[English] 日本語
Yorodumi
- EMDB-72244: CryoEM Structure of human MDA5 disease-linked mutant T331I with d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72244
TitleCryoEM Structure of human MDA5 disease-linked mutant T331I with dsRNA (one protein subunit on dsRNA)
Map data
Sample
  • Complex: Complex of human MDA5 disease-linked mutant T331I with dsRNA (one subunit on dsRNA)
    • Protein or peptide: Interferon-induced helicase C domain-containing protein 1
    • RNA: RNA-13mer
    • RNA: RNA-13mer
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: water
KeywordsRLR / MDA5 / MDA5 disease-linked mutant / T331I / IMMUNE SYSTEM
Function / homology
Function and homology information


MDA-5 signaling pathway / regulation of type III interferon production / detection of virus / positive regulation of response to cytokine stimulus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / Modulation of host responses by IFN-stimulated genes / TRAF6 mediated IRF7 activation / negative regulation of viral genome replication / cellular response to exogenous dsRNA / pattern recognition receptor activity ...MDA-5 signaling pathway / regulation of type III interferon production / detection of virus / positive regulation of response to cytokine stimulus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / Modulation of host responses by IFN-stimulated genes / TRAF6 mediated IRF7 activation / negative regulation of viral genome replication / cellular response to exogenous dsRNA / pattern recognition receptor activity / cytoplasmic pattern recognition receptor signaling pathway / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / protein complex oligomerization / protein sumoylation / ribonucleoprotein complex binding / Dengue virus activates/modulates innate and adaptive immune responses / positive regulation of interferon-beta production / antiviral innate immune response / cellular response to virus / Negative regulators of DDX58/IFIH1 signaling / positive regulation of interleukin-6 production / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Evasion by RSV of host interferon responses / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of tumor necrosis factor production / Ovarian tumor domain proteases / double-stranded RNA binding / defense response to virus / TRAF3-dependent IRF activation pathway / RNA helicase activity / innate immune response / single-stranded RNA binding / Ub-specific processing proteases / RNA helicase / protein domain specific binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / Caspase recruitment domain / Caspase recruitment domain / Helicase/UvrB, N-terminal ...RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / Caspase recruitment domain / Caspase recruitment domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Death-like domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Interferon-induced helicase C domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsXu L / Chung K / Pyle A
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Unraveling the molecular basis for MDA5 T331I disease-linked mutation
Authors: Xu L / Chung K / Guo R / Pan A / Pyle AM
History
DepositionAug 21, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72244.png

Downloads & links

-
Map

FileDownload / File: emd_72244.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 425.984 Å		0.83 Å/pix.
x 512 pix.
= 425.984 Å		0.83 Å/pix.
x 512 pix.
= 425.984 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.7523527 - 1.3419125
Average (Standard dev.)0.0010695736 (±0.022533508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 425.984 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_72244_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_72244_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_72244_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of human MDA5 disease-linked mutant T331I with dsRNA (one...

EntireName: Complex of human MDA5 disease-linked mutant T331I with dsRNA (one subunit on dsRNA)
Components
  • Complex: Complex of human MDA5 disease-linked mutant T331I with dsRNA (one subunit on dsRNA)
    • Protein or peptide: Interferon-induced helicase C domain-containing protein 1
    • RNA: RNA-13mer
    • RNA: RNA-13mer
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: water

-
Supramolecule #1: Complex of human MDA5 disease-linked mutant T331I with dsRNA (one...

SupramoleculeName: Complex of human MDA5 disease-linked mutant T331I with dsRNA (one subunit on dsRNA)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Interferon-induced helicase C domain-containing protein 1

MacromoleculeName: Interferon-induced helicase C domain-containing protein 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.714484 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: ARASPEPELQ LRPYQMEVAQ PALEGKNIII CLPIGSGKTR VAVYIAKDHL DKKKKASEPG KVIVLVNKVL LVEQLFRKEF QPFLKKWYR VIGLSGDTQL KISFPEVVKS CDIIISTAQI LENSLLNLEN GEDAGVQLSD FSLIIIDECH HTNKEAVYNN I MRHYLMQK ...String:
ARASPEPELQ LRPYQMEVAQ PALEGKNIII CLPIGSGKTR VAVYIAKDHL DKKKKASEPG KVIVLVNKVL LVEQLFRKEF QPFLKKWYR VIGLSGDTQL KISFPEVVKS CDIIISTAQI LENSLLNLEN GEDAGVQLSD FSLIIIDECH HTNKEAVYNN I MRHYLMQK LKNNRLKKEN KPVIPLPQIL GLTASPGVGG ATKQAKAEEH ILKLCANLDA FTIKTVKENL DQLKNQIQEP CK KFAIADA TREDPFKEKL LEIMTRIQTY CQMSPMSDFG TQPYEQWAIQ MEKKAAKEGN RKERVCAEHL RKYNEALQIN DTI RMIDAY THLETFYNEE KDKKFAVIED DSDEGGDDEY CDGDEDEDDL KKPLKLDETD RFLMTLFFEN NKMLKRLAEN PEYE NEKLT KLRNTIMEQY TRTEESARGI IFTKTRQSAY ALSQWITENE KFAEVGVKAH HLIGAGHSSE FKPMTQNEQK EVISK FRTG KINLLIATTV AEEGLDIKEC NIVIRYGLVT NEIAMVQARG RARADESTYV LVAHSGSGVI EHETVNDFRE KMMYKA IHC VQNMKPEEYA HKILELQMQS IMEKKMKTKR NIAKHYKNNP SLITFLCKNC SVLACSGEDI HVIEKMHHVN MTPEFKE LY IVRENKALQK KCADYQINGE IICKCGQAWG TMMVHKGLDL PCLKIRNFVV VFKNNSTKKQ YKKWVELPIT FPNLDYSE C CLFSDED

UniProtKB: Interferon-induced helicase C domain-containing protein 1

-
Macromolecule #2: RNA-13mer

MacromoleculeName: RNA-13mer / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.21355 KDa
SequenceString:
CGGUUAGGGG CUA

-
Macromolecule #3: RNA-13mer

MacromoleculeName: RNA-13mer / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.076494 KDa
SequenceString:
UAGCCCCUAA CCG

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.589 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: alphafold predicted model of protein
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 75762
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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