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- EMDB-24622: Negative stain electron microscopy single particle reconstruction... -

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Entry
Database: EMDB / ID: EMD-24622
TitleNegative stain electron microscopy single particle reconstruction of monoclonal antibody DH1028 Fab in complex with HIV-1 Env CH505 SOSIP trimer.
Map dataFinal sharpened map of negative stain electron microscopy single particle reconstruction of monoclonal antibody DH1028 Fab in complex with HIV-1 Env CH505 SOSIP trimer.
Sample
  • Complex: Complex of HIV Env CH505TFchim.6R.SOSIP.664.v4.1 with DH1028 antibody Fab
    • Complex: HIV Env CH505TFchim.6R.SOSIP.664.v4.1 trimer
      • Protein or peptide: HIV Env CH505TFchim.6R.SOSIP.664.v4.1
    • Complex: DH1028 Antibody Fab
      • Complex: DH1028 Antibody Fab Heavy Chain
        • Protein or peptide: DH1028 Antibody Fab Heavy Chain
      • Complex: DH1028 Antibody Fab Light Chain
        • Protein or peptide: DH1028 Antibody Fab Light Chain
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 / 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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 2 / Macaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 12.9 Å
AuthorsEdwards RJ / Mansouri K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1-AI144371 United States
CitationJournal: Sci Transl Med / Year: 2022
Title: Stabilized HIV-1 envelope immunization induces neutralizing antibodies to the CD4bs and protects macaques against mucosal infection.
Authors: Kevin O Saunders / Robert J Edwards / Kedamawit Tilahun / Kartik Manne / Xiaozhi Lu / Derek W Cain / Kevin Wiehe / Wilton B Williams / Katayoun Mansouri / Giovanna E Hernandez / Laura ...Authors: Kevin O Saunders / Robert J Edwards / Kedamawit Tilahun / Kartik Manne / Xiaozhi Lu / Derek W Cain / Kevin Wiehe / Wilton B Williams / Katayoun Mansouri / Giovanna E Hernandez / Laura Sutherland / Richard Scearce / Robert Parks / Maggie Barr / Todd DeMarco / Chloe M Eater / Amanda Eaton / Georgeanna Morton / Benjamin Mildenberg / Yunfei Wang / R Wes Rountree / Mark A Tomai / Christopher B Fox / M Anthony Moody / S Munir Alam / Sampa Santra / Mark G Lewis / Thomas N Denny / George M Shaw / David C Montefiori / Priyamvada Acharya / Barton F Haynes /
Abstract: A successful HIV-1 vaccine will require induction of a polyclonal neutralizing antibody (nAb) response, yet vaccine-mediated induction of such a response in primates remains a challenge. We found ...A successful HIV-1 vaccine will require induction of a polyclonal neutralizing antibody (nAb) response, yet vaccine-mediated induction of such a response in primates remains a challenge. We found that a stabilized HIV-1 CH505 envelope (Env) trimer formulated with a Toll-like receptor 7/8 agonist induced potent HIV-1 polyclonal nAbs that correlated with protection from homologous simian-human immunodeficiency virus (SHIV) infection. The serum dilution that neutralized 50% of virus replication (ID titer) required to protect 90% of macaques was 1:364 against the challenge virus grown in primary rhesus CD4 T cells. Structural analyses of vaccine-induced nAbs demonstrated targeting of the Env CD4 binding site or the N156 glycan and the third variable loop base. Autologous nAb specificities similar to those elicited in macaques by vaccination were isolated from the human living with HIV from which the CH505 Env immunogen was derived. CH505 viral isolates were isolated that mutated the V1 to escape both the infection-induced and vaccine-induced antibodies. These results define the specificities of a vaccine-induced nAb response and the protective titers of HIV-1 vaccine-induced nAbs required to protect nonhuman primates from low-dose mucosal challenge by SHIVs bearing a primary transmitted/founder Env.
History
DepositionAug 4, 2021-
Header (metadata) releaseAug 25, 2021-
Map releaseAug 25, 2021-
UpdateMar 8, 2023-
Current statusMar 8, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.154
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.154
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24622.png

