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- EMDB-23780: BG505 SOSIP MD39 in complex with the monoclonal antibodies Rh.331... -

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Basic information

Entry
Database: EMDB / ID: EMD-23780
TitleBG505 SOSIP MD39 in complex with the monoclonal antibodies Rh.33104 mAb.1 and RM20A3
Map data3D map of BG505 SOSIP MD39 in complex with the monoclonal antibody Rh.33104 mAb.1 (as Fab fragment). Obtained by cryoEM. Main map
Sample
  • Complex: BG505 SOSIP MD39 in complex with the monoclonal antibodies Rh.33104 mAb.1 and RM20A3
    • Protein or peptide: Rh.33104 mAb.1 Heavy Chain
    • Protein or peptide: Surface protein gp120
    • Protein or peptide: RM20A3 mAb Heavy Chain
    • Protein or peptide: RM20A3 mAb Light Chain
    • Protein or peptide: Rh.33104 mAb.1 Light Chain
    • Protein or peptide: Transmembrane protein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsmonoclonal antibody / immune complex / VIRAL PROTEIN
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / virion attachment to host cell / host cell plasma membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / 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 speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsAntanasijevic A / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1115782 United States
Bill & Melinda Gates FoundationOPP1196345 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 6, 2021-
Header (metadata) releaseJan 26, 2022-
Map releaseJan 26, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mdu
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7mdu
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23780.png

Downloads & links

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Map

FileDownload / File: emd_23780.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map of BG505 SOSIP MD39 in complex with the monoclonal antibody Rh.33104 mAb.1 (as Fab fragment). Obtained by cryoEM. Main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 360 pix.
= 370.8 Å		1.03 Å/pix.
x 360 pix.
= 370.8 Å		1.03 Å/pix.
x 360 pix.
= 370.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.029183544 - 0.056320462
Average (Standard dev.)0.000014482969 (±0.0016611055)
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
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0290.0560.000

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Supplemental data

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Mask #1

Fileemd_23780_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 MD39 in complex...

Fileemd_23780_half_map_1.map
Annotation3D map of BG505 SOSIP MD39 in complex with the monoclonal antibody Rh.33104 mAb.1 (as Fab fragment). Obtained by cryoEM. 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 MD39 in complex...

Fileemd_23780_half_map_2.map
Annotation3D map of BG505 SOSIP MD39 in complex with the monoclonal antibody Rh.33104 mAb.1 (as Fab fragment). Obtained by cryoEM. 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 MD39 in complex with the monoclonal antibodies Rh.331...

EntireName: BG505 SOSIP MD39 in complex with the monoclonal antibodies Rh.33104 mAb.1 and RM20A3
Components
  • Complex: BG505 SOSIP MD39 in complex with the monoclonal antibodies Rh.33104 mAb.1 and RM20A3
    • Protein or peptide: Rh.33104 mAb.1 Heavy Chain
    • Protein or peptide: Surface protein gp120
    • Protein or peptide: RM20A3 mAb Heavy Chain
    • Protein or peptide: RM20A3 mAb Light Chain
    • Protein or peptide: Rh.33104 mAb.1 Light Chain
    • Protein or peptide: Transmembrane protein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BG505 SOSIP MD39 in complex with the monoclonal antibodies Rh.331...

SupramoleculeName: BG505 SOSIP MD39 in complex with the monoclonal antibodies Rh.33104 mAb.1 and RM20A3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Details: The complexes were created by combining BG505 SOSIP MD39 and the two antibodies (as Fab fragments) and subsequent SEC purification.
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Macromolecule #1: Rh.33104 mAb.1 Heavy Chain

MacromoleculeName: Rh.33104 mAb.1 Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 12.421753 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSETLSL TCAVSGGSFS GYSWGWIRQP PGKGLEWIGS IIGRTGSTAY NPSLTSRVTI SRDTSNNQFS LKLTSLTAA DTAVYYCARQ QSNFDFWGQG VLVTVSS

