolytic cleavage of IgG antibody |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293F |
-Macromolecule #1: BG505 HIV-1 Env gp120
Macromolecule | Name: BG505 HIV-1 Env gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 57.945977 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKKQK ...String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKKQK VYSLFYRLDV VQINENQGNR SNNSNKEYRL INCNTSAITQ ACPKVSFEPI PIHYCAPAGF AILKCKDKKF NG TGPCPSV STVQCTHGIK PVVSTQLLLN GSLAEEEVMI RSENITNNAK NILVQFNTPV QINCTRPNNN TRKSIRIGPG QAF YATGDI IGDIRQAHCN VSKATWNETL GKVVKQLRKH FGNNTIIRFA NSSGGDLEVT THSFNCGGEF FYCNTSGLFN STWI SNTSV QGSNSTGSND SITLPCRIKQ IINMWQRIGQ AMYAPPIQGV IRCVSNITGL ILTRDGGSTN STTETFRPGG GDMRD NWRS ELYKYKVVKI EPLGVAPTRC KRRVVGRRRR RR |
-Macromolecule #2: BG505 HIV-1 Env gp41
Macromolecule | Name: BG505 HIV-1 Env gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 17.146482 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD |
-Macromolecule #3: monoclonal antibody 11B kappa chain
Macromolecule | Name: monoclonal antibody 11B kappa chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 25.161066 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MYRMQLLSCI ALSLALVTNS DIVMTQTPSS VSAAVGGTVT INCQASESIY SGLAWYQQKP GQPPKLLIYR ASTLTSGVSS RFKGSGSGA RFTLTINDLE CADAATYYCQ SCYDTTIGTY GSWAFGGGTE VVVKGDPVAP SVLIFPPAAD QVATGTVTIV C VANKYFPD ...String: MYRMQLLSCI ALSLALVTNS DIVMTQTPSS VSAAVGGTVT INCQASESIY SGLAWYQQKP GQPPKLLIYR ASTLTSGVSS RFKGSGSGA RFTLTINDLE CADAATYYCQ SCYDTTIGTY GSWAFGGGTE VVVKGDPVAP SVLIFPPAAD QVATGTVTIV C VANKYFPD VTVTWEVDGT TQTTGIENSK TPQNSADCTY NLSSTLTLTS TQYNSHKEYT CKVTQGTTSV VQSFNRGDC |
-Macromolecule #4: monoclonal antibody 11B fragment antigen binding heavy chain
Macromolecule | Name: monoclonal antibody 11B fragment antigen binding heavy chain type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 25.312748 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MYRMQLLSCI ALSLALVTNS QLVESGGGLV KPGGTLTLTC KASGFSLSDS YWMCWVRQAP GKGLEWVACV FTGNGKAYYA RWVEGRFTI SRSTSLNTAT LQMTSLTAAD TATYFCARGD YDDPLDGVAT LWGPGTLVTV SSGQPKAPSV FPLAPCCGDT P SSTVTLGC ...String: MYRMQLLSCI ALSLALVTNS QLVESGGGLV KPGGTLTLTC KASGFSLSDS YWMCWVRQAP GKGLEWVACV FTGNGKAYYA RWVEGRFTI SRSTSLNTAT LQMTSLTAAD TATYFCARGD YDDPLDGVAT LWGPGTLVTV SSGQPKAPSV FPLAPCCGDT P SSTVTLGC LVKGYLPEPV TVTWNSGTLT NGVRTFPSVR QSSGLYSLSS VVSVTSSSQP VTCNVAHPAT NTKVDKTVAP ST C |
-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: 36 / 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 | 6 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
Details: Detergent (DDM) added shortly prior to freezing | ||||||||||||
Grid | Model: C-flat-2/2 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1518 / Average exposure time: 8.0 sec. / Average electron dose: 65.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |