[English] 日本語
Yorodumi
- EMDB-9395: Electron Cryo-Microscopy of Chikungunya in Complex with Mouse Mxr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9395
TitleElectron Cryo-Microscopy of Chikungunya in Complex with Mouse Mxra8 Receptor
Map dataChikungunya in Complex with Mouse Mxra8 Receptor
Sample
  • Complex: Chikungunya virus with Mxra8 receptor
    • Complex: Chikungunya virus
      • Protein or peptide: E1 glycoprotein
      • Protein or peptide: E2 glycoprotein
      • Protein or peptide: Capsid protein
      • Protein or peptide: E3 glycoprotein
    • Complex: mouse Mxra8 receptor ectodomain
      • Protein or peptide: Matrix remodeling-associated protein 8
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsChikungunya / viral receptor / Mxra8 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / VIRUS
Function / homology
Function and homology information


establishment of glial blood-brain barrier / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / T=4 icosahedral viral capsid / ciliary membrane / bicellular tight junction / host cell cytoplasm / cell adhesion / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane ...establishment of glial blood-brain barrier / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / T=4 icosahedral viral capsid / ciliary membrane / bicellular tight junction / host cell cytoplasm / cell adhesion / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / cell surface / proteolysis / RNA binding / nucleus / membrane / cytoplasm
Similarity search - Function
Matrix remodeling-associated protein 8 / Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein ...Matrix remodeling-associated protein 8 / Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin E-set / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein / Structural polyprotein / Matrix remodeling-associated protein 8
Similarity search - Component
Biological speciesChikungunya virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.99 Å
AuthorsBasore K / Kim AS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United 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.
History
DepositionJan 4, 2019-
Header (metadata) releaseFeb 27, 2019-
Map releaseMay 22, 2019-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6nk7
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6nk7
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9395.png

Downloads & links

-
Map

FileDownload / File: emd_9395.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChikungunya in Complex with Mouse Mxra8 Receptor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 600 pix.
= 841.8 Å		1.4 Å/pix.
x 600 pix.
= 841.8 Å		1.4 Å/pix.
x 600 pix.
= 841.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.403 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-4.306646 - 6.398281
Average (Standard dev.)0.14662306 (±0.7393429)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-300-300-300
Dimensions600600600
Spacing600600600
CellA=B=C: 841.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4031.4031.403
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z841.800841.800841.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ513513513
MAP C/R/S123
start NC/NR/NS-300-300-300
NC/NR/NS600600600
D min/max/mean-4.3076.3980.147

-
Supplemental data

-
Sample components

-
Entire : Chikungunya virus with Mxra8 receptor

EntireName: Chikungunya virus with Mxra8 receptor
Components
  • Complex: Chikungunya virus with Mxra8 receptor
    • Complex: Chikungunya virus
      • Protein or peptide: E1 glycoprotein
      • Protein or peptide: E2 glycoprotein
      • Protein or peptide: Capsid protein
      • Protein or peptide: E3 glycoprotein
    • Complex: mouse Mxra8 receptor ectodomain
      • Protein or peptide: Matrix remodeling-associated protein 8
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Chikungunya virus with Mxra8 receptor

SupramoleculeName: Chikungunya virus with Mxra8 receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

-
Supramolecule #2: Chikungunya virus

SupramoleculeName: Chikungunya virus / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Chikungunya virus / Strain: 181/25

-
Supramolecule #3: mouse Mxra8 receptor ectodomain

SupramoleculeName: mouse Mxra8 receptor ectodomain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: E1 glycoprotein

MacromoleculeName: E1 glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Chikungunya virus / Strain: 181/25
Molecular weightTheoretical: 47.497906 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELLSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMW GGAYCFCDTE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNVTVSAYAN GDHAVTVKDA K FIVGPMSS ...String:
YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELLSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMW GGAYCFCDTE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNVTVSAYAN GDHAVTVKDA K FIVGPMSS AWTPFDNKIV VYKGDVYNMD YPPFGAGRPG QFGDIQSRTP ESEDVYANTQ LVLQRPSAGT VHVPYSQAPS GF KYWLKER GASLQHTAPF GCQIATNPVR AMNCAVGNMP ISIDIPDAAF TRVVDAPSLT DMSCEVPACT HSSDFGGVAI IKY AASKKG KCAVHSMTNA VTIREAEIEV EGNSQLQISF STALASAEFR VQVCSTQVHC AAECHPPKDH IVNYPASHTT LGVQ DISVT AMSWVQKITG GVGLVVAVAA LILIVVLCVS FSRH

