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- EMDB-23237: BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAb... -

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Basic information

Entry
Database: EMDB / ID: EMD-23237
TitleBG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-2 from animal Rh.33311 (Wk26 time point)
Map data3D map of BG505 SOSIP v5.2 N241/N289 in complex with the polyclonal Fab pAbC-2 from animal Rh.33311 (Wk26 time point). Main map
Sample
  • Complex: BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-2 from animal Rh.33311 (Wk26 time point)
    • Complex: BG505 SOSIP.v5.2 N241/N289
      • Protein or peptide: BG505 SOSIP.v5.2 N241/N289 - gp120
      • Protein or peptide: BG505 SOSIP.v5.2 N241/N289 - gp41
    • Complex: polyclonal Fab pAbC-2 from animal Rh.33311
      • Protein or peptide: Rh.33311 pAbC-2 - Heavy Chain
      • Protein or peptide: Rh.33311 pAbC-2 - Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV / vaccine design / BG505 / VIRAL PROTEIN-IMMUNE SYSTEM complex / Polyclonal antibodies / EMPEM
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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsAntanasijevic A / Sewall LM
Funding support United States, 1 items
OrganizationGrant numberCountry
International AIDS Vaccine InitiativeOPP1196345 United States
CitationJournal: Nat Commun / Year: 2021
Title: Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM.
Authors: Antanasijevic A / Sewall LM / Cottrell CA / Carnathan DG / Jimenez LE / Ngo JT / Silverman JB / Groschel B / Georgeson E / Bhiman J / Bastidas R / LaBranche C / Allen JD / Copps J / Perrett ...Authors: Antanasijevic A / Sewall LM / Cottrell CA / Carnathan DG / Jimenez LE / Ngo JT / Silverman JB / Groschel B / Georgeson E / Bhiman J / Bastidas R / LaBranche C / Allen JD / Copps J / Perrett HR / Rantalainen K / Cannac F / Yang YR / de la Pena AT / Rocha RF / Berndsen ZT / Baker D / King NP / Sanders RW / Moore JP / Crotty S / Crispin M / Montefiori DC / Burton DR / Schief WR / Silvestri G / Ward AB
History
DepositionJan 1, 2021-
Header (metadata) releaseAug 4, 2021-
Map releaseAug 4, 2021-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7l8u
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7l8u
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23237.png

Downloads & links

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Map

FileDownload / File: emd_23237.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map of BG505 SOSIP v5.2 N241/N289 in complex with the polyclonal Fab pAbC-2 from animal Rh.33311 (Wk26 time point). 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: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.034501478 - 0.05685334
Average (Standard dev.)0.0001485421 (±0.002374285)
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-0.0350.0570.000

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Supplemental data

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Mask #1

Fileemd_23237_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 N241/N289 in...

Fileemd_23237_half_map_1.map
Annotation3D map of BG505 SOSIP v5.2 N241/N289 in complex with the polyclonal Fab pAbC-2 from animal Rh.33311 (Wk26 time point). 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 N241/N289 in...

Fileemd_23237_half_map_2.map
Annotation3D map of BG505 SOSIP v5.2 N241/N289 in complex with the polyclonal Fab pAbC-2 from animal Rh.33311 (Wk26 time point). 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 N241/N289 in complex with the polyclonal Fab pAb...

EntireName: BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-2 from animal Rh.33311 (Wk26 time point)
Components
  • Complex: BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-2 from animal Rh.33311 (Wk26 time point)
    • Complex: BG505 SOSIP.v5.2 N241/N289
      • Protein or peptide: BG505 SOSIP.v5.2 N241/N289 - gp120
      • Protein or peptide: BG505 SOSIP.v5.2 N241/N289 - gp41
    • Complex: polyclonal Fab pAbC-2 from animal Rh.33311
      • Protein or peptide: Rh.33311 pAbC-2 - Heavy Chain
      • Protein or peptide: Rh.33311 pAbC-2 - Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAb...

SupramoleculeName: BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-2 from animal Rh.33311 (Wk26 time point)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Polyclonal complexes were generated by incubation of isolated polyclonal Fabs with recombinantly expressed BG505 SOSIP and subsequent SEC purification. Map and model were reconstructed from ...Details: Polyclonal complexes were generated by incubation of isolated polyclonal Fabs with recombinantly expressed BG505 SOSIP and subsequent SEC purification. Map and model were reconstructed from the immune complex dataset using the focused classification approach.

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Supramolecule #2: BG505 SOSIP.v5.2 N241/N289

SupramoleculeName: BG505 SOSIP.v5.2 N241/N289 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #3: polyclonal Fab pAbC-2 from animal Rh.33311

SupramoleculeName: polyclonal Fab pAbC-2 from animal Rh.33311 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Macromolecule #1: BG505 SOSIP.v5.2 N241/N289 - gp120

MacromoleculeName: BG505 SOSIP.v5.2 N241/N289 - gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 56.417125 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 CTRPNNNTRK SIRIGPGQWF YAT GDIIGD IRQAHCNVSK ATWNETLGKV VKQLRKHFGN NTIIRFANSS GGDLEVTTHS FNCGGEFFYC NTSGLFNSTW ISNT SVQGS NSTGSNDSIT LPCRIKQIIN MWQRIGQAMY APPIQGVIRC VSNITGLILT RDGGSTNSTT ETFRPGGGDM RDNWR SELY KYKVVKIEPL GVAPTRCKR

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Macromolecule #2: BG505 SOSIP.v5.2 N241/N289 - gp41

MacromoleculeName: BG505 SOSIP.v5.2 N241/N289 - gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 16.477719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LGFLGAAGST MGAASMTLTV QARNLLSGIV QQQSNLLRAP ECQQHLLKLT VWGIKQLQAR VLAVERYLRD QQLLGIWGCS GKLICCTNV PWNSTWSNRN LSEIWDNMTW LQWDKEISNY TQIIYGLLEE SQNQQEKNEQ DLLALD

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Macromolecule #3: Rh.33311 pAbC-2 - Heavy Chain

MacromoleculeName: Rh.33311 pAbC-2 - Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 9.634868 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

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Macromolecule #4: Rh.33311 pAbC-2 - Light Chain

MacromoleculeName: Rh.33311 pAbC-2 - Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 8.954028 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

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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: 47 / 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 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris-HCl
150.0 mMNaClSodium chloride

Details: TBS buffer prepared from a 10X stock
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / 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: Blotting time varied between 3 and 7 seconds..
DetailsPolyclonal complexes were generated by incubation of isolated polyclonal Fabs with recombinantly expressed BG505 SOSIP and subsequent SEC purification.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-39 / Number grids imaged: 4 / Number real images: 6268 / Average exposure time: 9.75 sec. / Average electron dose: 44.3 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: 0.6 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsFrames were aligned using MotionCorr and GCTF was applied for estimation of CTF parameters.
Particle selectionNumber selected: 1267693 / Details: Particles picked using template picker
Startup modelType of model: OTHER
Details: 3D map of the free HIV Env trimer ectodomain, low-pass filtered to 20A
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0)
Details: 28188 symmetry-expanded particles. See the Methods section in the manuscript for details.
Number images used: 28188
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Details: Multi-step focused classification was applied to isolate the particles featuring this type fo polyclonal antibody. See the Method section of the manuscript for details
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6vl5

source_name: PDB, initial_model_type: experimental model

4kte

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7l8u:
BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-2 from animal Rh.33311 (Wk26 time point)

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