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- EMDB-8761: CryoEM structure of rhinovirus B14 in complex with C5 Fab (4 degr... -

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Basic information

Entry
Database: EMDB / ID: EMD-8761
TitleCryoEM structure of rhinovirus B14 in complex with C5 Fab (4 degrees Celsius, molar ratio 1:3, full particle)
Map dataInner density masked out. The map has been sharpened.
Sample
  • Virus: Human rhinovirus B14
    • Protein or peptide: viral protein 1
    • Protein or peptide: viral protein 3
    • Protein or peptide: viral protein 2
    • Protein or peptide: viral protein 4
    • Protein or peptide: C5 antibody variable heavy domain
    • Protein or peptide: C5 antibody variable light domain
  • Ligand: water
Function / homology
Function and homology information


lysis of host organelle involved in viral entry into host cell / protein complex oligomerization / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / monoatomic ion channel activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane ...lysis of host organelle involved in viral entry into host cell / protein complex oligomerization / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / monoatomic ion channel activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHRV-14, Human rhinovirus B14 / Mouse (mice) / Human rhinovirus B14
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsLiu Y / Dong Y / Rossmann MG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI011219 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Antibody-induced uncoating of human rhinovirus B14.
Authors: Yangchao Dong / Yue Liu / Wen Jiang / Thomas J Smith / Zhikai Xu / Michael G Rossmann /
Abstract: Rhinoviruses (RVs) are the major causes of common colds in humans. They have a nonenveloped, icosahedral capsid surrounding a positive-strand RNA genome. Here we report that the antigen-binding (Fab) ...Rhinoviruses (RVs) are the major causes of common colds in humans. They have a nonenveloped, icosahedral capsid surrounding a positive-strand RNA genome. Here we report that the antigen-binding (Fab) fragment of a neutralizing antibody (C5) can trigger genome release from RV-B14 to form emptied particles and neutralize virus infection. Using cryo-electron microscopy, structures of the C5 Fab in complex with the full and emptied particles have been determined at 2.3 Å and 3.0 Å resolution, respectively. Each of the 60 Fab molecules binds primarily to a region on viral protein 3 (VP3). Binding of the C5 Fabs to RV-B14 results in significant conformational changes around holes in the capsid through which the viral RNA might exit. These results are so far the highest resolution view of an antibody-virus complex and elucidate a mechanism whereby antibodies neutralize RVs and related viruses by inducing virus uncoating.
History
DepositionJun 8, 2017-
Header (metadata) releaseJun 21, 2017-
Map releaseJul 12, 2017-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10.8
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 10.8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5w3l
  • Surface level: 10.8
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5w3l
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8761.png

Downloads & links

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Map

FileDownload / File: emd_8761.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationInner density masked out. The map has been sharpened.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 672 pix.
= 672. Å		1 Å/pix.
x 672 pix.
= 672. Å		1 Å/pix.
x 672 pix.
= 672. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 10.8 / Movie #1: 10.8
Minimum - Maximum-53.73968 - 71.794525
Average (Standard dev.)0.025925875 (±2.6715336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions672672672
Spacing672672672
CellA=B=C: 672.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z672672672
origin x/y/z0.0000.0000.000
length x/y/z672.000672.000672.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-36
NX/NY/NZ528549
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS672672672
D min/max/mean-53.74071.7950.026

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Supplemental data

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Half map: Unmasked, unsharpened half map #1

Fileemd_8761_half_map_1.map
AnnotationUnmasked, unsharpened half map #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unmasked, unsharpened half map #2

Fileemd_8761_half_map_2.map
AnnotationUnmasked, unsharpened 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 : Human rhinovirus B14

EntireName: Human rhinovirus B14
Components
  • Virus: Human rhinovirus B14
    • Protein or peptide: viral protein 1
    • Protein or peptide: viral protein 3
    • Protein or peptide: viral protein 2
    • Protein or peptide: viral protein 4
    • Protein or peptide: C5 antibody variable heavy domain
    • Protein or peptide: C5 antibody variable light domain
  • Ligand: water

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Supramolecule #1: Human rhinovirus B14

SupramoleculeName: Human rhinovirus B14 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 / Details: Viruses were grown in HeLa-H1 cells. / NCBI-ID: 12131 / Sci species name: Human rhinovirus B14 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: viral protein 1

MacromoleculeName: viral protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: HRV-14, Human rhinovirus B14
Molecular weightTheoretical: 32.560549 KDa
SequenceString: GLGDELEEVI VEKTKQTVAS ISSGPKHTQK VPILTANETG ATMPVLPSDS IETRTTYMHF NGSETDVECF LGRAACVHVT EIQNKDATG IDNHREAKLF NDWKINLSSL VQLRKKLELF TYVRFDSEYT ILATASQPDS ANYSSNLVVQ AMYVPPGAPN P KEWDDYTW ...String:
GLGDELEEVI VEKTKQTVAS ISSGPKHTQK VPILTANETG ATMPVLPSDS IETRTTYMHF NGSETDVECF LGRAACVHVT EIQNKDATG IDNHREAKLF NDWKINLSSL VQLRKKLELF TYVRFDSEYT ILATASQPDS ANYSSNLVVQ AMYVPPGAPN P KEWDDYTW QSASNPSVFF KVGDTSRFSV PYVGLASAYN CFYDGYSHDD AETQYGITVL NHMGSMAFRI VNEHDEHKTL VK IRVYHRA KHVEAWIPRA PRALPYTSIG RTNYPKNTEP VIKKRKGDIK SY

