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- EMDB-23801: BG505 SOSIP.v5.2(7S) in complex with the monoclonal antibodies Rh... -

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Basic information

Entry
Database: EMDB / ID: EMD-23801
TitleBG505 SOSIP.v5.2(7S) in complex with the monoclonal antibodies Rh.33172 mAb.1 and RM19R
Map data3D map of BG505 SOSIP.v5.2(7S) in complex with the monoclonal antibody Rh.33172 mAb.1 (as Fab fragment). The main map
Sample
  • Complex: BG505 SOSIP.v5.2(7S) in complex with the monoclonal antibodies Rh.33172 mAb.1 and RM19R
    • Complex: monoclonal antibodies Rh.33172 mAb.1 and RM19R
      • Protein or peptide: RM19R mAb Light chain
      • Protein or peptide: RM19R mAb Heavy chain
      • Protein or peptide: Rh.33172 mAb.1 Heavy chain
      • Protein or peptide: Rh.33172 mAb.1 Light chain
    • Complex: BG505 SOSIP.v5.2(7S)
      • Protein or peptide: BG505 SOSIPv5.2(7S) - gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Biological speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsAntanasijevic A / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1115782, OPP1196345 United States
CitationJournal: Sci Adv / Year: 2022
Title: From structure to sequence: Antibody discovery using cryoEM.
Authors: Aleksandar Antanasijevic / Charles A Bowman / Robert N Kirchdoerfer / Christopher A Cottrell / Gabriel Ozorowski / Amit A Upadhyay / Kimberly M Cirelli / Diane G Carnathan / Chiamaka A ...Authors: Aleksandar Antanasijevic / Charles A Bowman / Robert N Kirchdoerfer / Christopher A Cottrell / Gabriel Ozorowski / Amit A Upadhyay / Kimberly M Cirelli / Diane G Carnathan / Chiamaka A Enemuo / Leigh M Sewall / Bartek Nogal / Fangzhu Zhao / Bettina Groschel / William R Schief / Devin Sok / Guido Silvestri / Shane Crotty / Steven E Bosinger / Andrew B Ward /
Abstract: One of the rate-limiting steps in analyzing immune responses to vaccines or infections is the isolation and characterization of monoclonal antibodies. Here, we present a hybrid structural and ...One of the rate-limiting steps in analyzing immune responses to vaccines or infections is the isolation and characterization of monoclonal antibodies. Here, we present a hybrid structural and bioinformatic approach to directly assign the heavy and light chains, identify complementarity-determining regions, and discover sequences from cryoEM density maps of serum-derived polyclonal antibodies bound to an antigen. When combined with next-generation sequencing of immune repertoires, we were able to specifically identify clonal family members, synthesize the monoclonal antibodies, and confirm that they interact with the antigen in a manner equivalent to the corresponding polyclonal antibodies. This structure-based approach for identification of monoclonal antibodies from polyclonal sera opens new avenues for analysis of immune responses and iterative vaccine design.
History
DepositionApr 7, 2021-
Header (metadata) releaseJan 26, 2022-
Map releaseJan 26, 2022-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.009
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mep
  • Surface level: 0.009
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7mep
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23801.png

Downloads & links

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Map

FileDownload / File: emd_23801.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map of BG505 SOSIP.v5.2(7S) in complex with the monoclonal antibody Rh.33172 mAb.1 (as Fab fragment). The main map
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.009
Minimum - Maximum-0.02561706 - 0.043500807
Average (Standard dev.)5.9354163e-05 (±0.0016315497)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 370.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z370.800370.800370.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0260.0440.000

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Supplemental data

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Mask #1

Fileemd_23801_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 3D map of BG505 SOSIP.v5.2(7S) in complex with...

Fileemd_23801_half_map_1.map
Annotation3D map of BG505 SOSIP.v5.2(7S) in complex with the monoclonal antibody Rh.33172 mAb.1 (as Fab fragment). Half-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 3D map of BG505 SOSIP.v5.2(7S) in complex with...

Fileemd_23801_half_map_2.map
Annotation3D map of BG505 SOSIP.v5.2(7S) in complex with the monoclonal antibody Rh.33172 mAb.1 (as Fab fragment). Half-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BG505 SOSIP.v5.2(7S) in complex with the monoclonal antibodies Rh...

EntireName: BG505 SOSIP.v5.2(7S) in complex with the monoclonal antibodies Rh.33172 mAb.1 and RM19R
Components
  • Complex: BG505 SOSIP.v5.2(7S) in complex with the monoclonal antibodies Rh.33172 mAb.1 and RM19R
    • Complex: monoclonal antibodies Rh.33172 mAb.1 and RM19R
      • Protein or peptide: RM19R mAb Light chain
      • Protein or peptide: RM19R mAb Heavy chain
      • Protein or peptide: Rh.33172 mAb.1 Heavy chain
      • Protein or peptide: Rh.33172 mAb.1 Light chain
    • Complex: BG505 SOSIP.v5.2(7S)
      • Protein or peptide: BG505 SOSIPv5.2(7S) - gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BG505 SOSIP.v5.2(7S) in complex with the monoclonal antibodies Rh...

