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- PDB-4gl2: Structural Basis for dsRNA duplex backbone recognition by MDA5 -

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Basic information

Entry
Database: PDB / ID: 4gl2
TitleStructural Basis for dsRNA duplex backbone recognition by MDA5
Components
  • Interferon-induced helicase C domain-containing protein 1
  • RNA (5'-R(*AP*UP*CP*CP*GP*CP*GP*GP*CP*CP*CP*U)-3')
  • RNA (5'-R(P*AP*GP*GP*GP*CP*CP*GP*CP*GP*GP*AP*U)-3')
KeywordsRNA BINDING PROTEIN/RNA / MDA5 / dsRNA / anti-viral signaling / RIG-I / MAVS / oligomerization / helicase / ATPase / filament formation / RNA BINDING PROTEIN-RNA complex
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 / negative regulation of viral genome replication / cytoplasmic pattern recognition receptor signaling pathway / 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 / negative regulation of viral genome replication / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / protein complex oligomerization / positive regulation of interferon-alpha production / TRAF6 mediated NF-kB activation / protein sumoylation / ribonucleoprotein complex binding / antiviral innate immune response / positive regulation of interferon-beta production / Negative regulators of DDX58/IFIH1 signaling / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / cellular response to virus / Evasion by RSV of host interferon responses / 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 / 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
phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / 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 ...phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / 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 nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RNA / RNA (> 10) / Interferon-induced helicase C domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.557 Å
AuthorsWu, B. / Hur, S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Structural Basis for dsRNA Recognition, Filament Formation, and Antiviral Signal Activation by MDA5.
Authors: Wu, B. / Peisley, A. / Richards, C. / Yao, H. / Zeng, X. / Lin, C. / Chu, F. / Walz, T. / Hur, S.
History
DepositionAug 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Oct 30, 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 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon-induced helicase C domain-containing protein 1
B: Interferon-induced helicase C domain-containing protein 1
C: RNA (5'-R(*AP*UP*CP*CP*GP*CP*GP*GP*CP*CP*CP*U)-3')
E: RNA (5'-R(*AP*UP*CP*CP*GP*CP*GP*GP*CP*CP*CP*U)-3')
F: RNA (5'-R(P*AP*GP*GP*GP*CP*CP*GP*CP*GP*GP*AP*U)-3')
D: RNA (5'-R(P*AP*GP*GP*GP*CP*CP*GP*CP*GP*GP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,41810
Polymers176,2746
Non-polymers1,1434
Water00
1
A: Interferon-induced helicase C domain-containing protein 1
C: RNA (5'-R(*AP*UP*CP*CP*GP*CP*GP*GP*CP*CP*CP*U)-3')
D: RNA (5'-R(P*AP*GP*GP*GP*CP*CP*GP*CP*GP*GP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7095
Polymers88,1373
Non-polymers5722
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-57 kcal/mol
Surface area32620 Å2
MethodPISA
2
B: Interferon-induced helicase C domain-containing protein 1
E: RNA (5'-R(*AP*UP*CP*CP*GP*CP*GP*GP*CP*CP*CP*U)-3')
F: RNA (5'-R(P*AP*GP*GP*GP*CP*CP*GP*CP*GP*GP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7095
Polymers88,1373
Non-polymers5722
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-61 kcal/mol
Surface area31790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.112, 154.748, 185.006
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Interferon-induced helicase C domain-containing protein 1 / Clinically amyopathic dermatomyositis autoantigen 140 kDa / CADM-140 autoantigen / Helicase with 2 ...Clinically amyopathic dermatomyositis autoantigen 140 kDa / CADM-140 autoantigen / Helicase with 2 CARD domains / Helicard / Interferon-induced with helicase C domain protein 1 / Melanoma differentiation-associated protein 5 / MDA-5 / Murabutide down-regulated protein / RIG-I-like receptor 2 / RLR-2 / RNA helicase-DEAD box protein 116


Mass: 80467.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFIH1, MDA5, RH116 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BYX4, RNA helicase
#2: RNA chain RNA (5'-R(*AP*UP*CP*CP*GP*CP*GP*GP*CP*CP*CP*U)-3')


Mass: 3763.288 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: RNA chain RNA (5'-R(P*AP*GP*GP*GP*CP*CP*GP*CP*GP*GP*AP*U)-3')


