+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25755 | |||||||||||||||
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Title | ApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | HIV / germline targeting vaccine / VIRAL PROTEIN / VIRAL 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 / virion membrane / structural molecule activity / identical protein binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Human immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey) / Mus musculus (house mouse) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.72 Å | |||||||||||||||
Authors | Berndsen ZT / Ward AB | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Immunity / Year: 2022 Title: Priming HIV Envelope V2 Apex-directed broadly neutralizing antibody responses with protein or mRNA immunogens Authors: Melzi E / Willis J / Ma K / Lin Y / Kratochvil S / Berndsen ZT / Nair U / Warner J / Steichen J / Pecetta S / Perez M / Kirsch K / Ward AB / Schief W / Batista FD | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25755.map.gz | 97.4 MB | EMDB map data format | |
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Header (meta data) | emd-25755-v30.xml emd-25755.xml | 20.3 KB 20.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25755_fsc.xml | 10.4 KB | Display | FSC data file |
Images | emd_25755.png | 74.4 KB | ||
Masks | emd_25755_msk_1.map | 103 MB | Mask map | |
Others | emd_25755_half_map_1.map.gz emd_25755_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25755 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25755 | HTTPS FTP |
-Validation report
Summary document | emd_25755_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_25755_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_25755_validation.xml.gz | 18 KB | Display | |
Data in CIF | emd_25755_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25755 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25755 | HTTPS FTP |
-Related structure data
Related structure data | 7t9bMC 7t9aC 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_25755.map.gz / Format: CCP4 / Size: 103 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: 1.15 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_25755_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_25755_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_25755_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HIV-1 Envelope ApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs
Entire | Name: HIV-1 Envelope ApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs |
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Components |
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-Supramolecule #1: HIV-1 Envelope ApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs
Supramolecule | Name: HIV-1 Envelope ApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
-Macromolecule #1: HIV-1 Envelope ApexGT5 gp120
Macromolecule | Name: HIV-1 Envelope ApexGT5 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: 53.196496 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNATTELRN KRQKVYSLFY RLDIVPMVDL WTNYRLINCN T SAITQACP ...String: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNATTELRN KRQKVYSLFY RLDIVPMVDL WTNYRLINCN T SAITQACP KVSFEPIPIH YCAPAGFAIL KCKDKKFNGT GPCPSVSTVQ CTHGIKPVVS TQLLLNGSLA EEEVIIRSEN IT NNAKNIL VQLNTPVQIN CTRPNNNTVK SIRIGPGQAF YYTGDIIGDI RQAHCNVSKA TWNETLGKVV KQLRKHFGNN TII RFAQSS GGDLEVTTHS FNCGGEFFYC NTSGLFNSTW ISNTSVQGSN STGSNDSITL PCRIKQIINM WQRIGQAMYA PPIQ GVIRC VSNITGLILT RDGGSTNSTT ETFRPGGGDM RDNWRSELYK YKVVKIEPLG VAPTRCKRRV VGRRRRRR |
-Macromolecule #2: HIV-1 Envelope ApexGT5 gp41
Macromolecule | Name: HIV-1 Envelope ApexGT5 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: 17.134324 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AVGIGAVSLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEP QQHLLKDTHW GIKQLQARVL AVEHYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD |
-Macromolecule #3: RM20A3 Fab Heavy Chain
Macromolecule | Name: RM20A3 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Molecular weight | Theoretical: 13.511111 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVETGGG LVQPGGSLKL SCRASGYTFS SFAMSWVRQA PGKGLEWVSL INDRGGLTFY VDSVKGRFTI SRDNSKNTLS LQMHSLRDG DTAVYYCATG GMSSALQSSK YYFDFWGQGA LVTVSS |
-Macromolecule #4: RM20A3 Fab Light Chain
Macromolecule | Name: RM20A3 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Molecular weight | Theoretical: 13.5088 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ALTQPPSVSG SPGQSVTISC TGTSSDIGSY NYVSWYQQHP GKAPKLMIYD VTQRPSGVSD RFSGSKSGNT ASLTISGLQA DDEADYYCS AYAGRQTFYI FGGGTRLTVL GQPKASPTVT LFPPSSEEL |
-Macromolecule #5: GT5-d42.16 Fab Heavy Chain
Macromolecule | Name: GT5-d42.16 Fab Heavy Chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 15.126627 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGGG LVKPGGSLRL SCTASGFTFS NAWMSWVRQA PGKGLEWVGR IKSKTEGGTT DYATPVKGRF TISRDDSKDT LFLQMNSLK TEDTAVYYCN TGVETYDFWS G(TYS)DDH(TYS)YDYY FRDVWGKGTT VTVSS |
-Macromolecule #6: GT5-d42.16 Fab Light Chain
Macromolecule | Name: GT5-d42.16 Fab Light Chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 11.605943 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPGT LSLSPGERAT LSCRASQIIS SIYFAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGSSFTFG PGTKVDIK |
-Macromolecule #13: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 13 / Number of copies: 41 / 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 |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |