+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25754 | |||||||||||||||
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Title | ApexGT2 in complex with GT2-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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / 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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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: 3.54 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_25754.map.gz | 154.6 MB | EMDB map data format | |
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Header (meta data) | emd-25754-v30.xml emd-25754.xml | 20.3 KB 20.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25754_fsc.xml | 12.1 KB | Display | FSC data file |
Images | emd_25754.png | 91.5 KB | ||
Masks | emd_25754_msk_1.map | 163.6 MB | Mask map | |
Others | emd_25754_half_map_1.map.gz emd_25754_half_map_2.map.gz | 151.8 MB 151.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25754 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25754 | HTTPS FTP |
-Related structure data
Related structure data | 7t9aMC 7t9bC 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_25754.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_25754_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_25754_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_25754_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HIV-1 Envelope ApexGT2 in complex with PCT64_LMCA.HL_GT2_d42.16 F...
Entire | Name: HIV-1 Envelope ApexGT2 in complex with PCT64_LMCA.HL_GT2_d42.16 Fab and RM20A3 Fab |
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Components |
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-Supramolecule #1: HIV-1 Envelope ApexGT2 in complex with PCT64_LMCA.HL_GT2_d42.16 F...
Supramolecule | Name: HIV-1 Envelope ApexGT2 in complex with PCT64_LMCA.HL_GT2_d42.16 Fab and RM20A3 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
-Macromolecule #1: HIV Envelope ApexGT2 gp120
Macromolecule | Name: HIV Envelope ApexGT2 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: 53.070258 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNATTELRN KRQKVYSLFY RLDIVPMGEN STNYRLINCN T SAITQACP ...String: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNATTELRN KRQKVYSLFY RLDIVPMGEN STNYRLINCN 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 Envelope ApexGT2 gp41
Macromolecule | Name: HIV Envelope ApexGT2 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: 18.250541 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AVGIGAVSLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEP QQHLLKDTHW GIKQLQARVL AVEHYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALDGTKHHH H HH |
-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: GT2-d42.16 Fab Heavy Chain
Macromolecule | Name: GT2-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: 15.138617 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGGD LVKPGGSLRL SCAASGFTFS DAWMSWVRQA PGKGLEWVGR IKSNIDGGTT DYVAPVKGRF TISRDDSKNT LYLQMNSLK TEDTAVYYCT TGVETYDFWS G(TYS)DDH(TYS)YDYY FRDVWGKGTT VTVSS |
-Macromolecule #6: GT2-d42.16 Fab Light Chain
Macromolecule | Name: GT2-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: 11.479702 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPGT LSLSAGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGSSFTFG PGTKVDIK |
-Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 42 / 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 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 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |