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- EMDB-22104: Cryo-EM reconstruction of HIV-1 Env BG505 SOSIP.664 in complex wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-22104
TitleCryo-EM reconstruction of HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 11B fragment antigen binding
Map dataSharpened map
Sample
  • Complex: HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 11B fragment antigen binding
    • Complex: HIV-1 Env BG505 SOSIP.664
      • Protein or peptide: BG505 HIV-1 Env gp120
      • Protein or peptide: BG505 HIV-1 Env gp41
    • Complex: rabbit monoclonal antibody 11B fragment antigen
      • Protein or peptide: monoclonal antibody 11B kappa chain
      • Protein or peptide: monoclonal antibody 11B fragment antigen binding heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / Env / glycan hole / antibody / vaccine design / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 speciesHuman immunodeficiency virus 1 / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsOzorowski G / Cottrell CA
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1AI100663 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
Bill & Melinda Gates FoundationOPP1115782 United States
CitationJournal: To Be Published
Title: Limited breadth of anti-HIV Env glycan hole antibodies is further hindered by strain-specific peptide interactions
Authors: Ozorowski G / Cottrell CA / de Val N / Scaringi N / Polveroni TM / Ward AB
History
DepositionJun 2, 2020-
Header (metadata) releaseDec 8, 2021-
Map releaseDec 8, 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: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6x98
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22104.png

Downloads & links

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Map

FileDownload / File: emd_22104.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 288 pix.
= 296.64 Å		1.03 Å/pix.
x 288 pix.
= 296.64 Å		1.03 Å/pix.
x 288 pix.
= 296.64 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: 0.5 / Movie #1: 0.5
Minimum - Maximum-2.0052269 - 3.3897152
Average (Standard dev.)0.0052753617 (±0.10126981)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 296.63998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z296.640296.640296.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-2.0053.3900.005

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Supplemental data

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Mask #1

Fileemd_22104_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_22104_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_22104_half_map_2.map
AnnotationHalf map 1
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 SOSIP.664 in complex with rabbit monoclonal antib...

EntireName: HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 11B fragment antigen binding
Components
  • Complex: HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 11B fragment antigen binding
    • Complex: HIV-1 Env BG505 SOSIP.664
      • Protein or peptide: BG505 HIV-1 Env gp120
      • Protein or peptide: BG505 HIV-1 Env gp41
    • Complex: rabbit monoclonal antibody 11B fragment antigen
      • Protein or peptide: monoclonal antibody 11B kappa chain
      • Protein or peptide: monoclonal antibody 11B fragment antigen binding heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antib...

SupramoleculeName: HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 11B fragment antigen binding
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 570 KDa

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Supramolecule #2: HIV-1 Env BG505 SOSIP.664

SupramoleculeName: HIV-1 Env BG505 SOSIP.664 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #3: rabbit monoclonal antibody 11B fragment antigen

SupramoleculeName: rabbit monoclonal antibody 11B fragment antigen / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Details: Fab fragment generated by proteolytic cleavage of IgG antibody
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: BG505 HIV-1 Env gp120

MacromoleculeName: BG505 HIV-1 Env gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 57.945977 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKKQK ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKKQK VYSLFYRLDV VQINENQGNR SNNSNKEYRL INCNTSAITQ ACPKVSFEPI PIHYCAPAGF AILKCKDKKF NG TGPCPSV STVQCTHGIK PVVSTQLLLN GSLAEEEVMI RSENITNNAK NILVQFNTPV QINCTRPNNN TRKSIRIGPG QAF YATGDI IGDIRQAHCN VSKATWNETL GKVVKQLRKH FGNNTIIRFA NSSGGDLEVT THSFNCGGEF FYCNTSGLFN STWI SNTSV QGSNSTGSND SITLPCRIKQ IINMWQRIGQ AMYAPPIQGV IRCVSNITGL ILTRDGGSTN STTETFRPGG GDMRD NWRS ELYKYKVVKI EPLGVAPTRC KRRVVGRRRR RR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: BG505 HIV-1 Env gp41

MacromoleculeName: BG505 HIV-1 Env gp41 / type: protein_or_peptide / ID: 2 / 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

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: monoclonal antibody 11B kappa chain

MacromoleculeName: monoclonal antibody 11B kappa chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 25.161066 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYRMQLLSCI ALSLALVTNS DIVMTQTPSS VSAAVGGTVT INCQASESIY SGLAWYQQKP GQPPKLLIYR ASTLTSGVSS RFKGSGSGA RFTLTINDLE CADAATYYCQ SCYDTTIGTY GSWAFGGGTE VVVKGDPVAP SVLIFPPAAD QVATGTVTIV C VANKYFPD ...String:
MYRMQLLSCI ALSLALVTNS DIVMTQTPSS VSAAVGGTVT INCQASESIY SGLAWYQQKP GQPPKLLIYR ASTLTSGVSS RFKGSGSGA RFTLTINDLE CADAATYYCQ SCYDTTIGTY GSWAFGGGTE VVVKGDPVAP SVLIFPPAAD QVATGTVTIV C VANKYFPD VTVTWEVDGT TQTTGIENSK TPQNSADCTY NLSSTLTLTS TQYNSHKEYT CKVTQGTTSV VQSFNRGDC

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Macromolecule #4: monoclonal antibody 11B fragment antigen binding heavy chain

MacromoleculeName: monoclonal antibody 11B fragment antigen binding heavy chain
type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 25.312748 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYRMQLLSCI ALSLALVTNS QLVESGGGLV KPGGTLTLTC KASGFSLSDS YWMCWVRQAP GKGLEWVACV FTGNGKAYYA RWVEGRFTI SRSTSLNTAT LQMTSLTAAD TATYFCARGD YDDPLDGVAT LWGPGTLVTV SSGQPKAPSV FPLAPCCGDT P SSTVTLGC ...String:
MYRMQLLSCI ALSLALVTNS QLVESGGGLV KPGGTLTLTC KASGFSLSDS YWMCWVRQAP GKGLEWVACV FTGNGKAYYA RWVEGRFTI SRSTSLNTAT LQMTSLTAAD TATYFCARGD YDDPLDGVAT LWGPGTLVTV SSGQPKAPSV FPLAPCCGDT P SSTVTLGC LVKGYLPEPV TVTWNSGTLT NGVRTFPSVR QSSGLYSLSS VVSVTSSSQP VTCNVAHPAT NTKVDKTVAP ST C

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 36 / 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
150.0 mMNaClsodium chloride
50.0 mMTris
0.06 mMn-Dodecyl beta-D-maltoside

Details: Detergent (DDM) added shortly prior to freezing
GridModel: C-flat-2/2 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1518 / Average exposure time: 8.0 sec. / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4zmj

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 96896
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5cez


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6x98:
Cryo-EM model of HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 11B fragment antigen binding variable domain

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