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- PDB-3zgq: Crystal structure of human interferon-induced protein IFIT5 -

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Basic information

Entry
Database: PDB / ID: 3zgq
TitleCrystal structure of human interferon-induced protein IFIT5
ComponentsINTERFERON-INDUCED PROTEIN WITH TETRATRICOPEPTIDE REPEATS 5
KeywordsIMMUNE SYSTEM / RNA BINDING / INTERFERON RESPONSE
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
DI(HYDROXYETHYL)ETHER / Interferon-induced protein with tetratricopeptide repeats 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.203 Å
AuthorsKatibah, G.E. / Lee, H.J. / Huizar, J.P. / Vogan, J.M. / Alber, T. / Collins, K.
CitationJournal: Mol.Cell / Year: 2013
Title: TRNA Binding, Structure, and Localization of the Human Interferon-Induced Protein Ifit5.
Authors: Katibah, G.E. / Lee, H.J. / Huizar, J.P. / Vogan, J.M. / Alber, T. / Collins, K.
History
DepositionDec 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0402
Polymers55,9341
Non-polymers1061
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.833, 71.793, 116.920
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: 55933.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RESIDUES 190-195 ARE DISORDERED / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q13325
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1111
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Details: DOUBLE CRYSTAL SI(111)
RadiationMonochromator: DOUBLE FLAT CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1111 Å / Relative weight: 1
ReflectionResolution: 2.2→47.7 Å / Num. obs: 27780 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 27.28 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.203→47.704 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 23.16 / Stereochemistry target values: ML / Details: RESIDUES 190-195 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2398 2000 7.2 %
Rwork0.1778 --
obs0.1821 27780 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.203→47.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3885 0 7 232 4124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084006
X-RAY DIFFRACTIONf_angle_d1.1215395
X-RAY DIFFRACTIONf_dihedral_angle_d15.721527
X-RAY DIFFRACTIONf_chiral_restr0.08582
X-RAY DIFFRACTIONf_plane_restr0.005687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2034-2.25850.25091370.22211764X-RAY DIFFRACTION98
2.2585-2.31950.2831410.21851816X-RAY DIFFRACTION100
2.3195-2.38780.29541410.20461810X-RAY DIFFRACTION100
2.3878-2.46490.28221410.19821833X-RAY DIFFRACTION100
2.4649-2.5530.27491420.191823X-RAY DIFFRACTION100
2.553-2.65520.27521420.191824X-RAY DIFFRACTION100
2.6552-2.7760.30011400.19371819X-RAY DIFFRACTION100
2.776-2.92230.25431420.18581831X-RAY DIFFRACTION100
2.9223-3.10540.27551430.18871829X-RAY DIFFRACTION100
3.1054-3.34510.2661430.18271845X-RAY DIFFRACTION100
3.3451-3.68160.23211430.15931852X-RAY DIFFRACTION100
3.6816-4.21410.19661440.14661863X-RAY DIFFRACTION100
4.2141-5.30820.17391470.15561888X-RAY DIFFRACTION100
5.3082-47.71490.23321540.18341983X-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)
13.1213-0.79580.92031.7361-0.00922.0469-0.0733-0.0850.45720.09110.05970.0704-0.1795-0.0632-0.01490.0957-0.0270.01030.08210.01050.2345.939799.5934137.488
21.983-0.9297-0.17921.49021.03271.6790.03770.25570.7378-0.36780.0350.385-0.5626-0.16710.06070.1120.0477-0.02480.18110.08440.47190.0264104.6484130.7761
32.0784-0.4305-0.09771.8870.04660.53290.11190.61340.1115-0.4012-0.02660.2055-0.1279-0.0658-0.04380.08250.0295-0.03650.15470.09250.029516.971698.283120.7398
41.5384-0.1646-0.02321.5506-1.16682.5722-0.02970.16830.16260.0267-0.1363-0.2483-0.11780.30280.09450.0643-0.0140.00880.08470.04530.109233.486794.5393130.1712
52.9775-0.53830.32632.3822-1.0111.59870.117-0.0116-0.1306-0.1619-0.231-0.34970.08580.37390.01410.1025-0.0114-0.06490.0892-0.00020.030537.626374.9756139.8427
62.11591.32261.60681.93570.31962.22640.12670.1589-0.2856-0.1778-0.0280.39510.1593-0.0985-0.04550.11020.0032-0.06070.0952-0.02960.198420.451566.684134.2327
76.08571.30790.00457.14761.96054.9902-0.2768-0.2049-0.3232-0.35070.48850.0370.55350.2126-0.14930.2770.0241-0.0430.2734-0.02040.290615.859959.6592118.2154
87.0885-0.2840.39392.12241.84254.68330.3586-0.4516-0.6485-0.67760.42620.59440.43710.0855-0.84080.4405-0.0669-0.16240.23610.1140.74381.43856.7668116.0054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2 THROUGH 106 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 107 THROUGH 152 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 153 THROUGH 188 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 189 THROUGH 282 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 283 THROUGH 333 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 334 THROUGH 406 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 407 THROUGH 450 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 451 THROUGH 482 )

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