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- PDB-3ga3: Crystal structure of the C-terminal domain of human MDA5 -

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Basic information

Entry
Database: PDB / ID: 3ga3
TitleCrystal structure of the C-terminal domain of human MDA5
ComponentsInterferon-induced helicase C domain-containing protein 1, MDA5
KeywordsHYDROLASE / Innate immune receptor / RNA biniding / helicase / RLR / Alternative splicing / Antiviral defense / ATP-binding / Cytoplasm / Diabetes mellitus / Host-virus interaction / Immune response / Innate immunity / Nucleotide-binding / Nucleus / Phosphoprotein / Polymorphism / RNA-binding
Function / homology
Function and homology information


MDA-5 signaling pathway / regulation of type III interferon production / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / pattern recognition receptor activity / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / negative regulation of viral genome replication / type I interferon-mediated signaling pathway ...MDA-5 signaling pathway / regulation of type III interferon production / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / pattern recognition receptor activity / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / protein sumoylation / ribonucleoprotein complex binding / antiviral innate immune response / positive regulation of interferon-beta production / Negative regulators of DDX58/IFIH1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / Evasion by RSV of host interferon responses / cellular response to virus / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of tumor necrosis factor production / double-stranded RNA binding / Ovarian tumor domain proteases / protein complex oligomerization / TRAF3-dependent IRF activation pathway / defense response to virus / RNA helicase activity / single-stranded RNA binding / Ub-specific processing proteases / RNA helicase / innate immune response / 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 regulatory domain / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / 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 ...RIG-I-like receptor, C-terminal regulatory domain / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / 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 / Beta Complex / 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 / Mainly Beta
Similarity search - Domain/homology
Interferon-induced helicase C domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLi, P.
CitationJournal: To be Published
Title: Crystal structure of the C-terminal domain of human MDA5
Authors: Li, P. / Li, X. / Lu, C.
History
DepositionFeb 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon-induced helicase C domain-containing protein 1, MDA5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6542
Polymers15,5881
Non-polymers651
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.410, 60.920, 36.443
Angle α, β, γ (deg.)90.00, 102.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Interferon-induced helicase C domain-containing protein 1, MDA5 / Interferon-induced with helicase C domain protein 1 / Helicase with 2 CARD domains / Helicard / ...Interferon-induced with helicase C domain protein 1 / Helicase with 2 CARD domains / Helicard / Melanoma differentiation-associated protein 5 / MDA-5 / RNA helicase-DEAD box protein 116 / Murabutide down-regulated protein


Mass: 15588.222 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 893-1017
Source method: isolated from a genetically manipulated source
Details: 15 degrees overnight expression / Source: (gene. exp.) Homo sapiens (human) / Gene: IFIH1, IFIH1 or MDA5, MDA5, RH116 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: Q9BYX4, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.71 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 8.5
Details: 0.1 M Tris, 14 to 18% ethanol, pH 8.5, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: Osmic
RadiationMonochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 21528 / Num. obs: 20278 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 64.5
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.064 / Mean I/σ(I) obs: 45.6 / Num. unique all: 1868 / Rsym value: 0.064 / % possible all: 86.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RIG-I CTD

Resolution: 1.45→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: individual B refinement with CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1590 -Random
Rwork0.18 ---
all0.18 21528 --
obs0.18 20278 7.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20.162 Å2
2---0.913 Å20 Å2
3----0.129 Å2
Refinement stepCycle: LAST / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 1 204 1296
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.56
X-RAY DIFFRACTIONc_bond_d0.01
LS refinement shellResolution: 1.45→1.47 Å
RfactorNum. reflection% reflection
Rfree0.265 39 -
Rwork0.222 --
obs-1868 86.8 %

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