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- PDB-5udj: IFIT1 monomeric mutant (L457E/L464E) with Gppp-AAAA -

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Basic information

Entry
Database: PDB / ID: 5udj
TitleIFIT1 monomeric mutant (L457E/L464E) with Gppp-AAAA
Components
  • Interferon-induced protein with tetratricopeptide repeats 1
  • RNA (5'-D(*(G3A))-R(P*AP*AP*A)-3')
KeywordsRNA BINDING PROTEIN / mRNA cap / Guanosine-triphosphate RNA / tetratricopeptide repeat
Function / homology
Function and homology information


intracellular transport of viral protein in host cell / cellular response to type I interferon / negative regulation of helicase activity / cellular response to exogenous dsRNA / negative regulation of viral genome replication / positive regulation of viral genome replication / antiviral innate immune response / negative regulation of protein binding / response to virus / ISG15 antiviral mechanism ...intracellular transport of viral protein in host cell / cellular response to type I interferon / negative regulation of helicase activity / cellular response to exogenous dsRNA / negative regulation of viral genome replication / positive regulation of viral genome replication / antiviral innate immune response / negative regulation of protein binding / response to virus / ISG15 antiviral mechanism / Interferon alpha/beta signaling / host cell / defense response to virus / RNA binding / cytosol / cytoplasm
Similarity search - Function
Tetratricopeptide repeat 2 / 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: 1.69 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 / Database references / Category: pdbx_audit_support / struct_ref_seq_dif
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq_dif.details
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(*(G3A))-R(P*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4925
Polymers57,2612
Non-polymers2303
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-32 kcal/mol
Surface area22270 Å2
MethodPISA
2
A: Interferon-induced protein with tetratricopeptide repeats 1
B: RNA (5'-D(*(G3A))-R(P*AP*AP*A)-3')
hetero molecules

A: Interferon-induced protein with tetratricopeptide repeats 1
B: RNA (5'-D(*(G3A))-R(P*AP*AP*A)-3')
hetero molecules

A: Interferon-induced protein with tetratricopeptide repeats 1
B: RNA (5'-D(*(G3A))-R(P*AP*AP*A)-3')
hetero molecules

A: Interferon-induced protein with tetratricopeptide repeats 1
B: RNA (5'-D(*(G3A))-R(P*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,96720
Polymers229,0468
Non-polymers92112
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation5_652-x+1,y,-z-31
crystal symmetry operation6_552x,-y,-z-31
Buried area21280 Å2
ΔGint-137 kcal/mol
Surface area80480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.536, 112.536, 93.470
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-765-

HOH

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Components

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


Mass: 55564.328 Da / Num. of mol.: 1 / Mutation: 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(*(G3A))-R(P*AP*AP*A)-3')


Mass: 1697.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Chemical ChemComp-PGE / TRIETHYLENE 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


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
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: Jan 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 67695 / % possible obs: 100 % / Redundancy: 14.5 % / Biso Wilson estimate: 19.04 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 22.2
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsCC1/2Diffraction-ID% possible allRmerge(I) obs
1.69-1.7212.21.90.7041100
1.72-1.7513.80.7871100
1.75-1.7814.50.8211100
1.78-1.8214.70.871100
1.82-1.8614.80.91100
1.86-1.914.80.93111000.904
1.9-1.9514.80.94911000.689
1.95-214.80.96811000.551
2-2.0614.80.97811000.418
2.06-2.1314.80.98411000.327
2.13-2.2114.90.98811000.274
2.21-2.2914.80.9911000.226
2.29-2.414.80.99311000.187
2.4-2.5214.90.99511000.153
2.52-2.6814.80.99711000.124
2.68-2.8914.80.99711000.107
2.89-3.1814.80.99611000.11
3.18-3.6414.60.99711000.085
3.64-4.5914.50.99911000.064
4.59-5013.80.998199.80.061