Downloads & links

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Map

FileDownload / File: emd_24622.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal sharpened map of negative stain electron microscopy single particle reconstruction of monoclonal antibody DH1028 Fab in complex with HIV-1 Env CH505 SOSIP trimer.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.02 Å/pix.
x 96 pix.
= 385.92 Å		4.02 Å/pix.
x 96 pix.
= 385.92 Å		4.02 Å/pix.
x 96 pix.
= 385.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1541 / Movie #1: 0.154
Minimum - Maximum-0.08474229 - 0.3660044
Average (Standard dev.)0.0019296634 (±0.024363931)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 385.91998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.024.024.02
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z385.920385.920385.920
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
D min/max/mean-0.0850.3660.002

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Supplemental data

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Additional map: Raw,unsharpened map of negative stain electron microscopy single...

Fileemd_24622_additional_1.map
AnnotationRaw,unsharpened map of negative stain electron microscopy single particle reconstruction of monoclonal antibody DH1028 Fab in complex with HIV-1 Env CH505 SOSIP trimer.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 of negative stain electron microscopy single...

Fileemd_24622_half_map_1.map
AnnotationHalf-map 2 of negative stain electron microscopy single particle reconstruction of monoclonal antibody DH1028 Fab in complex with HIV-1 Env CH505 SOSIP trimer.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1 of negative stain electron microscopy single...

Fileemd_24622_half_map_2.map
AnnotationHalf-map 1 of negative stain electron microscopy single particle reconstruction of monoclonal antibody DH1028 Fab in complex with HIV-1 Env CH505 SOSIP trimer.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of HIV Env CH505TFchim.6R.SOSIP.664.v4.1 with DH1028 anti...

EntireName: Complex of HIV Env CH505TFchim.6R.SOSIP.664.v4.1 with DH1028 antibody Fab
Components
  • Complex: Complex of HIV Env CH505TFchim.6R.SOSIP.664.v4.1 with DH1028 antibody Fab
    • Complex: HIV Env CH505TFchim.6R.SOSIP.664.v4.1 trimer
      • Protein or peptide: HIV Env CH505TFchim.6R.SOSIP.664.v4.1
    • Complex: DH1028 Antibody Fab
      • Complex: DH1028 Antibody Fab Heavy Chain
        • Protein or peptide: DH1028 Antibody Fab Heavy Chain
      • Complex: DH1028 Antibody Fab Light Chain
        • Protein or peptide: DH1028 Antibody Fab Light Chain

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Supramolecule #1: Complex of HIV Env CH505TFchim.6R.SOSIP.664.v4.1 with DH1028 anti...

SupramoleculeName: Complex of HIV Env CH505TFchim.6R.SOSIP.664.v4.1 with DH1028 antibody Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 2
Molecular weightTheoretical: 23 KDa

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Supramolecule #2: HIV Env CH505TFchim.6R.SOSIP.664.v4.1 trimer

SupramoleculeName: HIV Env CH505TFchim.6R.SOSIP.664.v4.1 trimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human immunodeficiency virus 2

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Supramolecule #3: DH1028 Antibody Fab

SupramoleculeName: DH1028 Antibody Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Supramolecule #4: DH1028 Antibody Fab Heavy Chain

SupramoleculeName: DH1028 Antibody Fab Heavy Chain / type: complex / ID: 4 / Parent: 3 / Macromolecule list: #2
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Supramolecule #5: DH1028 Antibody Fab Light Chain

SupramoleculeName: DH1028 Antibody Fab Light Chain / type: complex / ID: 5 / Parent: 3 / Macromolecule list: #3
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Macromolecule #1: HIV Env CH505TFchim.6R.SOSIP.664.v4.1

