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- EMDB-21372: Cryo-EM structure of stabilized HIV-1 Env trimer CAP256.wk34.c80 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-21372
TitleCryo-EM structure of stabilized HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2
Map dataSharpened map
Sample
  • Complex: HIV-1 Env trimer CAP256 SU.wk34.80 SOSIP.RnS2
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
  • 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 / 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
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsGorman J / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
CitationJournal: Cell Rep / Year: 2020
Title: Structure of Super-Potent Antibody CAP256-VRC26.25 in Complex with HIV-1 Envelope Reveals a Combined Mode of Trimer-Apex Recognition.
Authors: Jason Gorman / Gwo-Yu Chuang / Yen-Ting Lai / Chen-Hsiang Shen / Jeffrey C Boyington / Aliaksandr Druz / Hui Geng / Mark K Louder / Krisha McKee / Reda Rawi / Raffaello Verardi / Yongping ...Authors: Jason Gorman / Gwo-Yu Chuang / Yen-Ting Lai / Chen-Hsiang Shen / Jeffrey C Boyington / Aliaksandr Druz / Hui Geng / Mark K Louder / Krisha McKee / Reda Rawi / Raffaello Verardi / Yongping Yang / Baoshan Zhang / Nicole A Doria-Rose / Bob Lin / Penny L Moore / Lynn Morris / Lawrence Shapiro / John R Mascola / Peter D Kwong /
Abstract: Antibodies targeting the V1V2 apex of the HIV-1 envelope (Env) trimer comprise one of the most commonly elicited categories of broadly neutralizing antibodies. Structures of these antibodies indicate ...Antibodies targeting the V1V2 apex of the HIV-1 envelope (Env) trimer comprise one of the most commonly elicited categories of broadly neutralizing antibodies. Structures of these antibodies indicate diverse modes of Env recognition typified by antibodies of the PG9 class and the PGT145 class. The mode of recognition, however, has been unclear for the most potent of the V1V2 apex-targeting antibodies, CAP256-VRC26.25 (named for donor-lineage.clone and referred to hereafter as VRC26.25). Here, we determine the cryoelectron microscopy structure at 3.7 Å resolution of the antigen-binding fragment of VRC26.25 in complex with the Env trimer thought to have initiated the lineage. The 36-residue protruding loop of VRC26.25 displays recognition incorporating both strand-C interactions similar to the PG9 class and V1V2 apex insertion similar to the PGT145 class. Structural elements of separate antibody classes can thus intermingle to form a "combined" class, which in this case yields an antibody of extraordinary potency.
History
DepositionFeb 10, 2020-
Header (metadata) releaseMar 11, 2020-
Map releaseMar 11, 2020-
UpdateOct 6, 2021-
Current statusOct 6, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vrw
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21372.png

Downloads & links

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Map

FileDownload / File: emd_21372.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Voxel sizeX=Y=Z: 1.061 Å
Density
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-1.1037374 - 2.7860277
Average (Standard dev.)0.011395817 (±0.078729734)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0611.0611.061
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z339.520339.520339.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.1042.7860.011

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Supplemental data

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Mask #1

Fileemd_21372_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unnsharpened map

Fileemd_21372_additional.map
AnnotationUnnsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_21372_half_map_1.map
AnnotationHalf map A
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 B

Fileemd_21372_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : HIV-1 Env trimer CAP256 SU.wk34.80 SOSIP.RnS2

EntireName: HIV-1 Env trimer CAP256 SU.wk34.80 SOSIP.RnS2
Components
  • Complex: HIV-1 Env trimer CAP256 SU.wk34.80 SOSIP.RnS2
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 Env trimer CAP256 SU.wk34.80 SOSIP.RnS2

SupramoleculeName: HIV-1 Env trimer CAP256 SU.wk34.80 SOSIP.RnS2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.322434 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLWVTVYYGV PVWREAKTTL FCASDAKSYE KEVHNVWATH ACVPTDPNPQ ELVLENVTEN FNMWKNDMVD QMHEDIISLW DQSLKPCVK LTPLCVTLNC SDAKVNATYK GTREEIKNCS FNATTELRDK KRREYALFYR LDIVPLSGEG NNNSEYRLIN C NTSVITQI ...String:
GLWVTVYYGV PVWREAKTTL FCASDAKSYE KEVHNVWATH ACVPTDPNPQ ELVLENVTEN FNMWKNDMVD QMHEDIISLW DQSLKPCVK LTPLCVTLNC SDAKVNATYK GTREEIKNCS FNATTELRDK KRREYALFYR LDIVPLSGEG NNNSEYRLIN C NTSVITQI CPKVTFDPIP IHYCAPAGYA ILKCNNKTFN GTGPCNNVST VQCTHGIKPV VSTQLLLNGS LAEEEIIIRS EN LTDNVKT IIVHLNESVE ITCTRPNNMT RKSVRIGPGQ TFYALGDIIG DIRQPHCNIS EIKWEKTLQR VSEKLREHFN KTI IFNQSS GGDLEITTHS FNCGGEFFYC NTSDLFFNKT FNETYSTGSN STNSTITLPC RIKQIINMWQ EVGRAMYAPP IAGN ITCKS NITGLLLTRD GGGNNSTKET FRPGGGNMRD NWRSELYKYK VVEVKPLGIA PTECNRTVVQ RRRRRR

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Macromolecule #2: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.355703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVVGLGAVFL GFLGAAGSTM GAASNTLTVQ ARQLLSGIVQ QQSNLLRAPE AQQHMLQLGV WGFKQLQARV LAIERYLEVQ QLLGMWGCS GKLICCTNVP WNSSWSNKTY NEIWDNMTWM QWDREIGNYT DTIYKLLEVS QFQQEINEKD NLTLD

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 39 / 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 mg/mL
BufferpH: 7.4 / Component - Formula: PBS
GridModel: C-flat-1.2/1.3 4C / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
DetailsCAP256 SU.wk34.80 SOSIP.RnS2

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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 / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1760 / Average exposure time: 10.0 sec. / Average electron dose: 74.41 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. 2.12)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12) / Number images used: 34008

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Atomic model buiding 1

Initial modelPDB ID:

6nf2

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6vrw:
Cryo-EM structure of stabilized HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2

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