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- EMDB-21232: BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20E1 and PG... -
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Open data
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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 | ||||||||||||||||||
![]() | BG505 SOSIP.v5.2 in complex with Rhesus macaque Fab RM20E1 and PGT122 Fab | ||||||||||||||||||
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Function / homology | ![]() 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 / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.42 Å | ||||||||||||||||||
![]() | Cottrell CA / Ward AB | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 95.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.1 KB 25.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.7 KB | Display | ![]() |
Images | ![]() | 131.6 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Others | ![]() ![]() | 95.5 MB 95.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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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 |
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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: ![]() ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 53.268371 KDa |
Recombinant expression | Organism: ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 17.178549 KDa |
Recombinant expression | Organism: ![]() |
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: ![]() |
Molecular weight | Theoretical: 14.838731 KDa |
Recombinant expression | Organism: ![]() |
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: ![]() |
Molecular weight | Theoretical: 11.510612 KDa |
Recombinant expression | Organism: ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 13.878558 KDa |
Recombinant expression | Organism: ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 12.370759 KDa |
Recombinant expression | Organism: ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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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: ![]() |
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 |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | ![]() PDB-6vlr: |