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- PDB-5udl: IFIT1 N216A monomeric mutant (L457E/L464E) with m7Gppp-AAAA (anti... -

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Basic information

Entry
Database: PDB / ID: 5udl
TitleIFIT1 N216A monomeric mutant (L457E/L464E) with m7Gppp-AAAA (anti conformation of cap)
Components
  • Interferon-induced protein with tetratricopeptide repeats 1
  • RNA (5'-D(*(GTA))-R(P*AP*AP*A)-3')
KeywordsRNA BINDING PROTEIN / mRNA cap / N7-Methylguanosine-triphosphate RNA / tetratricopeptide repeat
Function / homology
Function and homology information


intracellular transport of viral protein in host cell / cellular response to type I interferon / host cell / negative regulation of helicase activity / negative regulation of viral genome replication / cellular response to exogenous dsRNA / antiviral innate immune response / positive regulation of viral genome replication / negative regulation of protein binding / response to virus ...intracellular transport of viral protein in host cell / cellular response to type I interferon / host cell / negative regulation of helicase activity / negative regulation of viral genome replication / cellular response to exogenous dsRNA / antiviral innate immune response / positive regulation of viral genome replication / negative regulation of protein binding / response to virus / ISG15 antiviral mechanism / Interferon alpha/beta signaling / defense response to virus / RNA binding / cytosol / cytoplasm
Similarity search - Function
Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / RNA / Interferon-induced protein with tetratricopeptide repeats 1
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAbbas, Y.M. / Martinez-Montero, S. / Damha, M.J. / Nagar, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-133535 Canada
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of human IFIT1 with capped RNA reveals adaptable mRNA binding and mechanisms for sensing N1 and N2 ribose 2'-O methylations.
Authors: Abbas, Y.M. / Laudenbach, B.T. / Martinez-Montero, S. / Cencic, R. / Habjan, M. / Pichlmair, A. / Damha, M.J. / Pelletier, J. / Nagar, B.
History
DepositionDec 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon-induced protein with tetratricopeptide repeats 1
B: RNA (5'-D(*(GTA))-R(P*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4645
Polymers57,2332
Non-polymers2303
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-21 kcal/mol
Surface area22110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.760, 111.760, 92.992
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-717-

HOH

21A-845-

HOH

31A-888-

HOH

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Components

#1: Protein Interferon-induced protein with tetratricopeptide repeats 1 / IFIT-1 / Interferon-induced 56 kDa protein / P56


Mass: 55521.305 Da / Num. of mol.: 1 / Mutation: N216A, L457E, L464E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFIT1, G10P1, IFI56, IFNAI1, ISG56 / Production host: Escherichia coli (E. coli) / References: UniProt: P09914
#2: RNA chain RNA (5'-D(*(GTA))-R(P*AP*AP*A)-3')


Mass: 1712.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: 27 - 32 % PEG 200, 0.1 M Tris pH 8.1, 200 mM CaCl2

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Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 71832 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 21.08 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.028 / Rrim(I) all: 0.099 / Χ2: 1.07 / Net I/σ(I): 8 / Num. measured all: 1048686
Reflection shell
Resolution (Å)Redundancy (%)CC1/2Diffraction-ID% possible allRmerge(I) obs
1.65-1.6812.30.794199.9
1.68-1.7114.40.8581100
1.71-1.7414.70.8991100
1.74-1.7814.70.91211000.891
1.78-1.8214.80.94111000.743
1.82-1.8614.80.95411000.627
1.86-1.914.80.96911000.506
1.9-1.9614.80.97611000.409
1.96-2.0114.80.98411000.322
2.01-2.0814.80.98911000.258
2.08-2.1514.90.99211000.207
2.15-2.2414.80.99311000.18
2.24-2.3414.80.99511000.149
2.34-2.4614.90.99711000.124
2.46-2.6214.80.99711000.102
2.62-2.8214.80.99711000.091
2.82-3.1114.80.99611000.1
3.11-3.5514.70.99811000.077
3.55-4.4814.60.99911000.056
4.48-5013.90.999199.80.049

