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- EMDB-8981: Cryo-EM reconstruction of domain-swapped, glycan-reactive, neutra... -

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Entry
Database: EMDB / ID: EMD-8981
TitleCryo-EM reconstruction of domain-swapped, glycan-reactive, neutralizing antibody 2G12 bound to HIV-1 Env BG505 DS-SOSIP, which was also bound to CD4-binding site antibody VRC03
Map dataRefined map from cryoSparc postprocessed in Relion using map fro cryoSparc
Sample
  • Complex: Ternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of antibodies 2G12 and VRC03.
    • Protein or peptide: 2G12 Light chain
    • Protein or peptide: 2G12 heavy chain
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: VRC03 heavy chain
    • Protein or peptide: VRC03 Light chain
KeywordsHIV-1 Env / complex / neutralizing / VIRAL PROTEIN / domain-swapped antibody
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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsAcharya P / Kwong PD
CitationJournal: Structure / Year: 2019
Title: Structural Survey of Broadly Neutralizing Antibodies Targeting the HIV-1 Env Trimer Delineates Epitope Categories and Characteristics of Recognition.
Authors: Gwo-Yu Chuang / Jing Zhou / Priyamvada Acharya / Reda Rawi / Chen-Hsiang Shen / Zizhang Sheng / Baoshan Zhang / Tongqing Zhou / Robert T Bailer / Venkata P Dandey / Nicole A Doria-Rose / ...Authors: Gwo-Yu Chuang / Jing Zhou / Priyamvada Acharya / Reda Rawi / Chen-Hsiang Shen / Zizhang Sheng / Baoshan Zhang / Tongqing Zhou / Robert T Bailer / Venkata P Dandey / Nicole A Doria-Rose / Mark K Louder / Krisha McKee / John R Mascola / Lawrence Shapiro / Peter D Kwong /
Abstract: Over the past decade, structures have been determined for broadly neutralizing antibodies that recognize all major exposed surfaces of the prefusion-closed HIV-1-envelope (Env) trimer. To understand ...Over the past decade, structures have been determined for broadly neutralizing antibodies that recognize all major exposed surfaces of the prefusion-closed HIV-1-envelope (Env) trimer. To understand this recognition and its implications, we analyzed 206 antibody-HIV-1 Env structures from the Protein Data Bank with resolution suitable to define interaction chemistries and measured antibody neutralization on a 208-strain panel. Those with >25% breadth segregated into almost two dozen classes based on ontogeny and recognition and into six epitope categories based on recognized Env residues. For paratope, the number of protruding loops and level of somatic hypermutation were significantly higher for broad HIV-1 neutralizing antibodies than for a comparison set of non-HIV-1 antibodies (p < 0.0001). For epitope, the number of independent sequence segments was higher (p < 0.0001), as well as the glycan component surface area (p = 0.0005). The unusual characteristics of epitope and paratope delineated here are likely to reflect respectively virus-immune evasion and antibody-recognition solutions that allow effective neutralization of HIV-1.
History
DepositionJul 21, 2018-
Header (metadata) releaseAug 29, 2018-
Map releaseFeb 13, 2019-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.734
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.734
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6e5p
  • Surface level: 0.734
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8981.png

Downloads & links

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Map

FileDownload / File: emd_8981.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefined map from cryoSparc postprocessed in Relion using map fro cryoSparc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 420.902 Å		1.1 Å/pix.
x 384 pix.
= 420.902 Å		1.1 Å/pix.
x 384 pix.
= 420.902 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0961 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.734 / Movie #1: 0.734
Minimum - Maximum-0.29414085 - 2.2027838
Average (Standard dev.)0.018640218 (±0.12520622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 420.9024 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.09609895833331.09609895833331.0960989583333
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z420.902420.902420.902
α/β/γ90.00090.00090.000
start NX/NY/NZ989663
NX/NY/NZ108125172
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.2942.2030.019

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Supplemental data

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Additional map: Unsharpened map from cryoSparc

Fileemd_8981_additional.map
AnnotationUnsharpened map from cryoSparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map from cryoSparc

Fileemd_8981_additional_1.map
AnnotationUnsharpened map from cryoSparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of an...

EntireName: Ternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of antibodies 2G12 and VRC03.
Components
  • Complex: Ternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of antibodies 2G12 and VRC03.
    • Protein or peptide: 2G12 Light chain
    • Protein or peptide: 2G12 heavy chain
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: VRC03 heavy chain
    • Protein or peptide: VRC03 Light chain

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Supramolecule #1: Ternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of an...

SupramoleculeName: Ternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of antibodies 2G12 and VRC03.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: 2G12 Light chain

MacromoleculeName: 2G12 Light chain / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.130762 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VVMTQSPSTL SASVGDTITI TCRASQSIET WLAWYQQKPG KAPKLLIYKA STLKTGVPSR FSGSGSGTEF TLTISGLQFD DFATYHCQH YAGYSATFGQ GTRVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
VVMTQSPSTL SASVGDTITI TCRASQSIET WLAWYQQKPG KAPKLLIYKA STLKTGVPSR FSGSGSGTEF TLTISGLQFD DFATYHCQH YAGYSATFGQ GTRVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGE

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Macromolecule #2: 2G12 heavy chain

MacromoleculeName: 2G12 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.932869 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVKAGGSLIL SCGVSNFRIS AHTMNWVRRV PGGGLEWVAS ISTSSTYRDY ADAVKGRFTV SRDDLEDFVY LQMHKMRVE DTAIYYCARK GSDRLSDNDP FDAWGPGTVV TVSPASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
EVQLVESGGG LVKAGGSLIL SCGVSNFRIS AHTMNWVRRV PGGGLEWVAS ISTSSTYRDY ADAVKGRFTV SRDDLEDFVY LQMHKMRVE DTAIYYCARK GSDRLSDNDP FDAWGPGTVV TVSPASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKS

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Macromolecule #3: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.086102 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 PTRCKRRVV

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #4: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 19.102811 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALDGSAPTK A KRRVVQRE KR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #5: VRC03 heavy chain

MacromoleculeName: VRC03 heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.699861 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAV IKTPGSSVKI SCRASGYNFR DYSIHWVRLI PDKGFEWIGW IKPLWGAVSY ARQLQGRVSM TRQLSQDPDD PDWGVAYME FSGLTPADTA EYFCVRRGSC DYCGDFPWQY WCQGTVVVVS SASTKGPSVF PLAPSSGGTA ALGCLVKDYF P EPVTVSWN ...String:
QVQLVQSGAV IKTPGSSVKI SCRASGYNFR DYSIHWVRLI PDKGFEWIGW IKPLWGAVSY ARQLQGRVSM TRQLSQDPDD PDWGVAYME FSGLTPADTA EYFCVRRGSC DYCGDFPWQY WCQGTVVVVS SASTKGPSVF PLAPSSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPK

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Macromolecule #6: VRC03 Light chain

MacromoleculeName: VRC03 Light chain / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.043652 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

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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

Concentration0.5 mg/mL
BufferpH: 7.01 / Component - Concentration: 150.0 mM / Component - Name: HEPES
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: SPOTITON
Details: 0.005% dodecyl maltoside was added to sample before vitification.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2206 / Average exposure time: 10.0 sec. / Average electron dose: 63.84 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 463860
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 5245
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6e5p:
Backbone model based on cryo-EM map at 8.5 A of domain-swapped, glycan-reactive, neutralizing antibody 2G12 bound to HIV-1 Env BG505 DS-SOSIP, which was also bound to CD4-binding site antibody VRC03

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