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- EMDB-20191: Cryo-EM structure of vaccine-elicited antibody 0PV-b.01 in comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-20191
TitleCryo-EM structure of vaccine-elicited antibody 0PV-b.01 in complex with HIV-1 Env BG505 DS-SOSIP and antibodies VRC03 and PGT122
Map dataSharpened map
Sample
  • Complex: HIV-1 Env BG505 DS-SOSIP and antibodies 0PV-b.01, VRC03 and PGT122
    • Complex: Envelope glycoprotein gp120
      • Protein or peptide: BG505 gp120
    • Complex: Envelope glycoprotein gp41
      • Protein or peptide: Envelope glycoprotein gp41
    • Complex: VRC03
      • Protein or peptide: VRC03 heavy
      • Protein or peptide: VRC03 light
    • Complex: PGT122
      • Protein or peptide: PGT122 heavy
      • Protein or peptide: PGT122 light
    • Complex: 0PV-b.01
      • Protein or peptide: 0PV-b.01 heavy
      • Protein or peptide: 0PV-b.01 light
  • 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 / Homo sapiens (human) / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsGorman J / Kwong PD
CitationJournal: Cell / Year: 2019
Title: Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization.
Authors: Rui Kong / Hongying Duan / Zizhang Sheng / Kai Xu / Priyamvada Acharya / Xuejun Chen / Cheng Cheng / Adam S Dingens / Jason Gorman / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / ...Authors: Rui Kong / Hongying Duan / Zizhang Sheng / Kai Xu / Priyamvada Acharya / Xuejun Chen / Cheng Cheng / Adam S Dingens / Jason Gorman / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / Tongqing Zhou / Gwo-Yu Chuang / Cara W Chao / Ying Gu / Alexander J Jafari / Mark K Louder / Sijy O'Dell / Ariana P Rowshan / Elise G Viox / Yiran Wang / Chang W Choi / Martin M Corcoran / Angela R Corrigan / Venkata P Dandey / Edward T Eng / Hui Geng / Kathryn E Foulds / Yicheng Guo / Young D Kwon / Bob Lin / Kevin Liu / Rosemarie D Mason / Martha C Nason / Tiffany Y Ohr / Li Ou / Reda Rawi / Edward K Sarfo / Arne Schön / John P Todd / Shuishu Wang / Hui Wei / Winston Wu / / James C Mullikin / Robert T Bailer / Nicole A Doria-Rose / Gunilla B Karlsson Hedestam / Diana G Scorpio / Julie Overbaugh / Jesse D Bloom / Bridget Carragher / Clinton S Potter / Lawrence Shapiro / Peter D Kwong / John R Mascola /
Abstract: The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be ...The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be elicited, we identified, characterized, and tracked five neutralizing Ab lineages targeting the HIV-1-fusion peptide (FP) in vaccinated macaques over time. Genetic and structural analyses revealed two of these lineages to belong to a reproducible class capable of neutralizing up to 59% of 208 diverse viral strains. B cell analysis indicated each of the five lineages to have been initiated and expanded by FP-carrier priming, with envelope (Env)-trimer boosts inducing cross-reactive neutralization. These Abs had binding-energy hotspots focused on FP, whereas several FP-directed Abs induced by immunization with Env trimer-only were less FP-focused and less broadly neutralizing. Priming with a conserved subregion, such as FP, can thus induce Abs with binding-energy hotspots coincident with the target subregion and capable of broad neutralization.
History
DepositionMay 2, 2019-
Header (metadata) releaseAug 7, 2019-
Map releaseAug 7, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ot1
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ot1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20191.png

Downloads & links

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Map

FileDownload / File: emd_20191.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Voxel sizeX=Y=Z: 1.07325 Å
Density
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-1.713928 - 3.7456234
Average (Standard dev.)0.0007876671 (±0.105980285)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 377.78403 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.073251.073251.07325
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z377.784377.784377.784
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ1128100
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-1.7143.7460.001

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Supplemental data

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Mask #1

Fileemd_20191_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_20191_additional.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_20191_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_20191_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV-1 Env BG505 DS-SOSIP and antibodies 0PV-b.01, VRC03 and PGT122

EntireName: HIV-1 Env BG505 DS-SOSIP and antibodies 0PV-b.01, VRC03 and PGT122
Components
  • Complex: HIV-1 Env BG505 DS-SOSIP and antibodies 0PV-b.01, VRC03 and PGT122
    • Complex: Envelope glycoprotein gp120
      • Protein or peptide: BG505 gp120
    • Complex: Envelope glycoprotein gp41
      • Protein or peptide: Envelope glycoprotein gp41
    • Complex: VRC03
      • Protein or peptide: VRC03 heavy
      • Protein or peptide: VRC03 light
    • Complex: PGT122
      • Protein or peptide: PGT122 heavy
      • Protein or peptide: PGT122 light
    • Complex: 0PV-b.01
      • Protein or peptide: 0PV-b.01 heavy
      • Protein or peptide: 0PV-b.01 light
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 Env BG505 DS-SOSIP and antibodies 0PV-b.01, VRC03 and PGT122

SupramoleculeName: HIV-1 Env BG505 DS-SOSIP and antibodies 0PV-b.01, VRC03 and PGT122
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8

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Supramolecule #2: Envelope glycoprotein gp120

SupramoleculeName: Envelope glycoprotein gp120 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: Envelope glycoprotein gp41

SupramoleculeName: Envelope glycoprotein gp41 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #4: VRC03

SupramoleculeName: VRC03 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #5: PGT122

SupramoleculeName: PGT122 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #6: 0PV-b.01

SupramoleculeName: 0PV-b.01 / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 1 / 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 #2: BG505 gp120

