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- EMDB-22295: Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV... -

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Basic information

Entry
Database: EMDB / ID: EMD-22295
TitleCryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV-1 Env BG505 DS-SOSIP.664
Map dataSharpened Map
Sample
  • Complex: Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV-1 Env BG505 DS-SOSIP
    • Complex: Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV-1 Env BG505 DS-SOSIP.664
      • Protein or peptide: Envelope glycoprotein gp160
      • Protein or peptide: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41
      • Protein or peptide: VRC01.23 Heavy Chain
      • Protein or peptide: VRC01.23 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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 / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsGorman J / Kwong PD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Other privateSF349247 United States
CitationJournal: Science / Year: 2021
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
DepositionJul 13, 2020-
Header (metadata) releaseOct 7, 2020-
Map releaseOct 7, 2020-
UpdateJan 20, 2021-
Current statusJan 20, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.55
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.55
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xrt
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22295.png

Downloads & links

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Map

FileDownload / File: emd_22295.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened Map
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.55 / Movie #1: 0.55
Minimum - Maximum-0.34115198 - 1.5054345
Average (Standard dev.)0.014455143 (±0.071347974)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 308.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z308.160308.160308.160
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ510510510
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.3411.5050.014

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Supplemental data

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Mask #1

Fileemd_22295_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened Map

Fileemd_22295_additional_1.map
AnnotationUnsharpened Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Density modified map

Fileemd_22295_additional_2.map
AnnotationDensity modified map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_22295_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_22295_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV...

EntireName: Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV-1 Env BG505 DS-SOSIP
Components
  • Complex: Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV-1 Env BG505 DS-SOSIP
    • Complex: Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV-1 Env BG505 DS-SOSIP.664
      • Protein or peptide: Envelope glycoprotein gp160
      • Protein or peptide: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41
      • Protein or peptide: VRC01.23 Heavy Chain
      • Protein or peptide: VRC01.23 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV...

SupramoleculeName: 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...

SupramoleculeName: 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
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.300348 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41

MacromoleculeName: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.146482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

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Macromolecule #3: VRC01.23 Heavy Chain

MacromoleculeName: VRC01.23 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 14.70429 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLRESGPG LVKPSETLVL TCAVSGGGDS FGFHYWNWIR QPPGKGLEWI GHIGGSSGST DFNPSLKSRV TISMDSSRNQ FSLRLKSVT AADTAVYFCA RKGEDFYEDD (TYS)GQYFTAGWF FDLWGPGTPI IISS

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Macromolecule #4: VRC01.23 Light Chain

MacromoleculeName: VRC01.23 Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.312331 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QFVLTQPPSV SGAPGQTVTI SCTGRSSNFG GHYVQWYQQL PGTAPRLVIF ENDRRPSGVS DRFSGSQSGA SASLTITGLQ SEDEADYYC QCYDSSVLFG RGTRLT

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 40 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.0 mg/mL
BufferpH: 7.4 / Component - Formula: PBS
GridModel: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.14)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.14) / Number images used: 21480

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Atomic model buiding 1

Initial modelPDB ID:

4tvp

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6xrt:
Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV-1 Env BG505 DS-SOSIP.664

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