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Yorodumi- EMDB-21232: BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20E1 and PG... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21232 | ||||||||||||||||||
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Title | BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20E1 and PGT122 Fab | ||||||||||||||||||
Map data | BG505 SOSIP.v5.2 in complex with Rhesus macaque Fab RM20E1 and PGT122 Fab | ||||||||||||||||||
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 / Homo sapiens (human) / Macaca mulatta (Rhesus monkey) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.42 Å | ||||||||||||||||||
Authors | Cottrell CA / Ward AB | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: PLoS Pathog / Year: 2020 Title: Mapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates. Authors: Christopher A Cottrell / Jelle van Schooten / Charles A Bowman / Meng Yuan / David Oyen / Mia Shin / Robert Morpurgo / Patricia van der Woude / Mariëlle van Breemen / Jonathan L Torres / ...Authors: Christopher A Cottrell / Jelle van Schooten / Charles A Bowman / Meng Yuan / David Oyen / Mia Shin / Robert Morpurgo / Patricia van der Woude / Mariëlle van Breemen / Jonathan L Torres / Raj Patel / Justin Gross / Leigh M Sewall / Jeffrey Copps / Gabriel Ozorowski / Bartek Nogal / Devin Sok / Eva G Rakasz / Celia Labranche / Vladimir Vigdorovich / Scott Christley / Diane G Carnathan / D Noah Sather / David Montefiori / Guido Silvestri / Dennis R Burton / John P Moore / Ian A Wilson / Rogier W Sanders / Andrew B Ward / Marit J van Gils / Abstract: The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown ...The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown promise as vaccine candidates as they can induce potent autologous neutralizing responses in rabbits and non-human primates. In this study, monoclonal antibodies were isolated and characterized from rhesus macaques immunized with the BG505 SOSIP.664 trimer to better understand vaccine-induced antibody responses. Our studies reveal a diverse landscape of antibodies recognizing immunodominant strain-specific epitopes and non-neutralizing neo-epitopes. Additionally, we isolated a subset of mAbs against an epitope cluster at the gp120-gp41 interface that recognize the highly conserved fusion peptide and the glycan at position 88 and have characteristics akin to several human-derived broadly neutralizing antibodies. #1: Journal: Biorxiv / Year: 2020 Title: Mapping the immunogenic landscape of native HIV-1 envelope trimers in non-human primates Authors: Cottrell CA / van Schooten J / Bowman CA / Yuan M / Oyen D / Shin M / Morpurgo R / van der Woude P / van Breemen M / Torres JL / Patel R / Gross J / Sewall LM / Copps J / Ozorowski G / Sok D ...Authors: Cottrell CA / van Schooten J / Bowman CA / Yuan M / Oyen D / Shin M / Morpurgo R / van der Woude P / van Breemen M / Torres JL / Patel R / Gross J / Sewall LM / Copps J / Ozorowski G / Sok D / Rakasz EG / Labranche C / Vigdorovich V / Christley S / Sather DN / Montefiori D / Moore JP / Burton DR / Wilson IA / Sanders RW / Ward AB / van Gils MJ | ||||||||||||||||||
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_21232.map.gz | 95.8 MB | EMDB map data format | |
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Header (meta data) | emd-21232-v30.xml emd-21232.xml | 25.1 KB 25.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21232_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_21232.png | 131.6 KB | ||
Masks | emd_21232_msk_1.map | 103 MB | Mask map | |
Others | emd_21232_half_map_1.map.gz emd_21232_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21232 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21232 | HTTPS FTP |
-Validation report
Summary document | emd_21232_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_21232_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_21232_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | emd_21232_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21232 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21232 | HTTPS FTP |
-Related structure data
Related structure data | 6vlrMC 6vn0C 6vo1C 6vorC 6vosC 6vsrC M: atomic model generated by this map C: citing same article (ref.) |
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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_21232.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | BG505 SOSIP.v5.2 in complex with Rhesus macaque Fab RM20E1 and PGT122 Fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 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_21232_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: BG505 SOSIP.v5.2 in complex with Rhesus macaque Fab...
File | emd_21232_half_map_1.map | ||||||||||||
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Annotation | BG505 SOSIP.v5.2 in complex with Rhesus macaque Fab RM20E1 and PGT122 Fab | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: BG505 SOSIP.v5.2 in complex with Rhesus macaque Fab...
File | emd_21232_half_map_2.map | ||||||||||||
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Annotation | BG505 SOSIP.v5.2 in complex with Rhesus macaque Fab RM20E1 and PGT122 Fab | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20E1
Entire | Name: BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20E1 |
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Components |
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-Supramolecule #1: BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20E1
Supramolecule | Name: BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20E1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
-Macromolecule #1: Envelope glycoprotein gp120
Macromolecule | Name: Envelope glycoprotein 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: 53.268371 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETKKHNVWA THCCVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETKKHNVWA THCCVPTDPN 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 RIGPGQWFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ AMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG |
-Macromolecule #2: BG505 SOSIPv5.2 gp41
Macromolecule | Name: BG505 SOSIPv5.2 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: 17.178549 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEC QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD |
-Macromolecule #3: PGT122 Fab Heavy Chain
Macromolecule | Name: PGT122 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: 14.838731 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVHLQESGPG LVKPSETLSL TCNVSGTLVR DNYWSWIRQP LGKQPEWIGY VHDSGDTNYN PSLKSRVHLS LDKSKNLVSL RLTGVTAAD SAIYYCATTK HGRRIYGVVA FKEWFTYFYM DVWGKGTSVT VSS |
-Macromolecule #4: PGT122 Fab Light Chain
Macromolecule | Name: PGT122 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: 11.510612 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: TFVSVAPGQT ARITCGEESL GSRSVIWYQQ RPGQAPSLII YNNNDRPSGI PDRFSGSPGS TFGTTATLTI TSVEAGDEAD YYCHIWDSR RPTNWVFGEG TTLIVLS |
-Macromolecule #5: RM20E1 Fab Heavy Chain
Macromolecule | Name: RM20E1 Fab Heavy Chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Molecular weight | Theoretical: 13.878558 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVQSEAE VKRPGESLKI SCQTSGYNFP NYWITWVRQM PGKGLEWMGT IDPRDSDTKY SPSFQGQVTI SADKSINTAY LQWTSLRAS DSATYYCVMW VYILTTGNIW VDVWGPGVLV TVSS |
-Macromolecule #6: RM20E1 Fab Kappa Chain
Macromolecule | Name: RM20E1 Fab Kappa Chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Molecular weight | Theoretical: 12.370759 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DVVMTQSPLS LPITPGQPAS ISCRSSQSLV HNNGNTYLTW YQQRPGQPPR RLIYQVSNRD SGVPDRFIGS GAGTDFTLKI SRVESEDVG IYYCGQITDF PYSFGQGTKV DIK |
-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: 24 / 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 / Instrument: FEI VITROBOT MARK IV |
-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: 51.3 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | PDB-6vlr: |