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- PDB-5w5i: Human IFIT1 dimer with PPP-AAAA -

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Basic information

Entry
Database: PDB / ID: 5w5i
TitleHuman IFIT1 dimer with PPP-AAAA
Components
  • Interferon-induced protein with tetratricopeptide repeats 1
  • RNA (5'-D(*(ATP))-R(P*AP*AP*A)-3')
KeywordsRNA binding protein/RNA / triphosphate RNA / tetratricopeptide repeat / RNA binding protein / RNA binding protein-RNA complex
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 / negative regulation of viral genome replication / cellular response to exogenous dsRNA / host cell / 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 / negative regulation of helicase activity / negative regulation of viral genome replication / cellular response to exogenous dsRNA / host cell / 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
RNA / Interferon-induced protein with tetratricopeptide repeats 1
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsAbbas, Y.M. / Martinez-Montero, S. / Damha, M.J. / Nagar, B.
CitationJournal: To Be Published
Title: Structural insights into IFIT1 dimerization and conformational changes associated with mRNA binding
Authors: Abbas, Y.M. / Martinez-Montero, S. / Cencic, R. / Pelletier, J. / Damha, M.J. / Pawelek, P.D. / Nagar, B.
History
DepositionJun 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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(*(ATP))-R(P*AP*AP*A)-3')
C: Interferon-induced protein with tetratricopeptide repeats 1
D: RNA (5'-D(*(ATP))-R(P*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)113,9284
Polymers113,9284
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, IFIT1 migrates as a dimer on gel filtration, light scattering, Calculated MW corresponds to IFIT1 homodimer, equilibrium centrifugation, Analytical ultracentrifugation shows ...Evidence: gel filtration, IFIT1 migrates as a dimer on gel filtration, light scattering, Calculated MW corresponds to IFIT1 homodimer, equilibrium centrifugation, Analytical ultracentrifugation shows reversible monomer-dimer interaction
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-19 kcal/mol
Surface area40510 Å2
2
A: Interferon-induced protein with tetratricopeptide repeats 1
B: RNA (5'-D(*(ATP))-R(P*AP*AP*A)-3')
C: Interferon-induced protein with tetratricopeptide repeats 1
D: RNA (5'-D(*(ATP))-R(P*AP*AP*A)-3')

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

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

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


Theoretical massNumber of molelcules
Total (without water)455,71416
Polymers455,71416
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
Buried area31600 Å2
ΔGint-115 kcal/mol
Surface area153360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.789, 184.789, 88.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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


Mass: 55532.414 Da / Num. of mol.: 2
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(*(ATP))-R(P*AP*AP*A)-3')