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Macromolecule #2: viral protein 3

MacromoleculeName: viral protein 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: HRV-14, Human rhinovirus B14
Molecular weightTheoretical: 26.236754 KDa
SequenceString: GLPTTTLPGS GQFLTTDDRQ SPSALPNYEP TPRIHIPGKV HNLLEIIQVD TLIPMNNTHT KDEVNSYLIP LNANRQNEQV FGTNLFIGD GVFKTTLLGE IVQYYTHWSG SLRFSLMYTG PALSSAKLIL AYTPPGARGP QDRREAMLGT HVVWDIGLQS T IVMTIPWT ...String:
GLPTTTLPGS GQFLTTDDRQ SPSALPNYEP TPRIHIPGKV HNLLEIIQVD TLIPMNNTHT KDEVNSYLIP LNANRQNEQV FGTNLFIGD GVFKTTLLGE IVQYYTHWSG SLRFSLMYTG PALSSAKLIL AYTPPGARGP QDRREAMLGT HVVWDIGLQS T IVMTIPWT SGVQFRYTDP DTYTSAGFLS CWYQTSLILP PETTGQVYLL SFISACPDFK LRLMKDTQTI SQTVALTE

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Macromolecule #3: viral protein 2

MacromoleculeName: viral protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: HRV-14, Human rhinovirus B14
Molecular weightTheoretical: 28.501361 KDa
SequenceString: SPNVEACGYS DRVQQITLGN STITTQEAAN AVVCYAEWPE YLPDVDASDV NKTSKPDTSV CRFYTLDSKT WTTGSKGWCW KLPDALKDM GVFGQNMFFH SLGRSGYTVH VQCNATKFHS GCLLVVVIPE HQLASHEGGN VSVKYTFTHP GERGIDLSSA N EVGGPVKD ...String:
SPNVEACGYS DRVQQITLGN STITTQEAAN AVVCYAEWPE YLPDVDASDV NKTSKPDTSV CRFYTLDSKT WTTGSKGWCW KLPDALKDM GVFGQNMFFH SLGRSGYTVH VQCNATKFHS GCLLVVVIPE HQLASHEGGN VSVKYTFTHP GERGIDLSSA N EVGGPVKD VIYNMNGTLL GNLLIFPHQF INLRTNNTAT IVIPYINSVP IDSMTRHNNV SLMVIPIAPL TVPTGATPSL PI TVTIAPM CTEFSGIRSK SIVPQ

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Macromolecule #4: viral protein 4

MacromoleculeName: viral protein 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: HRV-14, Human rhinovirus B14
Molecular weightTheoretical: 7.183863 KDa
SequenceString:
GAQVSTQKSG SHENQNILTN GSNQTFTVIN YYKDAASTSS AGQSLSMDPS KFTEPVKDLM LKGAPALN

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Macromolecule #5: C5 antibody variable heavy domain

MacromoleculeName: C5 antibody variable heavy domain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice)
Molecular weightTheoretical: 11.989335 KDa
SequenceString:
AVQLAESGPA LVAPSQALSI TCTVAGFSLT AYGVAWVRQP PGAGLEWLGA IWAAGATDYN AALKSRASIA KDNSKSQVFL AMASLATAD TAAYYCAREW DAYGDYWGQG TTVTVSA

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Macromolecule #6: C5 antibody variable light domain

MacromoleculeName: C5 antibody variable light domain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice)
Molecular weightTheoretical: 10.897161 KDa
SequenceString:
DIVLTQSPAA LSAAAGATVA ATCRASGNIH NALAWYQQKA GKSPQLLVYA AAALAAGVPS RFSGSGSGTA YALAINSLAA DDFGAYYCQ HFWSTPYTFG GGTKLEIK

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 166 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 8
Details: 20 mM Tris, 120 mM sodium chloride, 1 mM EDTA, pH 8.0
GridModel: Ted Pella, Ultrathin lacey carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 4-49 / Number grids imaged: 1 / Number real images: 537 / Average exposure time: 6.0 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 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

Particle selectionNumber selected: 26759
CTF correctionSoftware - Name: jspr
Details: On-the-fly CTF correction during 2D alignment and 3D reconstruction
Startup modelType of model: OTHER / Details: Particle orientations were randomly assigned.
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 16100
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: jspr
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 0.5 degrees
Software - Name: jspr
Final 3D classificationSoftware - Name: RELION (ver. 1.4)
Details: 23090 particles were selected after 2D classification.
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsA combination of the following approaches was used: (1) model rebuilding using Coot, (2) real space refinement using Phenix, (3) reciprocal space refinment using Phenix (as in standard crystallographic refinement).
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coeffcient
Output model

PDB-5w3l:
CryoEM structure of rhinovirus B14 in complex with C5 Fab (4 degrees Celsius, molar ratio 1:3, full particle)

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