MacromoleculeName: HIV Env CH505TFchim.6R.SOSIP.664.v4.1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKEAKT TLFCASDAKA YEKEVHNVWA THACVPTDPN PQEMVLKNVT ENFNMWKNDM VDQMHEDVIS LWDQSLKPCV KLTPLCVTLN CTNATASNSS IIEGMKNCSF NITTELRDKR EKKNALFYKL DIVQLDGNSS QYRLINCNTS VITQACPKVS ...String:
AENLWVTVYY GVPVWKEAKT TLFCASDAKA YEKEVHNVWA THACVPTDPN PQEMVLKNVT ENFNMWKNDM VDQMHEDVIS LWDQSLKPCV KLTPLCVTLN CTNATASNSS IIEGMKNCSF NITTELRDKR EKKNALFYKL DIVQLDGNSS QYRLINCNTS VITQACPKVS FDPIPIHYCA PAGYAILKCN NKTFTGTGPC NNVSTVQCTH GIKPVVSTQL LLNGSLAEGE IIIRSENITN NVKTIIVHLN ESVKIECTRP NNKTRTSIRI GPGQAFYATG QVIGDIREAY CNINESKWNE TLQRVSKKLK EYFPHKNITF QPSSGGDLEI TTHSFNCGGE FFYCNTSSLF NRTYMANSTD MANSTETNST RTITIHCRIK QIINMWQEVG RAMYAPPIAG NITCISNITG LLLTRDGGKN NTETFRPGGG NMKDNWRSEL YKYKVVKIEP LGVAPTRCKR RVVGRRRRRR AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSGK LICCTNVPWN SSWSNRNLSE IWDNMTWLQW DKEISNYTQI IYGLLEESQN QQEKNEQDLL ALD

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Macromolecule #2: DH1028 Antibody Fab Heavy Chain

MacromoleculeName: DH1028 Antibody Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVTLKESGPA LVKPTQTLTL TCTFSGFSLS TSGMAVAWIR QPSRKTLEWL AHIFWDDDKL YNTSLRDRLT ISKDTSKNQV VLTMTNMDPV DTATYYCARK SYYYGGSYYF DYWGQGVLVT VSS astkg psvfplapss rstsestaa l gclvkdyf pe pvtvswn sgs ...String:
QVTLKESGPA LVKPTQTLTL TCTFSGFSLS TSGMAVAWIR QPSRKTLEWL AHIFWDDDKL YNTSLRDRLT ISKDTSKNQV VLTMTNMDPV DTATYYCARK SYYYGGSYYF DYWGQGVLVT VSS astkg psvfplapss rstsestaa l gclvkdyf pe pvtvswn sgs ltsgvh tfpa vlqss glysl ssvv tvpsss lgt qtyvcnv nh kpsntkvd k rveiktcgg

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Macromolecule #3: DH1028 Antibody Fab Light Chain

MacromoleculeName: DH1028 Antibody Fab Light Chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPPSV SGDPGQRVTI SCTGSSSNIG GYYVYWCQQF PGTAPKLLIY DDYKRPSGVS DRFSGSKSGT SASLTITGLQ PGDEADYYCG VWDSSLNGYI FGSGTRLTVL gqpkasptv t lfppssee lq ankatlv cli sdfypg vvkv awkad gsavn agve ...String:
QSVLTQPPSV SGDPGQRVTI SCTGSSSNIG GYYVYWCQQF PGTAPKLLIY DDYKRPSGVS DRFSGSKSGT SASLTITGLQ PGDEADYYCG VWDSSLNGYI FGSGTRLTVL gqpkasptv t lfppssee lq ankatlv cli sdfypg vvkv awkad gsavn agve tttpsk qsn nkyaass yl sltsdqwk s hksyscqvt hegstvektv apaecs

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.8 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMHEPESN-2-Hydroxyethyl-piperazine-N-2-ethanesulfonic acid
150.0 mMNaClsodium chloride
5.0 g/dLglycerolglycerol
StainingType: NEGATIVE / Material: uranyl formate
Details: For negative staining, 5 microliter of the diluted filter retentate was applied to a freshly glow-discharged, 300 mesh, carbon-coated EM grid and incubated 10-12 s, then rinsed with 70 ...Details: For negative staining, 5 microliter of the diluted filter retentate was applied to a freshly glow-discharged, 300 mesh, carbon-coated EM grid and incubated 10-12 s, then rinsed with 70 microliter of 2% uranyl formate delivered in one smooth ejection from a pipet. The drop of uranyl formate remaining on the grid was allowed to incubate for 60 s, then the grid was blotted with filter paper and allowed to air dry.
GridModel: Homemade / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
DetailsFrozen aliquots of SOSIP and Fab were thawed in an Aluminum block at room temperature for 2-3 minutes, then 10 microgram of SOSIP were mixed with 36 microgram Fab (~1:15 molar ratio) and diluted to 100 microliter final volume with HEPES-buffered saline (HBS), containing 20 mM HEPES buffer and 150 mM NaCl, pH 7.4, augmented with 5% glycerol. Mixture was incubated at 22 degrees C overnight. The following day, a 0.08% glutaraldehyde fixative was prepared by diluting an 8% stock 1/100 with HBS. Then 400 microliter of fixative was added to the SOSIP-Fab mixture and incubated 5 min at room temperature to crosslink the complex, followed by addition of 40 microliter of a 1 M Tris solution, pH 7.4 to quench any unreacted glutaraldehyde. The reaction mixture was then transferred to a 0.5-ml Amicon Ultra centrifugal filter device with a 100-kDa cutoff filter (Millipore, #UFC510096) and spun 10 min at 14,000 g in a benchtop centrifuge held at 20 degrees C to remove excess Fab. The filter retentate, usually ~25 microliter, was collected and diluted 1:1 with HBS augmented with 5% glycerol.

