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- PDB-6nk7: Electron Cryo-Microscopy of Chikungunya in Complex with Mouse Mxr... -

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Basic information

Entry
Database: PDB / ID: 6nk7
TitleElectron Cryo-Microscopy of Chikungunya in Complex with Mouse Mxra8 Receptor
Components
  • Capsid proteinCapsid
  • E1 glycoprotein
  • E2 glycoprotein
  • E3 glycoprotein
  • Matrix remodeling-associated protein 8
KeywordsVIRUS / Chikungunya / viral receptor / Mxra8 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / establishment of glial blood-brain barrier / ec:3.4.21.90: / ciliary membrane / bicellular tight junction / host cell membrane / viral capsid / fusion of virus membrane with host endosome membrane / host cell cytoplasm ...Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / establishment of glial blood-brain barrier / ec:3.4.21.90: / ciliary membrane / bicellular tight junction / host cell membrane / viral capsid / fusion of virus membrane with host endosome membrane / host cell cytoplasm / cell adhesion / virion attachment to host cell / virion membrane / serine-type endopeptidase activity / structural molecule activity / cell surface / integral component of membrane / nucleus / cytoplasm
Alphavirus E1 glycoprotein / Peptidase S1, PA clan / Immunoglobulin subtype / Immunoglobulin V-set domain / Alphavirus E3 spike glycoprotein / Alphavirus E2 glycoprotein / Peptidase S3, togavirin / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulin E-set ...Alphavirus E1 glycoprotein / Peptidase S1, PA clan / Immunoglobulin subtype / Immunoglobulin V-set domain / Alphavirus E3 spike glycoprotein / Alphavirus E2 glycoprotein / Peptidase S3, togavirin / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulin E-set / Immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Immunoglobulin V-set domain / Ig-like domain profile. / Alphavirus core protein (CP) domain profile. / Immunoglobulin-like domain
Togavirin / Togavirin / Matrix remodeling-associated protein 8
Biological speciesChikungunya virus
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.99 Å
AuthorsBasore, K. / Kim, A.S. / Nelson, C.A. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding supportUnited States , 1件
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesHHSN272201700060CUnited States
CitationJournal: Cell / Year: 2019
Title: Cryo-EM Structure of Chikungunya Virus in Complex with the Mxra8 Receptor.
Authors: Katherine Basore / Arthur S Kim / Christopher A Nelson / Rong Zhang / Brittany K Smith / Carla Uranga / Lo Vang / Ming Cheng / Michael L Gross / Jonathan Smith / Michael S Diamond / Daved H Fremont /
Abstract: Mxra8 is a receptor for multiple arthritogenic alphaviruses that cause debilitating acute and chronic musculoskeletal disease in humans. Herein, we present a 2.2 Å resolution X-ray crystal ...Mxra8 is a receptor for multiple arthritogenic alphaviruses that cause debilitating acute and chronic musculoskeletal disease in humans. Herein, we present a 2.2 Å resolution X-ray crystal structure of Mxra8 and 4 to 5 Å resolution cryo-electron microscopy reconstructions of Mxra8 bound to chikungunya (CHIKV) virus-like particles and infectious virus. The Mxra8 ectodomain contains two strand-swapped Ig-like domains oriented in a unique disulfide-linked head-to-head arrangement. Mxra8 binds by wedging into a cleft created by two adjacent CHIKV E2-E1 heterodimers in one trimeric spike and engaging a neighboring spike. Two binding modes are observed with the fully mature VLP, with one Mxra8 binding with unique contacts. Only the high-affinity binding mode was observed in the complex with infectious CHIKV, as viral maturation and E3 occupancy appear to influence receptor binding-site usage. Our studies provide insight into how Mxra8 binds CHIKV and creates a path for developing alphavirus entry inhibitors.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 4, 2019 / Release: May 22, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 22, 2019Structure modelrepositoryInitial release
1.1May 29, 2019Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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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
  • EMDB-9395
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: E1 glycoprotein
B: E1 glycoprotein
C: E1 glycoprotein
D: E1 glycoprotein
E: E2 glycoprotein
F: E2 glycoprotein
G: E2 glycoprotein
H: E2 glycoprotein
I: Capsid protein
J: Capsid protein
K: Capsid protein
L: Capsid protein
U: E3 glycoprotein
V: E3 glycoprotein
W: E3 glycoprotein
X: E3 glycoprotein
N: Matrix remodeling-associated protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)502,96622
Polymers501,86017
Non-polymers1,1065
Water0
1
A: E1 glycoprotein
B: E1 glycoprotein
C: E1 glycoprotein
D: E1 glycoprotein
E: E2 glycoprotein
F: E2 glycoprotein
G: E2 glycoprotein
H: E2 glycoprotein
I: Capsid protein
J: Capsid protein
K: Capsid protein
L: Capsid protein
U: E3 glycoprotein
V: E3 glycoprotein
W: E3 glycoprotein
X: E3 glycoprotein
N: Matrix remodeling-associated protein 8
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)30,177,9511320
Polymers30,111,5881020
Non-polymers66,362300
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area49310 Å2
ΔGint-241 kcal/mol
Surface area211770 Å2
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: E1 glycoprotein
B: E1 glycoprotein
C: E1 glycoprotein
D: E1 glycoprotein
E: E2 glycoprotein
F: E2 glycoprotein
G: E2 glycoprotein
H: E2 glycoprotein
I: Capsid protein
J: Capsid protein
K: Capsid protein
L: Capsid protein
U: E3 glycoprotein
V: E3 glycoprotein
W: E3 glycoprotein
X: E3 glycoprotein
N: Matrix remodeling-associated protein 8
hetero molecules
x 5


