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- PDB-4hoq: Crystal Structure of Full-Length Human IFIT5 -

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Basic information

Entry
Database: PDB / ID: 4hoq
TitleCrystal Structure of Full-Length Human IFIT5
ComponentsInterferon-induced protein with tetratricopeptide repeats 5
KeywordsRNA BINDING PROTEIN / TPR / RNA binding / antiviral / RNA
Function / homology
Function and homology information


RNA cap binding / poly(U) RNA binding / negative regulation of viral genome replication / ruffle membrane / Interferon alpha/beta signaling / actin cytoskeleton / apical part of cell / double-stranded DNA binding / positive regulation of canonical NF-kappaB signal transduction / defense response to virus ...RNA cap binding / poly(U) RNA binding / negative regulation of viral genome replication / ruffle membrane / Interferon alpha/beta signaling / actin cytoskeleton / apical part of cell / double-stranded DNA binding / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / tRNA binding / single-stranded RNA binding / innate immune response / RNA binding / plasma membrane / cytosol
Similarity search - Function
Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat ...Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Interferon-induced protein with tetratricopeptide repeats 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.07 Å
AuthorsAbbas, Y.M. / Pichlmair, A. / Gorna, M.W. / Superti-Furga, G. / Nagar, B.
CitationJournal: Nature / Year: 2013
Title: Structural basis for viral 5'-PPP-RNA recognition by human IFIT proteins.
Authors: Abbas, Y.M. / Pichlmair, A. / Gorna, M.W. / Superti-Furga, G. / Nagar, B.
History
DepositionOct 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Feb 27, 2013Group: Database references

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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 5


Theoretical massNumber of molelcules
Total (without water)56,2621
Polymers56,2621
Non-polymers00
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.150, 71.428, 117.560
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 protein with tetratricopeptide repeats 5 / IFIT-5 / Interferon-induced 58 kDa protein / Retinoic acid- and interferon-inducible 58 kDa protein / P58


Mass: 56261.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFIT5, IFIT5/ISG58, ISG58, RI58 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13325
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2011
RadiationMonochromator: double crystal monochromator (DCM) with an indirectly cryo-cooled first crystal and sagittally focusing second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 37620 / Num. obs: 37620 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 2.07→2.14 Å / % possible all: 78.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.07→37.051 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 21.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 1902 6.08 %RANDOM
Rwork0.1654 ---
all0.1683 33178 --
obs0.1683 31276 92.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→37.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 0 258 4154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063977
X-RAY DIFFRACTIONf_angle_d0.9445353
X-RAY DIFFRACTIONf_dihedral_angle_d13.9941502
X-RAY DIFFRACTIONf_chiral_restr0.071576
X-RAY DIFFRACTIONf_plane_restr0.004683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0702-2.12190.29351250.21561539X-RAY DIFFRACTION71
2.1219-2.17930.31211160.20051715X-RAY DIFFRACTION78
2.1793-2.24340.25791030.19351887X-RAY DIFFRACTION84
2.2434-2.31580.26171080.19071996X-RAY DIFFRACTION89
2.3158-2.39860.23161340.18212080X-RAY DIFFRACTION93
2.3986-2.49460.24881630.18062086X-RAY DIFFRACTION95
2.4946-2.60810.26151130.16942188X-RAY DIFFRACTION97
2.6081-2.74550.25431490.18052191X-RAY DIFFRACTION98
2.7455-2.91750.21161450.17732209X-RAY DIFFRACTION98
2.9175-3.14260.21121590.17352201X-RAY DIFFRACTION99
3.1426-3.45870.21791500.1712260X-RAY DIFFRACTION100
3.4587-3.95870.18221380.14162296X-RAY DIFFRACTION100
3.9587-4.98560.17071530.13982300X-RAY DIFFRACTION100
4.9856-37.05740.17561460.15592426X-RAY DIFFRACTION100
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)
13.83113.6658-4.38984.7713-3.03166.1088-0.0464-0.0669-0.1439-0.1365-0.05930.32670.0132-0.2075-0.02720.1867-0.0002-0.05310.35130.01540.3731-12.547223.324918.3247
23.3345-1.6113-0.1993.43820.92291.20940.1890.1515-0.4553-0.1759-0.08290.3331-0.03120.0079-0.04210.1447-0.0161-0.00360.191-0.0110.17644.85318.921914.7454
35.21681.2751.2453.33881.60872.9442-0.25620.04710.1604-0.06720.2626-0.1512-0.31270.1442-0.05110.20090.0429-0.02690.2645-0.04550.335620.003322.66822.9377
43.00440.6155-0.72643.3054-0.91612.8010.0452-0.31150.0673-0.0309-0.1342-0.18770.0797-0.0711-0.00220.1590.00130.01320.17140.01910.16819.545723.046523.4686
53.95283.5587-1.1398.6177-3.25213.33120.0266-0.50460.12810.7863-0.0905-0.2207-0.37710.13250.02760.29950.0079-0.03510.3158-0.09510.26957.634530.703628.2726
62.77530.20090.42163.44820.15063.4908-0.1014-0.29190.51150.1708-0.06990.0285-0.26840.12930.02230.14580.0186-0.01860.1748-0.03030.24572.151533.01421.9023
73.20881.5767-1.36725.4332-3.0156.0153-0.0748-0.09890.36020.20040.14330.5046-0.3484-0.4361-0.14970.2070.1010.00170.2568-0.07070.3913-6.479535.586820.4775
82.2998-1.543-0.0711.8491-0.11150.3988-0.00940.16160.3338-0.15790.08690.1688-0.0361-0.1186-0.03180.19550.0078-0.00650.22350.03630.26235.947430.40969.725
92.04980.7395-0.13813.114-0.02631.37780.0040.34680.1003-0.1232-0.05490.0452-0.03790.00470.00750.1806-0.0014-0.01870.19410.0160.16617.559225.49344.2325
101.0496-0.31020.0590.7975-0.88361.22680.01350.055-0.0415-0.007-0.1718-0.11270.09220.20970.06270.1750.0048-0.00170.19820.0170.137934.989516.416414.7659
111.19820.48730.91780.81890.38021.12930.04870.04310.0025-0.0884-0.07860.18990.10970.02450.02290.28220.0172-0.04070.2230.01170.288717.5374-8.572710.9785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 30 )
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 49 )
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 66 )
5X-RAY DIFFRACTION5chain 'A' and (resid 67 through 82 )
6X-RAY DIFFRACTION6chain 'A' and (resid 83 through 109 )
7X-RAY DIFFRACTION7chain 'A' and (resid 110 through 126 )
8X-RAY DIFFRACTION8chain 'A' and (resid 127 through 152 )
9X-RAY DIFFRACTION9chain 'A' and (resid 153 through 189 )
10X-RAY DIFFRACTION10chain 'A' and (resid 193 through 310 )
11X-RAY DIFFRACTION11chain 'A' and (resid 311 through 481 )

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