Mass: 1431.826 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.46 Å3/Da / Density % sol: 64.5 %
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: Jun 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 43686 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rpim(I) all: 0.025 / Rsym value: 0.058 / Net I/σ(I): 29.6
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2 / CC1/2: 0.85 / Rpim(I) all: 0.383 / Rsym value: 0.899 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→44.397 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 2.65 / Phase error: 26.32
RfactorNum. reflection% reflection
Rfree0.2416 1922 4.97 %
Rwork0.2189 --
obs0.22 38680 88.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.65→44.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7072 194 0 35 7301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027416
X-RAY DIFFRACTIONf_angle_d0.47710002
X-RAY DIFFRACTIONf_dihedral_angle_d12.9034520
X-RAY DIFFRACTIONf_chiral_restr0.0331083
X-RAY DIFFRACTIONf_plane_restr0.0021243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6499-2.71620.2748520.291111X-RAY DIFFRACTION37
2.7162-2.78960.2909680.2911416X-RAY DIFFRACTION48
2.7896-2.87170.3169990.30451956X-RAY DIFFRACTION66
2.8717-2.96430.3281400.29772655X-RAY DIFFRACTION91
2.9643-3.07020.31981560.28952919X-RAY DIFFRACTION99
3.0702-3.19310.32271570.28962923X-RAY DIFFRACTION100
3.1931-3.33840.3031570.26822943X-RAY DIFFRACTION100
3.3384-3.51440.29271530.24952962X-RAY DIFFRACTION100
3.5144-3.73440.25981490.21852969X-RAY DIFFRACTION100
3.7344-4.02260.19511610.19052938X-RAY DIFFRACTION100
4.0226-4.42710.17631560.17342962X-RAY DIFFRACTION100
4.4271-5.06690.18481560.16722964X-RAY DIFFRACTION100
5.0669-6.38080.22611550.20222998X-RAY DIFFRACTION100
6.3808-44.40290.21581630.18473042X-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)
11.31671.1368-1.6241.7425-0.57013.88370.12450.00420.5405-0.10620.1740.0874-0.325-0.0636-0.24150.303-0.0226-0.05630.6824-0.18250.456812.1732247.9767-4.8103
20.2411-0.1340.06720.35660.24451.46110.3521-1.20020.5983-0.1226-0.4332-0.4378-0.45311.21760.01030.2639-0.364-0.11911.145-0.29530.463417.5318247.25373.4336
31.95530.49990.26570.8784-0.55061.4517-0.16940.075-0.7149-0.2301-0.1576-0.20990.3630.41240.1349-0.49460.3124-0.07771.05490.01780.50588.7202228.49693.4434
43.6097-2.51140.14362.6541-0.71910.4353-0.2517-0.3954-0.86410.23780.0273-0.21050.56580.74130.11240.5910.27230.01560.99460.19050.76845.9276220.309715.6729
51.50570.98761.60153.18290.58172.20770.0663-0.6477-0.39930.43590.2243-0.43570.16960.4628-0.29730.48030.0263-0.06141.66130.03950.4953.5145231.564927.4321
61.706-0.15050.50220.74410.34031.17410.0864-1.0383-0.32560.71170.0480.1611-0.1480.2462-0.0827-0.0786-0.287-0.61121.3009-0.4576-0.2095-10.7408238.533225.8141
72.0399-0.13820.36130.9412-0.95441.05740.079-0.4037-0.07170.11290.02960.2038-0.15640.4284-0.10040.2102-0.01390.02350.4652-0.16220.2966-22.259236.930112.1229
85.6361.49342.87052.0067-0.85183.08210.0385-0.36290.02060.6154-0.10780.65050.24-0.54360.02220.3168-0.05260.13010.4789-0.10130.5998-30.9461224.925310.8043
92.87290.58751.18620.94020.37362.830.2538-0.4566-0.4918-0.0541-0.24690.70530.3607-0.4418-0.11920.3268-0.0732-0.07440.4885-0.25580.9342-37.8327222.2408-0.5561
102.1896-0.95250.51322.1551-0.23092.7472-0.0646-0.3414-0.65820.14470.0676-0.00150.17120.11080.01810.2937-0.03450.02570.98370.0280.3324-6.9447231.003116.4098
110.814-0.4360.29311.7868-0.75341.4691-0.2033-0.0023-0.2913-0.39780.31611.06710.7303-0.7833-0.00570.599-0.349-0.14520.33710.04390.6431-67.1467172.148-13.3995
120.35650.248-0.46381.3138-0.97151.2804-0.2074-0.1316-0.1418-0.0698-0.0424-0.27490.44680.10.18410.49440.02540.02430.1349-0.03010.3052-49.6177175.0035-13.8467
132.6552-2.2449-0.59973.3494-0.05270.34630.0220.3699-0.194-0.6613-0.08-0.78490.42730.3554-0.12560.81040.14340.17520.4076-0.05330.4648-39.8314180.7251-30.5117
144.4091-0.51670.38771.95990.90042.2130.07670.60540.0259-1.2585-0.1370.07480.4801-0.08810.0640.9655-0.0434-0.12820.3572-0.05150.2467-55.1627191.8348-41.2448
151.0439-0.0323-0.75962.7907-0.10480.63920.05980.22140.1029-0.2486-0.03960.08170.2286-0.1391-0.01780.3178-0.024-0.10280.16390.01430.2704-54.5611207.9751-25.9558
160.86791.07920.71662.00031.61132.6743-0.26520.13190.5925-0.36780.1486-0.2977-0.55430.52420.01420.3527-0.1276-0.14490.3269-0.03560.7842-38.0655222.0821-17.5418
172.4097-1.6713-0.05081.82881.61843.73970.1360.11890.1989-0.314-0.1002-0.3772-0.11460.3366-0.05130.4992-0.0730.01860.21050.07770.2933-49.5689194.2588-29.5267
184.59990.1854-0.69521.8599-2.04772.3058-0.22720.42-0.3782-0.2827-0.09530.04340.3753-0.1980.24310.4379-0.0591-0.03220.3274-0.06640.2334-54.9015185.887-25.06
191.70210.0291-1.56015.3658-0.65261.5016-0.0833-0.15740.11390.4219-0.0423-0.6027-0.21150.38020.11330.2083-0.0632-0.06080.9728-0.10450.3751.9113236.425612.8946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 153 )
3X-RAY DIFFRACTION3chain 'A' and (resid 154 through 192 )
4X-RAY DIFFRACTION4chain 'A' and (resid 193 through 245 )
5X-RAY DIFFRACTION5chain 'A' and (resid 246 through 284 )
6X-RAY DIFFRACTION6chain 'A' and (resid 285 through 352 )
7X-RAY DIFFRACTION7chain 'A' and (resid 353 through 412 )
8X-RAY DIFFRACTION8chain 'A' and (resid 413 through 432 )
9X-RAY DIFFRACTION9chain 'A' and (resid 433 through 469 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 4 )
11X-RAY DIFFRACTION11chain 'C' and (resid 9 through 127 )
12X-RAY DIFFRACTION12chain 'C' and (resid 128 through 192 )
13X-RAY DIFFRACTION13chain 'C' and (resid 193 through 245 )
14X-RAY DIFFRACTION14chain 'C' and (resid 246 through 335 )
15X-RAY DIFFRACTION15chain 'C' and (resid 336 through 412 )
16X-RAY DIFFRACTION16chain 'C' and (resid 413 through 469 )
17X-RAY DIFFRACTION17chain 'D' and (resid 2 through 4 )
18X-RAY DIFFRACTION18chain 'D' and resid ' 1 '
19X-RAY DIFFRACTION19chain 'B' and resid ' 1 '

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