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

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Basic information

Entry
Database: PDB / ID: 6iry
TitleCrystal structure of the zebrafish cap-specific adenosine methyltransferase bound to SAH
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
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: 1.8 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 14, 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)58,0794
Polymers57,5711
Non-polymers5093
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint9 kcal/mol
Surface area22470 Å2
Unit cell
Length a, b, c (Å)71.379, 82.288, 92.811
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.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.37 Å3/Da / Density % sol: 48.04 % / Mosaicity: 0.08 °
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: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→46.623 Å / Num. obs: 51421 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 32.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.017 / Rrim(I) all: 0.044 / Net I/σ(I): 21.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.846.80.58730190.9380.2410.635100
9-46.626.10.0464840.9970.0190.0599.5

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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: 1.8→46.623 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.24
RfactorNum. reflection% reflection
Rfree0.2034 2568 5 %
Rwork0.179 --
obs0.1802 51336 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.29 Å2 / Biso mean: 46.4289 Å2 / Biso min: 22.47 Å2
Refinement stepCycle: final / Resolution: 1.8→46.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3813 0 34 242 4089
Biso mean--33.09 46.12 -
Num. residues----468
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.83460.34541360.289827032839
1.8346-1.87210.27831430.257926662809
1.8721-1.91280.27061400.23426542794
1.9128-1.95730.2541360.213826782814
1.9573-2.00620.251360.21126712807
2.0062-2.06050.24721210.198727152836
2.0605-2.12110.22281370.191926572794
2.1211-2.18960.22941630.190626502813
2.1896-2.26780.24651650.196326972862
2.2678-2.35860.24921300.187226992829
2.3586-2.4660.23961400.190126932833
2.466-2.5960.21821470.189227062853
2.596-2.75860.21521390.188427052844
2.7586-2.97150.22521390.199827242863
2.9715-3.27050.20531420.187427322874
3.2705-3.74360.20071560.166527442900
3.7436-4.71580.15721580.14727532911
4.7158-46.63850.16751400.164829213061
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)
11.7804-0.1234-0.99280.9901-0.53763.08940.035-0.04210.09670.15750.08110.0306-0.00490.0062-0.12630.2620.0172-0.02540.2792-0.02550.240151.81718.186419.0861
24.0061-2.216-1.43111.80781.00652.0254-0.207-0.2642-0.13870.10050.12210.276-0.0988-0.20710.06510.34160.0208-0.01410.22990.04420.263230.797212.596431.2318
31.96990.2201-0.40013.1160.01562.41290.16820.07850.44880.1159-0.05550.2004-0.27680.0956-0.08730.2120.00380.02470.2811-0.01640.285156.98218.09016.7845
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 389 )A275 - 389
3X-RAY DIFFRACTION3chain 'A' and (resid 390 through 673 )A390 - 673

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