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- EMDB-22295: Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22295 | |||||||||
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Title | Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV-1 Env BG505 DS-SOSIP.664 | |||||||||
![]() | Sharpened Map | |||||||||
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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 / apoptotic process / 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: 3.9 Å | |||||||||
![]() | Gorman J / Kwong PD | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Recapitulation of HIV-1 Env-antibody coevolution in macaques leading to neutralization breadth. Authors: Ryan S Roark / Hui Li / Wilton B Williams / Hema Chug / Rosemarie D Mason / Jason Gorman / Shuyi Wang / Fang-Hua Lee / Juliette Rando / Mattia Bonsignori / Kwan-Ki Hwang / Kevin O Saunders / ...Authors: Ryan S Roark / Hui Li / Wilton B Williams / Hema Chug / Rosemarie D Mason / Jason Gorman / Shuyi Wang / Fang-Hua Lee / Juliette Rando / Mattia Bonsignori / Kwan-Ki Hwang / Kevin O Saunders / Kevin Wiehe / M Anthony Moody / Peter T Hraber / Kshitij Wagh / Elena E Giorgi / Ronnie M Russell / Frederic Bibollet-Ruche / Weimin Liu / Jesse Connell / Andrew G Smith / Julia DeVoto / Alexander I Murphy / Jessica Smith / Wenge Ding / Chengyan Zhao / Neha Chohan / Maho Okumura / Christina Rosario / Yu Ding / Emily Lindemuth / Anya M Bauer / Katharine J Bar / David Ambrozak / Cara W Chao / Gwo-Yu Chuang / Hui Geng / Bob C Lin / Mark K Louder / Richard Nguyen / Baoshan Zhang / Mark G Lewis / Donald D Raymond / Nicole A Doria-Rose / Chaim A Schramm / Daniel C Douek / Mario Roederer / Thomas B Kepler / Garnett Kelsoe / John R Mascola / Peter D Kwong / Bette T Korber / Stephen C Harrison / Barton F Haynes / Beatrice H Hahn / George M Shaw / ![]() Abstract: Neutralizing antibodies elicited by HIV-1 coevolve with viral envelope proteins (Env) in distinctive patterns, in some cases acquiring substantial breadth. We report that primary HIV-1 envelope ...Neutralizing antibodies elicited by HIV-1 coevolve with viral envelope proteins (Env) in distinctive patterns, in some cases acquiring substantial breadth. We report that primary HIV-1 envelope proteins-when expressed by simian-human immunodeficiency viruses in rhesus macaques-elicited patterns of Env-antibody coevolution very similar to those in humans, including conserved immunogenetic, structural, and chemical solutions to epitope recognition and precise Env-amino acid substitutions, insertions, and deletions leading to virus persistence. The structure of one rhesus antibody, capable of neutralizing 49% of a 208-strain panel, revealed a V2 apex mode of recognition like that of human broadly neutralizing antibodies (bNAbs) PGT145 and PCT64-35S. Another rhesus antibody bound the CD4 binding site by CD4 mimicry, mirroring human bNAbs 8ANC131, CH235, and VRC01. Virus-antibody coevolution in macaques can thus recapitulate developmental features of human bNAbs, thereby guiding HIV-1 immunogen design. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 85.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 28.2 KB 28.2 KB | Display Display | ![]() |
Images | ![]() | 131.7 KB | ||
Masks | ![]() | 91.1 MB | ![]() | |
Others | ![]() ![]() ![]() ![]() | 24.5 MB 8.5 MB 84.5 MB 84.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xrtMC ![]() 6xcjC 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 | Sharpened Map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 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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-Additional map: Unsharpened Map
File | emd_22295_additional_1.map | ||||||||||||
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Annotation | Unsharpened Map | ||||||||||||
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-Additional map: Density modified map
File | emd_22295_additional_2.map | ||||||||||||
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Annotation | Density modified map | ||||||||||||
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Density Histograms |
-Half map: Half map A
File | emd_22295_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
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Density Histograms |
-Half map: Half map B
File | emd_22295_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV...
Entire | Name: Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV-1 Env BG505 DS-SOSIP |
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Components |
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-Supramolecule #1: Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV...
Supramolecule | Name: Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV-1 Env BG505 DS-SOSIP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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-Supramolecule #2: Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV...
Supramolecule | Name: Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV-1 Env BG505 DS-SOSIP.664 type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Macromolecule #1: Envelope glycoprotein gp160
Macromolecule | Name: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 53.300348 KDa |
Recombinant expression | Organism: ![]() |
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 SACTQACPKV 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 CMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG R |
-Macromolecule #2: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41
Macromolecule | Name: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 17.146482 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD |
-Macromolecule #3: VRC01.23 Heavy Chain
Macromolecule | Name: VRC01.23 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 14.70429 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QVQLRESGPG LVKPSETLVL TCAVSGGGDS FGFHYWNWIR QPPGKGLEWI GHIGGSSGST DFNPSLKSRV TISMDSSRNQ FSLRLKSVT AADTAVYFCA RKGEDFYEDD (TYS)GQYFTAGWF FDLWGPGTPI IISS |
-Macromolecule #4: VRC01.23 Light Chain
Macromolecule | Name: VRC01.23 Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.312331 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QFVLTQPPSV SGAPGQTVTI SCTGRSSNFG GHYVQWYQQL PGTAPRLVIF ENDRRPSGVS DRFSGSQSGA SASLTITGLQ SEDEADYYC QCYDSSVLFG RGTRLT |
-Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 40 / 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
Concentration | 2.0 mg/mL |
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Buffer | pH: 7.4 / Component - Formula: PBS |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1945 / Average exposure time: 10.0 sec. / Average electron dose: 71.06 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |