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Yorodumi- EMDB-36649: CNE55.664 trimer in complex with broadly neutralizing HIV antibod... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36649 | ||||||||||||
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Title | CNE55.664 trimer in complex with broadly neutralizing HIV antibody PGT145 | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | HIV / Envelope trimer / broadly neutralizing antibody / PGT145 / Cryo-EM / VIRAL PROTEIN | ||||||||||||
Biological species | Human immunodeficiency virus 1 / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.14 Å | ||||||||||||
Authors | Chatterjee A / Chen C / Lee K / Mangala Prasad V | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Npj Viruses / Year: 2023 Title: An HIV-1 broadly neutralizing antibody overcomes structural and dynamic variation through highly focused epitope targeting. Authors: Hodge EA / Chatterjee A / Chen C / Naika GS / Laohajaratsang M / Mangala Prasad V / Lee KK | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36649.map.gz | 45.3 MB | EMDB map data format | |
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Header (meta data) | emd-36649-v30.xml emd-36649.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36649_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_36649.png | 25.9 KB | ||
Filedesc metadata | emd-36649.cif.gz | 6.7 KB | ||
Others | emd_36649_half_map_1.map.gz emd_36649_half_map_2.map.gz | 40.5 MB 40.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36649 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36649 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_36649.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_36649_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36649_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CNE55.664 trimer in complex with broadly neutralizing HIV antibod...
Entire | Name: CNE55.664 trimer in complex with broadly neutralizing HIV antibody PGT145 |
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Components |
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-Supramolecule #1: CNE55.664 trimer in complex with broadly neutralizing HIV antibod...
Supramolecule | Name: CNE55.664 trimer in complex with broadly neutralizing HIV antibody PGT145 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
-Macromolecule #1: gp120 protein of HIV envelope trimer
Macromolecule | Name: gp120 protein of HIV envelope trimer / 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: 54.064277 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 SAITQACPKV 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 AMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG RRRRR R |
-Macromolecule #2: gp41 protein of HIV envelope trimer
Macromolecule | Name: gp41 protein of HIV envelope trimer / 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: PGT145 antibody fragment, heavy chain
Macromolecule | Name: PGT145 antibody fragment, heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 28.793164 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QASTMDWIWR ILFLVAAATS AHSQVQLVQS GAEVKKPGSS VKVSCKASGN SFSNHDVHWV RQATGQGLEW MGWMSHEGDK TGLAQKFQG RVTITRDSGA STVYMELRGL TADDTAIYYC LTGSKHRLRD YFLYNEYGPN YEEWGDYLAT LDVWGHGTAV T VSSASTKG ...String: QASTMDWIWR ILFLVAAATS AHSQVQLVQS GAEVKKPGSS VKVSCKASGN SFSNHDVHWV RQATGQGLEW MGWMSHEGDK TGLAQKFQG RVTITRDSGA STVYMELRGL TADDTAIYYC LTGSKHRLRD YFLYNEYGPN YEEWGDYLAT LDVWGHGTAV T VSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LG TQTYICN VNHKPSNTKV DKKVEPKSCD |
-Macromolecule #4: PGT145 antibody fragment, light chain
Macromolecule | Name: PGT145 antibody fragment, light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.95375 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVVITQSPLF LPVTPGEAAS LSCKCSHSLQ HSTGANYLAW YLQRPGQTPR LLIHLATHRA SGVPDRFSGS GSGTDFTLKI SRVESDDVG TYYCMQGLHS PWTFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String: EVVITQSPLF LPVTPGEAAS LSCKCSHSLQ HSTGANYLAW YLQRPGQTPR LLIHLATHRA SGVPDRFSGS GSGTDFTLKI SRVESDDVG TYYCMQGLHS PWTFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C |
-Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 20 / 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
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.75 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 43.89 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Rigid body fitting followed by real space refinement to improve map occupancy |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-8jtm: |