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- PDB-6c6k: Structural basis for preferential recognition of cap 0 RNA by a h... -

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Basic information

Entry
Database: PDB / ID: 6c6k
TitleStructural basis for preferential recognition of cap 0 RNA by a human IFIT1-IFIT3 protein complex
Components
  • Interferon-induced protein with tetratricopeptide repeats 1
  • Interferon-induced protein with tetratricopeptide repeats 3
  • RNA (5'-R((M7G)*P*AP*UP*AP*GP*GP*CP*GP*GP*CP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / innate immunity / Interferon stimulated genes / Host defense / antiviral / self/non-self RNA recognition / pathogen associated molecular patterns / flavivirus / 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 / cellular response to interferon-alpha / host cell / negative regulation of helicase activity / negative regulation of viral genome replication / cellular response to exogenous dsRNA / type I interferon-mediated signaling pathway / antiviral innate immune response / positive regulation of viral genome replication ...intracellular transport of viral protein in host cell / cellular response to type I interferon / cellular response to interferon-alpha / host cell / negative regulation of helicase activity / negative regulation of viral genome replication / cellular response to exogenous dsRNA / type I interferon-mediated signaling pathway / 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 / negative regulation of cell population proliferation / negative regulation of apoptotic process / mitochondrion / RNA binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Interferon-induced protein with tetratricopeptide repeats 3 / Tetratricopeptide repeat / Tetratricopeptide repeat 2 / Tetratricopeptide repeat / : / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. ...Interferon-induced protein with tetratricopeptide repeats 3 / Tetratricopeptide repeat / 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 / RNA (> 10) / Interferon-induced protein with tetratricopeptide repeats 3 / Interferon-induced protein with tetratricopeptide repeats 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Equine encephalosis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.54 Å
AuthorsAmarasinghe, G.K. / Leung, D.W. / Johnson, B. / Xu, W.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI10497 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI109680 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI083019 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103422 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI120943 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109945 United States
CitationJournal: Immunity / Year: 2018
Title: Human IFIT3 Modulates IFIT1 RNA Binding Specificity and Protein Stability.
Authors: Johnson, B. / VanBlargan, L.A. / Xu, W. / White, J.P. / Shan, C. / Shi, P.Y. / Zhang, R. / Adhikari, J. / Gross, M.L. / Leung, D.W. / Diamond, M.S. / Amarasinghe, G.K.
History
DepositionJan 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / struct_conn / struct_conn_type
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _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_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: Interferon-induced protein with tetratricopeptide repeats 1
C: Interferon-induced protein with tetratricopeptide repeats 3
D: Interferon-induced protein with tetratricopeptide repeats 3
E: RNA (5'-R((M7G)*P*AP*UP*AP*GP*GP*CP*GP*GP*CP*G)-3')
F: RNA (5'-R((M7G)*P*AP*UP*AP*GP*GP*CP*GP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,66310
Polymers125,5666
Non-polymers974
Water5,819323
1
A: Interferon-induced protein with tetratricopeptide repeats 1
E: RNA (5'-R((M7G)*P*AP*UP*AP*GP*GP*CP*GP*GP*CP*G)-3')
hetero molecules

C: Interferon-induced protein with tetratricopeptide repeats 3


Theoretical massNumber of molelcules
Total (without water)62,8566
Polymers62,7833
Non-polymers733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area5770 Å2
ΔGint-72 kcal/mol
Surface area23500 Å2
MethodPISA
2
B: Interferon-induced protein with tetratricopeptide repeats 1
F: RNA (5'-R((M7G)*P*AP*UP*AP*GP*GP*CP*GP*GP*CP*G)-3')
hetero molecules

D: Interferon-induced protein with tetratricopeptide repeats 3


Theoretical massNumber of molelcules
Total (without water)62,8074
Polymers62,7833
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area5340 Å2
ΔGint-57 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.957, 80.484, 88.054
Angle α, β, γ (deg.)79.820, 78.810, 90.040
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 54099.918 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: Protein/peptide Interferon-induced protein with tetratricopeptide repeats 3 / IFIT-3


Mass: 4986.707 Da / Num. of mol.: 2 / Fragment: UNP residues 416-459
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFIT3, CIG-49, IFI60, IFIT4, ISG60 / Production host: Escherichia coli (E. coli) / References: UniProt: O14879
#3: RNA chain RNA (5'-R((M7G)*P*AP*UP*AP*GP*GP*CP*GP*GP*CP*G)-3')


Mass: 3696.232 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Equine encephalosis virus
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.89 Å3/Da / Density % sol: 57.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.4 / Details: imidazole, PEG20000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97957 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2.54→84.96 Å / Num. obs: 41031 / % possible obs: 90.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.047 / Rrim(I) all: 0.09 / Χ2: 0.869 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.592.90.32617620.8670.2190.3941.04975.6
2.59-2.6430.29918490.8940.1930.3571.0284.1
2.64-2.693.10.31219520.8810.2020.3731.02786.4
2.69-2.753.10.28220960.9290.1810.3371.08291.7
2.75-2.813.20.26220380.9310.1680.3130.9892.1
2.81-2.873.30.23720990.9410.1520.2821.01691.4
2.87-2.943.30.20320640.9580.1290.2420.99692.8
2.94-3.023.40.18520490.9570.1160.2190.99390.3
3.02-3.113.30.16219120.9610.1030.1930.9484.8
3.11-3.213.40.13220980.9820.0820.1560.91592.5
3.21-3.333.50.11621290.9810.0720.1370.90895.2
3.33-3.463.60.09721670.9850.060.1140.87595.3
3.46-3.623.60.07820960.9880.0480.0920.79694.3
3.62-3.813.60.06620950.9920.040.0770.7292.8
3.81-4.053.50.05420600.9920.0340.0640.61390
4.05-4.363.60.04720880.9940.0280.0550.53193.3
4.36-4.83.70.04721540.9940.0280.0550.53895.5
4.8-5.493.70.04621300.9930.0280.0540.49894.3
5.49-6.923.60.04520650.990.0280.0530.46491.9
6.92-503.60.05521280.9440.0340.0651.69594.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.37 Å48.07 Å
Translation7.37 Å48.07 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASER2.7.17phasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→84.96 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.894 / SU B: 9.603 / SU ML: 0.209 / SU R Cruickshank DPI: 1.3403 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.34 / ESU R Free: 0.317
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 1947 5 %RANDOM
Rwork0.1686 ---
obs0.1722 37025 85.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 133.26 Å2 / Biso mean: 40.562 Å2 / Biso min: 1.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0.01 Å20.02 Å2
2--0.03 Å20.01 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 2.54→84.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8125 496 4 323 8948
Biso mean--56.31 33.31 -
Num. residues----1020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198885
X-RAY DIFFRACTIONr_bond_other_d0.0020.028100
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.93312060
X-RAY DIFFRACTIONr_angle_other_deg1.034318855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93751007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.42624.388417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.223151610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4281555
X-RAY DIFFRACTIONr_chiral_restr0.0890.21286
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029447
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021812
LS refinement shellResolution: 2.538→2.604 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 94 -
Rwork0.216 1686 -
all-1780 -
obs--52.11 %

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