SupramoleculeName: BG505 SOSIP.v5.2(7S) in complex with the monoclonal antibodies Rh.33172 mAb.1 and RM19R
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: The complexes were created by combining BG505 SOSIP.v5.2(7S) and the two antibodies (as Fab fragments) and subsequent SEC purification.

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Supramolecule #2: monoclonal antibodies Rh.33172 mAb.1 and RM19R

SupramoleculeName: monoclonal antibodies Rh.33172 mAb.1 and RM19R / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #4-#5
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Supramolecule #3: BG505 SOSIP.v5.2(7S)

SupramoleculeName: BG505 SOSIP.v5.2(7S) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Human immunodeficiency virus

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Macromolecule #1: RM19R mAb Light chain

MacromoleculeName: RM19R mAb Light chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.808134 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AIRMTQSPAI LSLSPGERAT LSCRASQSVD SRLAWYQQKP GQSPRLLIYD VSSRATGIPD RFSGSGSGTE FTLTISSLEP EDVAVYFCH QENDWPWTFG QGTKVEIK

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Macromolecule #2: RM19R mAb Heavy chain

MacromoleculeName: RM19R mAb Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 13.268667 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGPG LVRPSETLSL TCAVSGDSIS TNNGWSWIRQ TPGKGLEWIG YINGRSGSTR YNPSLQSRVT ISTDTSGNQF SLKVNSVTA ADTAKYYCAF FWSTYYKRFD VWGPGVRVTV SS

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Macromolecule #3: BG505 SOSIPv5.2(7S) - gp120

MacromoleculeName: BG505 SOSIPv5.2(7S) - gp120 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus
Molecular weightTheoretical: 74.987219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKRGLCCVLL LCGAVFVSPS QEIHARFRRG ARAENLWVTV YYGVPVWKDA ETTLFCASDA KAYETKKHNV WATHCCVPTD PNPQEIHLE NVTEEFNMWK NNMVEQMHTD IISLWDQSLK PCVKLTPLCV TLQCTNVTNN ITDDMRGELK NCSFNMTTEL R DKKQKVYS ...String:
MKRGLCCVLL LCGAVFVSPS QEIHARFRRG ARAENLWVTV YYGVPVWKDA ETTLFCASDA KAYETKKHNV WATHCCVPTD PNPQEIHLE NVTEEFNMWK NNMVEQMHTD IISLWDQSLK PCVKLTPLCV TLQCTNVTNN ITDDMRGELK NCSFNMTTEL R DKKQKVYS LFYRLDVVQI NENQGNRSNN SNKEYRLINC NTSAITQACP KVSFEPIPIH YCAPAGFAIL KCKDKKFNGT GP CTNVSTV QCTHGIKPVV STQLLLNGSL AEEEVIIRSE NITNNAKNIL VQLNESVQIN CTRPNNNTVK SIRIGPGQWF YYT GDIIGD IRQAHCNVSK ATWNETLGKV VKQLRKHFGN NTIIRFANSS GGDLEVTTHS FNCGGEFFYC NTSGLFNSTW ISNT SVQGS NSTGSNDSIT LPCRIKQIIN MWQRIGQAMY APPIQGVIRC VSNITGLILT RDGGSTNSTT ETFRPGGGDM RDNWR SELY KYKVVKIEPL GVAPTRCKRR VVGRRRRRRA VGIGAVSLGF LGAAGSTMGA ASMTLTVQAR NLLSGIVQQQ SNLLRA PEC QQHLLKDTHW GIKQLQARVL AVEHYLRDQQ LLGIWGCSGK LICCTNVPWN SSWSNRNLSE IWDNMTWLQW DKEISNY TQ IIYGLLEESQ NQQEKNEQDL LELD

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Macromolecule #4: Rh.33172 mAb.1 Heavy chain

MacromoleculeName: Rh.33172 mAb.1 Heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 14.306693 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKMPGTSVKL SCKTSGYTFT SYNINWVRQA PGQALEWMGW INPNNGTTDY AQKFQGRVTM TRDTSTTTAY MQLNSLRSE DTAVYYCARA RGGYEDDDGY HYTGYGLDSW GQGVVVTVSS

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Macromolecule #5: Rh.33172 mAb.1 Light chain

MacromoleculeName: Rh.33172 mAb.1 Light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.477829 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASIGDRVT VTCRASQGIN MQLCWYQLKP GKAPTLLIYG TSGLQTGVSS RFSGSGSGTN FTLTISSLQP EDVATYYCQ QDYTTPFTFG PGTKLDIK

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 51 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration6.0 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
10.0 mMTris-HClTris-HCl
150.0 mMNaClSodium Chloride

Details: TBS, 0.2um filtered
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force: 0 Wait time: 10s Blot time: 3-7s.
DetailsThe sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2050 / Average exposure time: 9.5 sec. / Average electron dose: 44.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 169887 / Details: template picked
CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER / Details: Ab initio model from cryosparc
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 35099
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0) / Details: Relion, regularized likelihood
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0) / Details: Relion, regularized likelihood
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6vfl

Output model

PDB-7mep:
BG505 SOSIP.v5.2(7S) in complex with the monoclonal antibodies Rh.33172 mAb.1 and RM19R

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