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Macromolecule #2: Surface protein gp120

MacromoleculeName: Surface protein gp120 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 57.652625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKRGLCCVLL LCGAVFVSPS QEIHARFRRG ARAENLWVTV YYGVPVWKDA ETTLFCASDA KAYETEKHNV WATHACVPTD PNPQEIHLE NVTEEFNMWK NNMVEQMHED IISLWDQSLK PCVKLTPLCV TLQCTNVTNN ITDDMRGELK NCSFNMTTEL R DKKQKVYS ...String:
MKRGLCCVLL LCGAVFVSPS QEIHARFRRG ARAENLWVTV YYGVPVWKDA ETTLFCASDA KAYETEKHNV WATHACVPTD PNPQEIHLE NVTEEFNMWK NNMVEQMHED IISLWDQSLK PCVKLTPLCV TLQCTNVTNN ITDDMRGELK NCSFNMTTEL R DKKQKVYS LFYRLDVVQI NENQGNRSNN SNKEYRLINC NTSAITQACP KVSFEPIPIH YCAPAGFAIL KCKDKKFNGT GP CPSVSTV QCTHGIKPVV STQLLLNGSL AEEEVIIRSE NITNNAKNIL VQLNTPVQIN CTRPNNNTVK SIRIGPGQAF YYT GDIIGD IRQAHCNVSK ATWNETLGKV VKQLRKHFGN NTIIRFAQSS GGDLEVTTHS FNCGGEFFYC NTSGLFNSTW ISNT SVQGS NSTGSNDSIT LPCRIKQIIN MWQRIGQAMY APPIQGVIRC VSNITGLILT RDGGSTNSTT ETFRPGGGDM RDNWR SELY KYKVVKIEPL GVAPTRCKRR VVGRRRRRR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: RM20A3 mAb Heavy Chain

MacromoleculeName: RM20A3 mAb Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 13.511111 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVETGGG LVQPGGSLKL SCRASGYTFS SFAMSWVRQA PGKGLEWVSL INDRGGLTFY VDSVKGRFTI SRDNSKNTLS LQMHSLRDG DTAVYYCATG GMSSALQSSK YYFDFWGQGA LVTVSS

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Macromolecule #4: RM20A3 mAb Light Chain

MacromoleculeName: RM20A3 mAb Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.755821 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSALTQPPSV SGSPGQSVTI SCTGTSSDIG SYNYVSWYQQ HPGKAPKLMI YDVTQRPSGV SDRFSGSKSG NTASLTISGL QADDEADYY CSAYAGRQTF YIFGGGTRLT VL

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Macromolecule #5: Rh.33104 mAb.1 Light Chain

MacromoleculeName: Rh.33104 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: 11.521576 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDTVT TTCRASQDIS NDLAWYQQKP GKAPKPLLYY ASNLESGVPS MFSGSGSGTD FTLTISSLQP EDFASYFCQ QYNSYPRTFG QGTKVEF

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Macromolecule #6: Transmembrane protein gp41

MacromoleculeName: Transmembrane protein gp41 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.134324 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVSLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEP QQHLLKDTHW GIKQLQARVL AVEHYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 12 / 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
150.0 mMNaClSodium Chloride

Details: TBS, 0.2um filtered
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / 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 specimen consisted of homogeneous antigen-antibody complexes

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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: 1022 / 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: 0.8 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: 109105 / Details: template picking
Startup modelType of model: OTHER / Details: Low-pass-filtered map of BG505 SOSIP
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 29009
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 model
PDB IDChain

6vfl

source_name: PDB, initial_model_type: experimental model

6x9r

source_name: PDB, initial_model_type: experimental model
Output model

PDB-7mdu:
BG505 SOSIP MD39 in complex with the monoclonal antibodies Rh.33104 mAb.1 and RM20A3

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