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- PDB-6irz: Crystal structure of the zebrafish cap-specific adenosine methylt... -

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Basic information

Entry
Database: PDB / ID: 6irz
TitleCrystal structure of the zebrafish cap-specific adenosine methyltransferase bound to SAH and m7G-capped RNA
ComponentsPDX1 C-terminal-inhibiting factor 1
KeywordsTRANSFERASE / RNA METHYLATION / METHYLTRANSFERASE / M6A / N6-METHYLADENOSINE
Function / homology
Function and homology information


mRNA (2'-O-methyladenosine-N6-)-methyltransferase / mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / S-adenosyl-L-methionine binding / RNA polymerase II C-terminal domain binding / positive regulation of translation / mRNA processing / methylation / nucleus
Similarity search - Function
PCIF1, WW domain / mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase PCIF1-like / Phosphorylated CTD interacting factor 1 WW domain / Heat shock protein 70kD, C-terminal domain superfamily / WW domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / S-ADENOSYL-L-HOMOCYSTEINE / mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHirano, S. / Nishimasu, H. / Ishitani, R. / Nureki, O.
CitationJournal: Science / Year: 2019
Title: Cap-specific terminal N 6 -methylation of RNA by an RNA polymerase II-associated methyltransferase.
Authors: Akichika, S. / Hirano, S. / Shichino, Y. / Suzuki, T. / Nishimasu, H. / Ishitani, R. / Sugita, A. / Hirose, Y. / Iwasaki, S. / Nureki, O. / Suzuki, T.
History
DepositionNov 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Oct 28, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: PDX1 C-terminal-inhibiting factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6016
Polymers57,5711
Non-polymers1,0305
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-1 kcal/mol
Surface area22430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.669, 83.165, 93.132
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PDX1 C-terminal-inhibiting factor 1


Mass: 57570.781 Da / Num. of mol.: 1 / Mutation: A308V, H344N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: pcif1 / Plasmid: pE-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: A0A0R4IKJ1
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 459.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N5O11P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.41 Å3/Da / Density % sol: 48.97 % / Mosaicity: 0.07 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 13% PEG 3350, 0.1M potassium thiocyanate, 0.1M bis-Tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→46.9 Å / Num. obs: 38329 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 37.69 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Net I/σ(I): 16.1 / Num. measured all: 259727 / Scaling rejects: 1553
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.057.10.65427710.9170.2650.706100
8.94-46.96.10.0475080.9970.020.05199.6

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IRX

6irx


Resolution: 2→46.566 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.14
RfactorNum. reflection% reflection
Rfree0.21 1884 4.95 %
Rwork0.1808 --
obs0.1823 38058 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.07 Å2 / Biso mean: 51.6435 Å2 / Biso min: 27.31 Å2
Refinement stepCycle: final / Resolution: 2→46.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 67 160 4041
Biso mean--57.08 47.18 -
Num. residues----467
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0001-2.05410.30221420.252527322874100
2.0541-2.11460.33921340.27862747288198
2.1146-2.18280.24461320.214227592891100
2.1828-2.26080.32541590.25842657281697
2.2608-2.35140.23821240.20652720284498
2.3514-2.45840.22931400.194627742914100
2.4584-2.5880.23731790.193527412920100
2.588-2.75010.20121260.192128042930100
2.7501-2.96240.25771690.203327792948100
2.9624-3.26040.23551400.198827992939100
3.2604-3.73210.21841190.179128442963100
3.7321-4.70130.17861530.146728473000100
4.7013-46.57860.15391670.153429713138100
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)
11.4611-0.2898-0.37481.0558-0.21312.3533-0.0436-0.04980.0950.13070.0414-0.005-0.0396-0.0026-0.0090.25380.0212-0.02610.29660.00380.258952.11058.198519.0965
22.1638-1.02280.37832.4976-1.01292.1427-0.3262-0.3230.0095-0.00250.09360.32720.0969-0.46720.27310.45780.13320.00130.5902-0.03180.500520.565816.563233.6505
31.5167-0.0057-0.6850.25090.55851.935-0.0843-0.4048-0.0291-0.07060.06070.0744-0.07070.12720.08450.39950.0213-0.04260.310.02580.279942.77438.74228.7235
41.48990.5038-0.52484.1823-0.44621.7586-0.1497-0.02210.05490.04990.0305-0.1670.06170.59220.05010.30790.081-0.04440.5370.00450.372872.69175.4738.7146
52.2596-0.21590.42392.63670.09252.33870.06720.6293-0.1908-0.3087-0.04910.21380.3508-0.2463-0.00090.41990.0072-0.02770.5251-0.04780.316853.31910.9123-3.596
61.2547-0.0347-0.08572.88070.16611.5356-0.08310.1630.2684-0.03120.11110.1249-0.1007-0.0241-0.01890.25960.0177-0.03420.35750.02970.319757.064513.08593.3039
72.52040.1433-0.62281.92490.16352.92420.0401-0.16110.63040.42660.03930.0325-0.61680.2281-0.03430.4759-0.0098-0.02390.2979-0.02230.469157.257426.580914.9429
81.6466-1.1458-0.13191.7050.18443.10740.23970.18990.66490.076-0.23510.1935-0.6364-0.4179-0.04050.68190.0462-0.06360.39450.14230.838752.081133.38074.3976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 178 through 274 )A178 - 274
2X-RAY DIFFRACTION2chain 'A' and (resid 275 through 334 )A275 - 334
3X-RAY DIFFRACTION3chain 'A' and (resid 335 through 389 )A335 - 389
4X-RAY DIFFRACTION4chain 'A' and (resid 390 through 423 )A390 - 423
5X-RAY DIFFRACTION5chain 'A' and (resid 424 through 459 )A424 - 459
6X-RAY DIFFRACTION6chain 'A' and (resid 460 through 532 )A460 - 532
7X-RAY DIFFRACTION7chain 'A' and (resid 533 through 616 )A533 - 616
8X-RAY DIFFRACTION8chain 'A' and (resid 617 through 673 )A617 - 673

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