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Electron microscopy

MicroscopeFEI/PHILIPS EM420
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number grids imaged: 1 / Number real images: 495 / Average exposure time: 0.25 sec. / Average electron dose: 32.0 e/Å2
Details: Images were collected with a minimal dose approach using a manually controlled low dose unit to keep the beam blanked except during initial grid orientation and image collection. To create ...Details: Images were collected with a minimal dose approach using a manually controlled low dose unit to keep the beam blanked except during initial grid orientation and image collection. To create an initial atlas, the entire grid was imaged once at 49x magnification at very low beam intensity by decreasing the emission current, strongly focusing C1 (Spot Size 6) and defocusing C2 (Intensity knob fully clockwise). The stage was then quickly translated to center the desired gridsquare, with an estimated exposure of < 2 s at this very low illumination level, at which point the beam was blanked. A 3,300x magnification was then selected so that a single gridsquare approximately fills the scintillator screen. The beam was then unblanked and the stage manually tilted and the eucentric height quickly adjusted by noting the movement of the gridbars, and then the stage was translated to center on the lower-left corner of the gridsquare, with an estimated exposure of < 2 s at this very low illumination level, at which point the beam was blanked. A magnfication of 82,000x was then selected and C2 focused by a known number of clicks of the Intensity knob so that the beam would approximately fill the scintillator screen. The beam was then unblanked, the objective lens focused by eye and then adjusted to approximately 0.5 micron underfocused, and C2 adjusted so the beam just filled the scintillator screen. Because this focusing step involved a long exposure to the focused beam, no data was collected in this area. For data collection, the stage was translated blindly, with the beam blanked, by noting the micrometer markings on the left-hand stage control, to move to an un-irradiated area that was approximately two screen-widths vertically away from the initial position. The beam was then unblanked, an image captured with 0.25 s exposure to the focused beam without any adjustment of the objective lens focus, and the beam then re-blanked. The FFT of the collected image was examined and the position of the first Thon ring noted and the objective lens focus adjusted if needed for subsequent images. The stage was then moved blindly in the same direction to an un-irradiated area and a new image collected. In this way images were collected until the gridbar was encountered, at which point the beam was unblanked and the stage moved so that the gridbar occluded all of the beam except a small sliver of the gridsquare at the bottom or top of the screen, and the right hand stage control was used to translate the specimen to a new location at least two screen widths away horizontally. In this way the entire gridsquare could be imaged in a rastered fashion with each area only irradiated with the full strength beam during the 0.25 s image capture.
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 82000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 305536
Startup modelType of model: INSILICO MODEL
In silico model: An unliganded (no Fab) Env trimer homology model was built with SwissModel using the CH505 sequence and PDB 5UM8 as template, then converted to a map using UCSF Chimera's molmap ...In silico model: An unliganded (no Fab) Env trimer homology model was built with SwissModel using the CH505 sequence and PDB 5UM8 as template, then converted to a map using UCSF Chimera's molmap function with 15 angstrom resolution and 4.02 angstrom gridspacing
Details: The starting model was further low-pass filtered to 60 angstroms for use in 3D classification. Resulting 3D classification map was used for as starting model for final 3d refinements.
Final reconstructionNumber classes used: 1 / Algorithm: EXACT BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 12.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 31969
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 8 / Avg.num./class: 5145 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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