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10_2142refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→40.299 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.86
RfactorNum. reflection% reflection
Rfree0.181 3325 4.91 %
Rwork0.1591 --
obs0.1602 67662 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.78 Å2 / Biso mean: 30.7515 Å2 / Biso min: 8.24 Å2
Refinement stepCycle: final / Resolution: 1.69→40.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 116 26 382 4284
Biso mean--52.96 30.82 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144077
X-RAY DIFFRACTIONf_angle_d1.2835524
X-RAY DIFFRACTIONf_chiral_restr0.061588
X-RAY DIFFRACTIONf_plane_restr0.009700
X-RAY DIFFRACTIONf_dihedral_angle_d12.9512507
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.689-1.71310.30331240.248426472771
1.7131-1.73870.25551400.236126242764
1.7387-1.76580.25971320.218926602792
1.7658-1.79480.24921370.211926282765
1.7948-1.82570.22111470.19726352782
1.8257-1.85890.18791190.184126432762
1.8589-1.89470.2111300.180326752805
1.8947-1.93330.19111460.171826372783
1.9333-1.97540.2161220.171326602782
1.9754-2.02130.18091470.169326462793
2.0213-2.07190.20011540.167526332787
2.0719-2.12790.18521400.157426722812
2.1279-2.19050.15921290.147426612790
2.1905-2.26120.18441430.139926482791
2.2612-2.3420.16111270.143627002827
2.342-2.43580.17971240.141326832807
2.4358-2.54660.18321290.142926762805
2.5466-2.68090.17091420.151127012843
2.6809-2.84880.21041290.156326932822
2.8488-3.06870.18311520.163526962848
3.0687-3.37730.17881550.170426902845
3.3773-3.86570.16591410.14827472888
3.8657-4.8690.15161540.132227672921
4.869-40.31030.16751620.16429153077
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)
10.06190.13360.00260.1671-0.12750.1274-0.01040.0890.0521-0.0887-0.0197-0.0436-0.01580.0975-0.00250.12320.0039-0.01040.15050.01540.157546.134818.3105-161.0563
20.21540.0507-0.02190.2035-0.06090.1625-0.01550.02120.172-0.0149-0.00880.0741-0.1102-0.0710.00340.1472-0.0009-0.00390.1162-0.00850.190543.232928.7131-156.2124
30.23640.2814-0.0990.4465-0.17780.6356-0.0058-0.040.00750.0420.01790.02390.0366-0.02960.00140.10930.021-0.00220.1020.01160.109130.58276.0519-153.655
40.0776-0.0589-0.0040.0391-0.00740.0329-0.00430.1233-0.01440.023-0.00720.16120.0802-0.035-0.00020.1932-0.0203-0.02080.1581-0.00870.163221.7016-7.4624-176.7911
50.0272-0.0452-0.01210.0454-0.00310.0477-0.08340.14870.0254-0.02290.08450.025-0.0092-0.0601-0.00010.1765-0.0403-0.01030.1855-0.01230.136824.377-1.9037-182.5603
60.0335-0.0694-0.00170.06510.01310.0256-0.07950.07570.0647-0.04450.07590.01230.06270.1565-00.19050.0128-0.00770.1658-0.00910.130339.1243-5.1364-178.37
70.1315-0.050400.0751-0.00340.10610.03070.0224-0.05390.05320.0652-0.04330.16220.13490.07170.25130.0795-0.02130.1908-0.03890.177343.052-16.8448-173.9806
80.11210.129-0.15270.2029-0.23370.48110.2951-0.0992-0.29290.0114-0.01750.14250.2-0.28990.1910.31160.0163-0.12910.1587-0.05390.326346.0497-32.9201-170.6066
90.00280.00090.00520.0053-0.00220.00670.0111-0.0942-0.07460.04770.03540.08890.08750.07400.1927-0.0055-0.0030.16540.00090.15232.684-4.3078-165.943
100.0027-0.01230.00280.0050.00990.0089-0.09860.05930.02390.01530.04170.02680.0085-0.03980.00020.14390.02060.00070.125200.154734.68268.336-160.4128
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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