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- PDB-4a36: Structure of duck RIG-I helicase domain bound to 19-mer dsRNA and... -

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Basic information

Entry
Database: PDB / ID: 4a36
TitleStructure of duck RIG-I helicase domain bound to 19-mer dsRNA and ATP transition state analogue
Components
  • 5'-R(*GP*CP*AP*UP*GP*CP*GP*AP*CP*CP*UP*CP*UP*GP *UP*UP*UP*GP*A)-3'
  • 5'-R(*UP*CP*AP*AP*AP*CP*AP*GP*AP*GP*GP*UP*CP*GP *CP*AP*UP*GP*C)-3'
  • RETINOIC ACID INDUCIBLE PROTEIN I
KeywordsRNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA COMPLEX / SUPERFAMILY 2 RNA HELICASE / ATP AND DSRNA BINDING / ANTIVIRAL SIGNALLING PATHWAY
Function / homology
Function and homology information


RNA helicase activity / RNA helicase / hydrolase activity / innate immune response / RNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / RIG-I, CARD domain repeat 2 / 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, CARD domain repeat 2 / 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 / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / RNA / RNA (> 10) / RNA helicase
Similarity search - Component
Biological speciesANAS PLATYRHYNCHOS (mallard)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsKowalinski, E. / Lunardi, T. / McCarthy, A.A. / Cusack, S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structural Basis for the Activation of Innate Immune Pattern Recognition Receptor Rig-I by Viral RNA.
Authors: Kowalinski, E. / Lunardi, T. / Mccarthy, A.A. / Louber, J. / Brunel, J. / Grigorov, B. / Gerlier, D. / Cusack, S.
History
DepositionSep 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2May 20, 2015Group: Source and taxonomy
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: RETINOIC ACID INDUCIBLE PROTEIN I
B: RETINOIC ACID INDUCIBLE PROTEIN I
R: 5'-R(*GP*CP*AP*UP*GP*CP*GP*AP*CP*CP*UP*CP*UP*GP *UP*UP*UP*GP*A)-3'
S: 5'-R(*UP*CP*AP*AP*AP*CP*AP*GP*AP*GP*GP*UP*CP*GP *CP*AP*UP*GP*C)-3'
T: 5'-R(*GP*CP*AP*UP*GP*CP*GP*AP*CP*CP*UP*CP*UP*GP *UP*UP*UP*GP*A)-3'
U: 5'-R(*UP*CP*AP*AP*AP*CP*AP*GP*AP*GP*GP*UP*CP*GP *CP*AP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,99512
Polymers150,9246
Non-polymers1,0716
Water0
1
A: RETINOIC ACID INDUCIBLE PROTEIN I
R: 5'-R(*GP*CP*AP*UP*GP*CP*GP*AP*CP*CP*UP*CP*UP*GP *UP*UP*UP*GP*A)-3'
S: 5'-R(*UP*CP*AP*AP*AP*CP*AP*GP*AP*GP*GP*UP*CP*GP *CP*AP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9976
Polymers75,4623
Non-polymers5353
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-39.8 kcal/mol
Surface area30090 Å2
MethodPISA
2
B: RETINOIC ACID INDUCIBLE PROTEIN I
T: 5'-R(*GP*CP*AP*UP*GP*CP*GP*AP*CP*CP*UP*CP*UP*GP *UP*UP*UP*GP*A)-3'
U: 5'-R(*UP*CP*AP*AP*AP*CP*AP*GP*AP*GP*GP*UP*CP*GP *CP*AP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9976
Polymers75,4623
Non-polymers5353
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-39.6 kcal/mol
Surface area29900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.270, 129.270, 106.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12T
22R
13U
23S

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
211LYSLYSPHEPHEBB245 - 4547 - 216
111LYSLYSPHEPHEAA245 - 4547 - 216
221ASPASPGLYGLYBB461 - 666223 - 428
121ASPASPGLYGLYAA461 - 666223 - 428
231THRTHRLYSLYSBB675 - 787437 - 549
131THRTHRLYSLYSAA675 - 787437 - 549
112GGCCTE1 - 101 - 10
212GGCCRC1 - 101 - 10
113GGCCUF11 - 1911 - 19
213GGCCSD11 - 1911 - 19

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.913917, 0.402081, -0.055563), (-0.403125, -0.915105, 0.008564), (-0.047402, 0.030226, 0.998418)-216.2274, 33.94608, 48.4082

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein RETINOIC ACID INDUCIBLE PROTEIN I / RIG-I


Mass: 63329.492 Da / Num. of mol.: 2 / Fragment: HELICASE DOMAIN, RESIDUES 242-794
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANAS PLATYRHYNCHOS (mallard) / Plasmid: PFASTBAC / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: D3TI84

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RNA chain , 2 types, 4 molecules RTSU

#2: RNA chain 5'-R(*GP*CP*AP*UP*GP*CP*GP*AP*CP*CP*UP*CP*UP*GP *UP*UP*UP*GP*A)-3' / 19-MER


Mass: 6031.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: RNA chain 5'-R(*UP*CP*AP*AP*AP*CP*AP*GP*AP*GP*GP*UP*CP*GP *CP*AP*UP*GP*C)-3' / 19-MER


Mass: 6100.713 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 3 types, 6 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF3

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Details

Sequence detailsEXTRA GAM AT N-TERMINUS AFTER HIS-TAG CLEAVAGE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 58.2 % / Description: NONE
Crystal growDetails: 12 MG/ML, 1.2 TIMES MOLAR RATIO OF 19-MER DSRNA, 4 MM ADP, 2 MM ALF3 AND 0.1 M HEPES PH 7.5, 5% (V/V) ISO-PROPANOL AND 10% (W/V) PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 18825 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.55 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 10.8
Reflection shellResolution: 3.7→3.8 Å / Redundancy: 7.53 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A2P

4a2p


Resolution: 3.7→45.95 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.893 / SU B: 38.592 / SU ML: 0.567 / Cross valid method: THROUGHOUT / ESU R Free: 0.739 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 940 5 %RANDOM
Rwork0.19278 ---
obs0.19628 17885 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 3.7→45.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8348 1562 64 0 9974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01810284
X-RAY DIFFRACTIONr_bond_other_d0.0020.026572
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.87414235
X-RAY DIFFRACTIONr_angle_other_deg0.931316078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1451038
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.8524.722396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.087151613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7011554
X-RAY DIFFRACTIONr_chiral_restr0.0710.21621
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022027
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
12B6828tight positional0.020.05
11A6828tight positional0.020.05
21T589tight positional0.030.05
22R589tight positional0.030.05
22U589tight positional0.030.05
22S589tight positional0.030.05
12B6828tight thermal15.710.5
11A6828tight thermal15.710.5
21T589tight thermal7.870.5
22R589tight thermal7.870.5
22U589tight thermal7.870.5
22S589tight thermal7.870.5
LS refinement shellResolution: 3.7→3.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 58 -
Rwork0.283 1274 -
obs--99.92 %

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