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

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Basic information

Entry
Database: PDB / ID: 6irx
TitleCrystal structure of the zebrafish cap-specific adenosine methyltransferase
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 / 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
mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PDX1 C-terminal-inhibiting factor 1


Theoretical massNumber of molelcules
Total (without water)58,0871
Polymers58,0871
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22930 Å2
Unit cell
Length a, b, c (Å)71.545, 84.132, 93.084
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: 58086.617 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.43 Å3/Da / Density % sol: 49.45 % / Mosaicity: 0.1 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 11% 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: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→47.033 Å / Num. obs: 38694 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 34.73 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.04 / Rrim(I) all: 0.141 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.0512.91.05428220.9130.3031.098100
8.94-47.03110.0855110.990.0260.08999.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.7.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→47.033 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.28
RfactorNum. reflection% reflection
Rfree0.2154 1860 4.82 %
Rwork0.191 --
obs0.1923 38620 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.74 Å2 / Biso mean: 45.7195 Å2 / Biso min: 20.63 Å2
Refinement stepCycle: final / Resolution: 2→47.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3915 0 0 198 4113
Biso mean---43.78 -
Num. residues----482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.05410.27781210.235428082929
2.0541-2.11450.241430.225227692912
2.1145-2.18280.23741480.215127852933
2.1828-2.26080.24591500.20527802930
2.2608-2.35130.2511470.219627952942
2.3513-2.45830.25251510.212627892940
2.4583-2.58790.27461230.222928252948
2.5879-2.750.25181400.224128082948
2.75-2.96230.21591200.218128512971
2.9623-3.26040.2481570.206928212978
3.2604-3.7320.20091480.180428422990
3.732-4.70120.18161460.160528883034
4.7012-47.04630.18881660.165329993165
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)
11.44280.1229-0.71331.864-0.48481.4834-0.0815-0.1658-0.13830.0092-0.0463-0.05240.20080.0310.12590.2619-0.0085-0.03680.2418-0.01150.216655.2555.891814.0303
23.7876-1.5212-1.2991.74311.39281.5877-0.00080.0878-0.0408-0.0645-0.13260.2658-0.1419-0.21880.13250.35690.04880.01690.41330.05020.305938.1511.777426.4085
31.7627-0.7309-1.56691.69910.93692.6273-0.04-0.2122-0.24840.0365-0.15020.5221-0.3149-0.32110.15240.4290.0805-0.03280.4264-0.02280.353234.276612.042932.6159
41.8712-0.2522-0.96535.7241-1.78572.5072-0.0614-0.0199-0.2034-0.0505-0.0855-0.40180.28930.35990.17450.29030.0775-0.01030.38340.00390.275272.64625.58778.4802
53.4099-0.1870.86763.13560.28624.12530.10050.1912-0.1724-0.0464-0.00610.17990.2408-0.3414-0.09030.2564-0.0003-0.00360.227-0.02810.208255.9951.173-0.2988
62.8824-2.25770.12632.1003-0.33753.55760.00140.17090.1091-0.08010.07980.2363-0.0729-0.3327-0.09290.25910.0182-0.030.25510.01990.264552.668922.67133.7425
71.5994-0.0874-0.33662.4154-0.07960.9685-0.0439-0.20220.24760.19840.0444-0.064-0.19050.0206-0.00390.2818-0.0083-0.01560.2804-0.00670.267559.810419.924412.4802
83.4423-0.3936-0.04032.07530.11122.79830.0995-0.08020.43050.02810.02120.217-0.3594-0.3682-0.10810.38610.0760.02220.24870.00480.422650.402631.166310.3371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 178 through 228 )A178 - 228
2X-RAY DIFFRACTION2chain 'A' and (resid 229 through 303 )A229 - 303
3X-RAY DIFFRACTION3chain 'A' and (resid 304 through 389 )A304 - 389
4X-RAY DIFFRACTION4chain 'A' and (resid 390 through 423 )A390 - 423
5X-RAY DIFFRACTION5chain 'A' and (resid 424 through 484 )A424 - 484
6X-RAY DIFFRACTION6chain 'A' and (resid 485 through 520 )A485 - 520
7X-RAY DIFFRACTION7chain 'A' and (resid 521 through 579 )A521 - 579
8X-RAY DIFFRACTION8chain 'A' and (resid 580 through 673 )A580 - 673

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