  • icosahedral pentamer
  • 2.51 MDa, 85 polymers
Theoretical massNumber of molelcules
Total (without water)2,514,829110
Polymers2,509,29985
Non-polymers5,53025
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: E1 glycoprotein
B: E1 glycoprotein
C: E1 glycoprotein
D: E1 glycoprotein
E: E2 glycoprotein
F: E2 glycoprotein
G: E2 glycoprotein
H: E2 glycoprotein
I: Capsid protein
J: Capsid protein
K: Capsid protein
L: Capsid protein
U: E3 glycoprotein
V: E3 glycoprotein
W: E3 glycoprotein
X: E3 glycoprotein
N: Matrix remodeling-associated protein 8
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 3.02 MDa, 102 polymers
Theoretical massNumber of molelcules
Total (without water)3,017,795132
Polymers3,011,159102
Non-polymers6,63630
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
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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Protein/peptide , 5 types, 17 molecules ABCDEFGHIJKLUVWXN

#1: Protein/peptide
E1 glycoprotein


Mass: 47497.906 Da / Num. of mol.: 4 / Fragment: UNP residues 810-1248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: 181/25 / Gene: CHIKVgp2 / Cell line (production host): Vero / Production host: Chlorocebus aethiops (grivet) / References: UniProt: Q88628, EC: 3.4.21.90
#2: Protein/peptide
E2 glycoprotein


Mass: 47077.719 Da / Num. of mol.: 4 / Fragment: UNP residues 330-748
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: 181/25 / Gene: CHIKVgp2 / Cell line (production host): Vero / Production host: Chlorocebus aethiops (grivet) / References: UniProt: Q88628, EC: 3.4.21.90
#3: Protein/peptide
Capsid protein / Capsid


Mass: 16428.607 Da / Num. of mol.: 4 / Fragment: UNP residues 111-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: 181/25 / Gene: CHIKVgp2 / Cell line (production host): Vero / Production host: Chlorocebus aethiops (grivet) / References: UniProt: Q88628, EC: 3.4.21.90
#4: Protein/peptide
E3 glycoprotein


Mass: 6955.070 Da / Num. of mol.: 4 / Fragment: UNP residues 266-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: 181/25 / Cell line (production host): Vero / Production host: Chlorocebus aethiops (grivet) / References: UniProt: D2KBQ2, EC: 3.4.21.90
#5: Protein/peptide Matrix remodeling-associated protein 8 / Adipocyte-specific protein 3 / Dual Ig domain-containing cell adhesion molecule / DICAM / Limitrin


Mass: 30022.596 Da / Num. of mol.: 1 / Fragment: ectodomain (UNP residues 39-291)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mxra8, Asp3, Dicam / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9DBV4

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Non-polymers , 1 types, 5 molecules

#6: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / N-Acetylglucosamine

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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

Component

Type: COMPLEX

IDNameEntity IDParent-IDSource
1Chikungunya virus with Mxra8 receptor1, 2, 3, 4, 50MULTIPLE SOURCES
2Chikungunya virusChikungunya1, 2, 3, 41RECOMBINANT
3mouse Mxra8 receptor ectodomain51RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
12Chikungunya virus37124181/25
23Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
12Chlorocebus aethiops (grivet)9534Vero
23Homo sapiens (human)9606HEK293
Details of virusEmpty: YES / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.2 / Details: Mxra8 at pH 7.4
Buffer component

Buffer-ID: 1

IDConc.Name
1218 mMsucrose
210 mMpotassium phosphate
325 mMcitrateCitric acid
4150 mMsodium chloride
525 mMHEPES
61 mMsodium azide
SpecimenDetails: Chikungunya virus grown in Vero cells + 15 mg/mL Mxra8 expressed in HEK293 cells
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 0.458 mbar.l/s O2 and 0.11 mbar.l/s H2 / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 0.3 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2RELION2.1image acquisition
4CTFFIND4CTF correction
7UCSF Chimera1.13.1model fitting
8Coot0.8.9.1model fitting
11FREALIGN10final Euler assignment
13cisTEM1.0.0-beta3D reconstruction
14PHENIX1.14model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8357 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDPdb chain residue range
13N42B5-342
23N42F1-393
33J0CA394-442
43J0CB394-423
55H23A111-261
66NK3A39-291
73N42A5-63

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