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- PDB-4hou: Crystal Structure of N-terminal Human IFIT1 -

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Basic information

Entry
Database: PDB / ID: 4hou
TitleCrystal Structure of N-terminal Human IFIT1
ComponentsInterferon-induced protein with tetratricopeptide repeats 1
KeywordsRNA BINDING PROTEIN / TPR / RNA binding / antiviral / RNA
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 domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...Tetratricopeptide repeat 2 / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 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 30, 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 1
B: Interferon-induced protein with tetratricopeptide repeats 1


Theoretical massNumber of molelcules
Total (without water)63,8772
Polymers63,8772
Non-polymers00
Water4,288238
1
A: Interferon-induced protein with tetratricopeptide repeats 1


Theoretical massNumber of molelcules
Total (without water)31,9381
Polymers31,9381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Interferon-induced protein with tetratricopeptide repeats 1


Theoretical massNumber of molelcules
Total (without water)31,9381
Polymers31,9381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.470, 176.952, 55.143
Angle α, β, γ (deg.)90.00, 130.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 31938.279 Da / Num. of mol.: 2 / Fragment: N-terminal human IFIT1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G10P1, IFI56, IFIT1, IFIT1/ISG56, IFNAI1, ISG56 / Production host: Escherichia coli (E. coli) / References: UniProt: P09914
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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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, 2010
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: 1.95→50 Å / Num. all: 45919 / Num. obs: 45919 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.6
Reflection shellResolution: 1.95→2.02 Å / % possible all: 95.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→30.521 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 24.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 2630 5.94 %
Rwork0.2016 --
obs0.2036 44239 95.59 %
all-46869 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→30.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 0 0 238 4284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074125
X-RAY DIFFRACTIONf_angle_d1.1385554
X-RAY DIFFRACTIONf_dihedral_angle_d15.2191547
X-RAY DIFFRACTIONf_chiral_restr0.078593
X-RAY DIFFRACTIONf_plane_restr0.004713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9302-1.96530.2874700.25271632X-RAY DIFFRACTION69
1.9653-2.00310.27731400.23681986X-RAY DIFFRACTION88
2.0031-2.0440.26351270.21912100X-RAY DIFFRACTION91
2.044-2.08840.28991240.22082151X-RAY DIFFRACTION93
2.0884-2.1370.27911460.20882151X-RAY DIFFRACTION95
2.137-2.19040.26021260.20262201X-RAY DIFFRACTION96
2.1904-2.24960.22591190.19472206X-RAY DIFFRACTION97
2.2496-2.31580.2341410.19792248X-RAY DIFFRACTION97
2.3158-2.39050.26381370.20172260X-RAY DIFFRACTION97
2.3905-2.47590.24191320.19952218X-RAY DIFFRACTION98
2.4759-2.5750.21821280.21042285X-RAY DIFFRACTION98
2.575-2.69220.2351630.20362219X-RAY DIFFRACTION99
2.6922-2.8340.26041460.20842245X-RAY DIFFRACTION99
2.834-3.01140.25961530.23112271X-RAY DIFFRACTION99
3.0114-3.24370.24811430.21642306X-RAY DIFFRACTION100
3.2437-3.56970.26131590.20132259X-RAY DIFFRACTION100
3.5697-4.08510.23011500.1852296X-RAY DIFFRACTION100
4.0851-5.14290.20141540.17752289X-RAY DIFFRACTION100
5.1429-30.52440.19561720.20622286X-RAY DIFFRACTION99
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)
14.8403-0.88210.67255.9161.16035.0441-0.1623-0.3280.51030.18690.09320.0475-0.3297-0.01630.05450.16430.0055-0.00450.1776-0.01030.2122-31.87016.881819.1146
21.240.09160.12245.05071.1760.6887-0.0741-0.0760.2798-0.1709-0.1160.9647-0.0485-0.15030.16740.19820.0315-0.02540.3091-0.01130.3825-42.062120.559817.9124
32.1265-2.45320.37168.40911.43816.7125-0.249-0.4608-0.63110.17120.38660.65090.8297-0.32680.12620.2362-0.0575-0.01040.40830.04160.362-25.154636.250523.762
45.2124-0.49150.80486.0369-1.27275.72930.00250.2510.0514-0.06470.1417-0.10620.0104-0.071-0.16090.26720.00580.01730.2401-0.03210.1707-28.4293-13.94691.8667
56.72-0.2014-1.6316.41881.86946.8361-0.2543-0.1126-0.18970.37210.4056-0.86790.4731.0428-0.09870.24410.0816-0.07390.3384-0.01540.2715-16.5485-16.19997.0208
63.4159-0.1740.05485.71012.01944.6074-0.05570.23010.1209-0.37990.1829-0.5596-0.02980.6011-0.10220.2384-0.01930.03690.22610.00870.2161-21.2105-6.4448-0.1855
71.7936-1.9570.41638.3003-0.12822.13710.20480.203-0.1211-0.906-0.09040.2257-0.0789-0.0225-0.10910.31820.0187-0.01950.2247-0.04210.2248-28.2419-26.871-4.3353
82.5127-2.54881.21824.51071.51944.52110.11450.0482-0.3153-0.411-0.1640.39140.5266-0.44120.06810.4483-0.0171-0.04290.2649-0.00660.194-26.0781-44.1076-4.9803
96.19421.30271.06579.10580.01625.2540.1665-0.0845-0.5994-0.68420.0689-0.01630.7451-0.1039-0.17830.39760.024-0.04790.28980.02810.2379-19.5803-49.00371.8713
107.6308-1.19111.66319.67970.12952.129-0.24850.27670.8725-0.51030.6048-0.2149-0.9793-0.4589-0.31560.4435-0.0251-0.0040.44590.0660.2511-16.0701-45.994713.0545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 107 )
2X-RAY DIFFRACTION2chain 'A' and (resid 108 through 246 )
3X-RAY DIFFRACTION3chain 'A' and (resid 247 through 278 )
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 47 )
5X-RAY DIFFRACTION5chain 'B' and (resid 48 through 91 )
6X-RAY DIFFRACTION6chain 'B' and (resid 92 through 127 )
7X-RAY DIFFRACTION7chain 'B' and (resid 128 through 191 )
8X-RAY DIFFRACTION8chain 'B' and (resid 192 through 216 )
9X-RAY DIFFRACTION9chain 'B' and (resid 217 through 245 )
10X-RAY DIFFRACTION10chain 'B' and (resid 246 through 278 )

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