Mass: 3906.400 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THIS IS A TRUNCATED VERSION OF HUMAN MDA5 PROTEIN (NP_071451).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2012
RadiationMonochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.557→118.699 Å / Num. all: 25225 / Num. obs: 24216 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
APSin house softwaredata collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.557→118.699 Å / SU ML: 0.55 / σ(F): 1.35 / Phase error: 36.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.32 1204 5.01 %
Rwork0.2761 --
obs0.2782 24044 95.1 %
all-25225 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.557→118.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9651 1020 64 0 10735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811013
X-RAY DIFFRACTIONf_angle_d1.27315084
X-RAY DIFFRACTIONf_dihedral_angle_d16.7214282
X-RAY DIFFRACTIONf_chiral_restr0.0631773
X-RAY DIFFRACTIONf_plane_restr0.0051716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.557-3.69940.43341330.35682548X-RAY DIFFRACTION97
3.6994-3.86780.31541330.32742510X-RAY DIFFRACTION96
3.8678-4.07180.3361320.30392486X-RAY DIFFRACTION95
4.0718-4.32690.36831320.28822521X-RAY DIFFRACTION96
4.3269-4.6610.31191350.2522548X-RAY DIFFRACTION96
4.661-5.130.29811340.24692545X-RAY DIFFRACTION95
5.13-5.87230.3581330.29522523X-RAY DIFFRACTION94
5.8723-7.39840.31421360.28032571X-RAY DIFFRACTION95
7.3984-118.76470.24951360.22792588X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.41431.2645-0.44812.4265-0.53782.5657-0.16910.19410.4040.22210.13590.31750.0009-0.27640.19480.40190.06450.06340.31110.04250.327129.835220.537-0.0015
21.2872-0.1546-0.20522.31880.74891.44340.08650.0772-0.0164-0.30640.10810.14310.1217-0.1854-0.25770.40250.1223-0.07690.52460.10420.344128.588510.6821-19.961
32.13970.1327-1.66591.2124-1.1272.1528-0.32760.3416-0.8756-0.28980.0499-0.27680.851-0.0677-0.09831.17030.24020.28060.18550.04250.723231.0515-31.907-2.553
43.3115-0.07490.75264.01890.35282.6518-0.01450.45230.19130.07050.0327-0.57490.51940.7387-0.04870.51980.2827-0.02060.36990.01690.266644.8689-5.5984-10.8588
52.5531-0.9617-0.04953.0630.40481.34980.12830.47560.1245-0.21280.06410.1881-0.0991-0.00120.13840.4879-0.004-0.06930.887-0.15660.402917.48438.7253-15.2
62.3108-1.5452-0.8992.62981.38052.69170.3585-0.2292-0.1044-0.1867-0.0427-0.002-0.0834-0.2464-0.47650.5588-0.0231-0.08090.2910.02860.345820.4858-19.217419.5178
72.72670.76330.45282.2215-0.34492.7004-0.06180.3105-0.2527-0.03880.27730.1219-0.0764-0.229-0.27970.4812-0.00780.04710.25870.05330.2547-5.474-21.471635.2735
81.1597-0.37840.87742.40630.76792.3529-0.1176-0.5694-0.21940.3640.10330.16430.58340.25780.12290.47290.22460.02870.5336-0.0520.2074-7.6364-12.239354.6192
90.9213-0.63770.07022.2296-0.56450.4934-0.2457-0.20570.50460.2575-0.0245-0.6502-0.42280.0774-0.02970.66360.1774-0.5179-0.08120.08780.6921-4.531830.596937.6169
102.15351.1378-0.98174.02840.64873.4486-0.1969-0.4398-0.15390.19740.2578-0.5071-0.22441.00780.13230.4026-0.0956-0.10980.50090.00470.40939.64665.047645.5915
112.3522-0.0572-0.15750.9376-0.79871.8336-0.4992-0.6507-0.1088-0.1107-0.31510.3845-0.0953-0.27560.13130.391-0.0183-0.07370.3481-0.00420.4681-17.0782-10.072152.0299
124.15391.44250.39382.8072-0.49391.9128-0.01140.36860.37050.38020.02380.0573-0.3723-0.3385-0.07730.44280.0469-0.06410.1770.03810.3208-15.130218.080715.564
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 306:490
2X-RAY DIFFRACTION2CHAIN A AND RESID 491:543
3X-RAY DIFFRACTION3CHAIN A AND RESID 550:694
4X-RAY DIFFRACTION4CHAIN A AND RESID 699:835
5X-RAY DIFFRACTION5CHAIN A AND RESID 836:889
6X-RAY DIFFRACTION6CHAIN A AND RESID 900:1013
7X-RAY DIFFRACTION7CHAIN B AND RESID 306:490
8X-RAY DIFFRACTION8CHAIN B AND RESID 491:541
9X-RAY DIFFRACTION9CHAIN B AND RESID 550:694
10X-RAY DIFFRACTION10CHAIN B AND RESID 698:835
11X-RAY DIFFRACTION11CHAIN B AND RESID 836:887
12X-RAY DIFFRACTION12CHAIN B AND RESID 900:1013

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