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- PDB-5w3l: CryoEM structure of rhinovirus B14 in complex with C5 Fab (4 degr... -

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Basic information

Entry
Database: PDB / ID: 5w3l
TitleCryoEM structure of rhinovirus B14 in complex with C5 Fab (4 degrees Celsius, molar ratio 1:3, full particle)
Components
  • (C5 antibody variable ...) x 2
  • (viral protein ...) x 4
KeywordsVIRUS/IMMUNE SYSTEM / virus / antibody / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


lysis of host organelle involved in viral entry into host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 ...lysis of host organelle involved in viral entry into host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / channel activity / monoatomic ion transmembrane transport / 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 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / 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 coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / 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 / Few Secondary Structures / Irregular / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / 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 / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman rhinovirus 14
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsLiu, Y. / Dong, Y. / Rossmann, M.G.
Funding support United States, 1items
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, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_audit_support.funding_organization
Revision 1.2Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: viral protein 1
B: viral protein 3
C: viral protein 2
D: viral protein 4
E: C5 antibody variable heavy domain
G: C5 antibody variable light domain


Theoretical massNumber of molelcules
Total (without water)117,3696
Polymers117,3696
Non-polymers00
Water2,990166
1
A: viral protein 1
B: viral protein 3
C: viral protein 2
D: viral protein 4
E: C5 antibody variable heavy domain
G: C5 antibody variable light domain
x 60


Theoretical massNumber of molelcules
Total (without water)7,042,141360
Polymers7,042,141360
Non-polymers00
Water6,485360
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: viral protein 1
B: viral protein 3
C: viral protein 2
D: viral protein 4
E: C5 antibody variable heavy domain
G: C5 antibody variable light domain
x 5


  • icosahedral pentamer
  • 587 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)586,84530
Polymers586,84530
Non-polymers00
Water54030
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: viral protein 1
B: viral protein 3
C: viral protein 2
D: viral protein 4
E: C5 antibody variable heavy domain
G: C5 antibody variable light domain
x 6


  • icosahedral 23 hexamer
  • 704 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)704,21436
Polymers704,21436
Non-polymers00
Water64936
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Viral protein ... , 4 types, 4 molecules ABCD

#1: Protein viral protein 1


Mass: 32560.549 Da / Num. of mol.: 1 / Fragment: UNP residues 568-856 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / References: UniProt: P03303
#2: Protein viral protein 3


Mass: 26236.754 Da / Num. of mol.: 1 / Fragment: UNP residues 332-567 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / References: UniProt: P03303
#3: Protein viral protein 2


Mass: 28501.361 Da / Num. of mol.: 1 / Fragment: UNP residues 70-331 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / References: UniProt: P03303
#4: Protein viral protein 4


Mass: 7183.863 Da / Num. of mol.: 1 / Fragment: UNP residues 2-69 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / References: UniProt: P03303

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Antibody , 2 types, 2 molecules EG

#5: Antibody C5 antibody variable heavy domain


Mass: 11989.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#6: Antibody C5 antibody variable light domain


Mass: 10897.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 1 types, 166 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human rhinovirus B14 / Type: VIRUS / Details: Viruses were grown in HeLa-H1 cells. / Entity ID: #1-#6 / Source: NATURAL
Source (natural)Organism: Human rhinovirus B14
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 8
Details: 20 mM Tris, 120 mM sodium chloride, 1 mM EDTA, pH 8.0
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Ted Pella, Ultrathin lacey carbon
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 29000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6 sec. / Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 537
Image scansSampling size: 5 µm / Width: 3710 / Height: 3838 / Movie frames/image: 50 / Used frames/image: 4-49

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Processing

EM software
IDNameVersionCategory
1EMAN22.07particle selection
2DoG Pickerparticle selection
3Leginon3.1image acquisition
5jsprCTF correction
8UCSF Chimeramodel fitting
10PHENIXmodel refinement
11Cootmodel refinement
12jsprinitial Euler assignment
13jsprfinal Euler assignment
14RELION1.4classification
15jspr3D reconstruction
CTF correctionDetails: On-the-fly CTF correction during 2D alignment and 3D reconstruction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 26759
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16100 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coeffcient
Details: A 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 ...Details: A 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).

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