UniProtKB: Structural polyprotein

-
Macromolecule #2: E2 glycoprotein

MacromoleculeName: E2 glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Chikungunya virus / Strain: 181/25
Molecular weightTheoretical: 47.077719 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: NFNVYKAIRP YLAHCPDCGE GHSCHSPVAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDNHM PADAERARLF VRTSAPCTI TGTMGHFILA RCPKGETLTV GFTDGRKISH SCTHPFHHDP PVIGREKFHS RPQHGRELPC STYAQSTAAT A EEIEVHMP ...String:
NFNVYKAIRP YLAHCPDCGE GHSCHSPVAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDNHM PADAERARLF VRTSAPCTI TGTMGHFILA RCPKGETLTV GFTDGRKISH SCTHPFHHDP PVIGREKFHS RPQHGRELPC STYAQSTAAT A EEIEVHMP PDTPDRTLMS QQSGNVKITV NSQTVRYKCN CGDSNEGLTT TDKVINNCKV DQCHAAVTNH KKWQYNSPLV PR NAELGDR KGKVHIPFPL ANVTCRVPKA RNPTVTYGKN QVIMLLYPDH PTLLSYRNMG EEPNYQEEWV THKKEIRLTV PTE GLEVTW GNNEPYKYWP QLSTNGTAHG HPHEIILYYY ELYPTMTVVV VSVASFVLLS MVGVAVGMCM CARRRCITPY ELTP GATVP FLLSLICCIR TAKA

UniProtKB: Structural polyprotein

-
Macromolecule #3: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Chikungunya virus / Strain: 181/25
Molecular weightTheoretical: 16.428607 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString:
NDCIFEVKHE GKVTGYACLV GDKVMKPAHV KGTIDNADLA KLAFKRSSKY DLECAQIPVH MKSDASKFTH EKPEGYYNWH HGAVQYSGG RFTIPTGAGK PGDSGRPIFD NKGRVVAIVL GGANEGARTA LSVVTWNKDI VTKITPEGAE EW

UniProtKB: Structural polyprotein

-
Macromolecule #4: E3 glycoprotein

MacromoleculeName: E3 glycoprotein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Chikungunya virus / Strain: 181/25
Molecular weightTheoretical: 6.95507 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString:
PVMCLLANTT FPCSQPPCTP CCYEKEPEET LRMLEDNVMR PGYYQLLQAS LTCSPHRQRR

UniProtKB: Structural polyprotein

-
Macromolecule #5: Matrix remodeling-associated protein 8

MacromoleculeName: Matrix remodeling-associated protein 8 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 30.022596 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SSSLVSESVV SLAAGTQAVL RCQSPRMVWT QDRLHDRQRV VHWDLSGGPG SQRRRLVDMY SAGEQRVYEP RDRDRLLLSP SAFHDGNFS LLIRAVDRGD EGVYTCNLHH HYCHLDESLA VRLEVTEDPL LSRAYWDGEK EVLVVAHGAP ALMTCINRAH V WTDRHLEE ...String:
SSSLVSESVV SLAAGTQAVL RCQSPRMVWT QDRLHDRQRV VHWDLSGGPG SQRRRLVDMY SAGEQRVYEP RDRDRLLLSP SAFHDGNFS LLIRAVDRGD EGVYTCNLHH HYCHLDESLA VRLEVTEDPL LSRAYWDGEK EVLVVAHGAP ALMTCINRAH V WTDRHLEE AQQVVHWDRQ LPGVSHDRAD RLLDLYASGE RRAYGPPFLR DRVSVNTNAF ARGDFSLRID ELERADEGIY SC HLHHHYC GLHERRVFHL QVTE

UniProtKB: Matrix remodeling-associated protein 8

-
Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.2
Component:
ConcentrationName
218.0 mMsucrose
10.0 mMpotassium phosphate
25.0 mMcitrate
150.0 mMsodium chloride
25.0 mMHEPES
1.0 mMsodium azide

Details: Mxra8 at pH 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 120 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Details: 0.458 mbar.l/s O2 and 0.11 mbar.l/s H2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.00 K / Instrument: FEI VITROBOT MARK IV
DetailsChikungunya virus grown in Vero cells + 15 mg/mL Mxra8 expressed in HEK293 cells

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 0.3 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0.0-beta) / Number images used: 8357
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: NOT APPLICABLE / Software - Name: FREALIGN (ver. 10)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

3n42

chain_id: B, residue_range: 5-342, source_name: PDB, initial_model_type: experimental model

3n42

chain_id: F, residue_range: 1-393, source_name: PDB, initial_model_type: experimental model

3j0c

chain_id: A, residue_range: 394-442, source_name: PDB, initial_model_type: experimental model

3j0c

chain_id: B, residue_range: 394-423, source_name: PDB, initial_model_type: experimental model

5h23

chain_id: A, residue_range: 111-261, source_name: PDB, initial_model_type: experimental model

6nk3

chain_id: A, residue_range: 39-291, source_name: PDB, initial_model_type: experimental model

3n42

chain_id: A, residue_range: 5-63, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6nk7:
Electron Cryo-Microscopy of Chikungunya in Complex with Mouse Mxra8 Receptor

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more