MacromoleculeName: BG505 gp120 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.987195 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 PTRCKRRVGR RRRRR

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Macromolecule #3: 0PV-b.01 heavy

MacromoleculeName: 0PV-b.01 heavy / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.430441 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG VVKPSETLSL TCGVSGGTIS SSHFYWSWIR QPPGKGLEWI GGLYINDERI NYNPSLESRV TISKDTSQNQ FALKLTSVT AADTAVYYCV REPVIAAAGT VDVWGRGVLV TVSSASTKGP SVFPLAPSSE STAALGCLVK DYFPEPVTVS W NSGSLTSG ...String:
QVQLQESGPG VVKPSETLSL TCGVSGGTIS SSHFYWSWIR QPPGKGLEWI GGLYINDERI NYNPSLESRV TISKDTSQNQ FALKLTSVT AADTAVYYCV REPVIAAAGT VDVWGRGVLV TVSSASTKGP SVFPLAPSSE STAALGCLVK DYFPEPVTVS W NSGSLTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYVCNVNHKP SNTKVDKRVE IKTCGGLEVL FQ

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Macromolecule #4: 0PV-b.01 light

MacromoleculeName: 0PV-b.01 light / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.843475 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQTPLS LSVTPGEPAS ISCRSSQSLL HSNGHTYVHW YLQKAGQSPQ LLIYEVSNRA SGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCEQTLQI PFTFGGGTKV EIKRTVAAPS VFIFPPSEDQ VKSGTVSVVC LLNNFYPREA SVKWKVDGAL K TGNSQESV ...String:
DIVMTQTPLS LSVTPGEPAS ISCRSSQSLL HSNGHTYVHW YLQKAGQSPQ LLIYEVSNRA SGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCEQTLQI PFTFGGGTKV EIKRTVAAPS VFIFPPSEDQ VKSGTVSVVC LLNNFYPREA SVKWKVDGAL K TGNSQESV TEQDSKDNTY SLSSTLTLSS TEYQSHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #5: PGT122 heavy

MacromoleculeName: PGT122 heavy / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.434691 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVHLQESGPG LVKPSETLSL TCNVSGTLVR DNYWSWIRQP LGKQPEWIGY VHDSGDTNYN PSLKSRVHLS LDKSKNLVSL RLTGVTAAD SAIYYCATTK HGRRIYGVVA FKEWFTYFYM DVWGKGTSVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
QVHLQESGPG LVKPSETLSL TCNVSGTLVR DNYWSWIRQP LGKQPEWIGY VHDSGDTNYN PSLKSRVHLS LDKSKNLVSL RLTGVTAAD SAIYYCATTK HGRRIYGVVA FKEWFTYFYM DVWGKGTSVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSC

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Macromolecule #6: PGT122 light

MacromoleculeName: PGT122 light / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.880275 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: APTFVSVAPG QTARITCGEE SLGSRSVIWY QQRPGQAPSL IIYNNNDRPS GIPDRFSGSP GSTFGTTATL TITSVEAGDE ADYYCHIWD SRRPTNWVFG EGTTLIVLSQ PKAAPSVTLF PPSSEELQAN KATLVCLISD FYPGAVTVAW KADSSPVKAG V ETTTPSKQ ...String:
APTFVSVAPG QTARITCGEE SLGSRSVIWY QQRPGQAPSL IIYNNNDRPS GIPDRFSGSP GSTFGTTATL TITSVEAGDE ADYYCHIWD SRRPTNWVFG EGTTLIVLSQ PKAAPSVTLF PPSSEELQAN KATLVCLISD FYPGAVTVAW KADSSPVKAG V ETTTPSKQ SNNKYAASSY LSLTPEQWKS HKSYSCQVTH EGSTVEKTVA PTECS

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Macromolecule #7: VRC03 heavy

MacromoleculeName: VRC03 heavy / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.248436 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAV IKTPGSSVKI SCRASGYNFR DYSIHWVRLI PDKGFEWIGW IKPLWGAVSY ARQLQGRVSM TRQLSQDPDD PDWGVAYME FSGLTPADTA EYFCVRRGSC DYCGDFPWQY WGQGTVVVVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT ...String:
QVQLVQSGAV IKTPGSSVKI SCRASGYNFR DYSIHWVRLI PDKGFEWIGW IKPLWGAVSY ARQLQGRVSM TRQLSQDPDD PDWGVAYME FSGLTPADTA EYFCVRRGSC DYCGDFPWQY WGQGTVVVVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSC

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Macromolecule #8: VRC03 light

MacromoleculeName: VRC03 light / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.146795 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGI LSLSPGETAT LFCKASQGGN AMTWYQKRRG QVPRLLIYDT SRRASGVPDR FVGSGSGTDF FLTINKLDRE DFAVYYCQQ FEFFGLGSEL EVHRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL QSGNSQESVT E QDSKDSTY ...String:
EIVLTQSPGI LSLSPGETAT LFCKASQGGN AMTWYQKRRG QVPRLLIYDT SRRASGVPDR FVGSGSGTDF FLTINKLDRE DFAVYYCQQ FEFFGLGSEL EVHRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL QSGNSQESVT E QDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #14: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 14 / Number of copies: 12 / 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

Concentration1.0 mg/mL
BufferpH: 7.4 / Component - Formula: PBS
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: SPOTITON

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2298 / Average exposure time: 10.0 sec. / Average electron dose: 73.46 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)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 57864

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Atomic model buiding 1

Initial modelPDB ID:

6cdi

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6ot1:
Cryo-EM structure of vaccine-elicited antibody 0PV-b.01 in complex with HIV-1 Env BG505 DS-SOSIP and antibodies VRC03 and PGT122

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