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10_2142refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→40.074 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.13
RfactorNum. reflection% reflection
Rfree0.1819 3547 4.94 %
Rwork0.1643 --
obs0.1652 71790 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.72 Å2 / Biso mean: 34.4929 Å2 / Biso min: 12.94 Å2
Refinement stepCycle: final / Resolution: 1.65→40.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3757 117 26 313 4213
Biso mean--68.22 32.63 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084039
X-RAY DIFFRACTIONf_angle_d1.0055469
X-RAY DIFFRACTIONf_chiral_restr0.048585
X-RAY DIFFRACTIONf_plane_restr0.006688
X-RAY DIFFRACTIONf_dihedral_angle_d13.5842492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6433-1.66580.24621470.24332491263892
1.6658-1.68960.27761370.24226712808100
1.6896-1.71480.27041280.221527152843100
1.7148-1.74160.22221540.203326892843100
1.7416-1.77020.22381210.198927042825100
1.7702-1.80070.23581470.196727152862100
1.8007-1.83350.23111470.185827032850100
1.8335-1.86870.21441170.17527062823100
1.8687-1.90690.23921450.17527062851100
1.9069-1.94830.21741370.172926932830100
1.9483-1.99360.20391280.172527432871100
1.9936-2.04350.19641660.167626692835100
2.0435-2.09870.17721490.161227242873100
2.0987-2.16050.19191350.158827332868100
2.1605-2.23020.15891460.150727152861100
2.2302-2.30990.17081270.149827562883100
2.3099-2.40240.17961340.147227232857100
2.4024-2.51170.19021270.150827642891100
2.5117-2.64410.17381410.154327422883100
2.6441-2.80980.17651370.161127692906100
2.8098-3.02660.18961470.177427632910100
3.0266-3.33110.17791630.18227442907100
3.3311-3.81280.1721450.160627962941100
3.8128-4.80240.14611570.134528282985100
4.8024-40.08620.17491650.16829813146100
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)
10.06820.11390.03120.1379-0.09320.0611-0.00480.09440.007-0.0441-0.0061-0.0476-0.03230.0764-00.1675-0.0052-0.01310.19520.00410.202746.029218.3292-159.9563
20.20580.09410.05690.158-0.0510.1317-0.05530.00910.1753-0.04230.00460.0503-0.1262-0.087500.2099-0.0047-0.01480.1713-0.00430.255342.847128.5227-155.3213
30.20070.2253-0.0540.3599-0.0520.4535-0.0059-0.0124-0.00910.04350.0068-0.00380.0267-0.0274-00.15960.0185-0.00380.14940.00480.15730.29036.026-152.939
40.0793-0.05620.00130.0347-0.01930.03080.00240.07630.01850.0137-0.0380.10860.1032-0.048100.2308-0.0235-0.0130.2006-0.0310.182821.3776-7.4288-175.9427
50.0325-0.0530.0020.0534-0.0140.056-0.15650.12280.0628-0.02490.0910.0328-0.014-0.0867-0.00020.2084-0.03710.00660.2344-0.02160.161923.9382-2.0097-181.7064
60.0503-0.0367-0.01230.04320.00930.0047-0.05830.06250.0992-0.06520.0597-0.00460.11270.0905-00.22250.0158-0.0020.2186-0.02120.174638.7311-5.1456-177.4852
70.1052-0.0128-0.00290.0936-0.08550.0620.0250.0558-0.10070.08360.0719-0.03260.2330.04570.01080.27930.0842-0.01630.2451-0.05440.223142.8116-16.7919-173.1317
80.01890.02660.0050.2837-0.09350.61990.3035-0.0727-0.3085-0.1010.01250.17580.2051-0.23840.18830.34290.0083-0.12830.2226-0.06680.387645.8309-32.8724-169.9886
9-0-0.00210.00390.01080.00620.0076-0.0295-0.1206-0.01850.04530.03090.08220.16630.13740.00020.2537-0.01440.00870.2164-0.01070.197932.2521-4.3681-165.1214
100.29890.08-0.21480.0425-0.04280.2153-0.25330.13040.00460.05680.2188-0.05120.0073-0.1149-0.01460.20240.027-0.01210.18010.01340.20534.36858.3985-159.4705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 45 )A8 - 45
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 127 )A46 - 127
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 284 )A128 - 284
4X-RAY DIFFRACTION4chain 'A' and (resid 285 through 311 )A285 - 311
5X-RAY DIFFRACTION5chain 'A' and (resid 312 through 335 )A312 - 335
6X-RAY DIFFRACTION6chain 'A' and (resid 336 through 373 )A336 - 373
7X-RAY DIFFRACTION7chain 'A' and (resid 374 through 412 )A374 - 412
8X-RAY DIFFRACTION8chain 'A' and (resid 413 through 467 )A413 - 467
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 4 )B2 - 4
10X-RAY DIFFRACTION10chain 'B' and resid ' 1 'B1

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