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- PDB-6irv: Crystal structure of the human cap-specific adenosine methyltrans... -

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Basic information

Entry
Database: PDB / ID: 6irv
TitleCrystal structure of the human cap-specific adenosine methyltransferase
ComponentsPhosphorylated CTD-interacting factor 1
KeywordsTRANSFERASE / RNA METHYLATION / METHYLTRANSFERASE / M6A / N6-METHYLADENOSINE
Function / homology
Function and homology information


mRNA (2'-O-methyladenosine-N6-)-methyltransferase / RNA polymerase II C-terminal domain phosphoserine binding / mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / : / S-adenosyl-L-methionine binding / intercellular bridge / RNA polymerase II C-terminal domain binding / positive regulation of translation / microtubule cytoskeleton / negative regulation of translation ...mRNA (2'-O-methyladenosine-N6-)-methyltransferase / RNA polymerase II C-terminal domain phosphoserine binding / mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / : / S-adenosyl-L-methionine binding / intercellular bridge / RNA polymerase II C-terminal domain binding / positive regulation of translation / microtubule cytoskeleton / negative regulation of translation / nucleoplasm / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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

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Assembly

Deposited unit
A: Phosphorylated CTD-interacting factor 1
B: Phosphorylated CTD-interacting factor 1


Theoretical massNumber of molelcules
Total (without water)118,7862
Polymers118,7862
Non-polymers00
Water1,15364
1
A: Phosphorylated CTD-interacting factor 1


Theoretical massNumber of molelcules
Total (without water)59,3931
Polymers59,3931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphorylated CTD-interacting factor 1


Theoretical massNumber of molelcules
Total (without water)59,3931
Polymers59,3931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.699, 120.309, 156.831
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 Phosphorylated CTD-interacting factor 1


Mass: 59393.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCIF1, C20orf67 / Plasmid: pE-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q9H4Z3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.81 Å3/Da / Density % sol: 56.19 % / Mosaicity: 0.04 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG 3350, 0.4M sodium nitrate, 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: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→48.125 Å / Num. obs: 37583 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 52.99 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.046 / Rrim(I) all: 0.119 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.7-2.826.60.75145350.90.3160.816100
9.35-48.125.80.0410180.9980.0180.04499.4

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IRX

6irx


Resolution: 2.7→48.125 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.37
RfactorNum. reflection% reflection
Rfree0.2518 1876 5.01 %
Rwork0.2143 --
obs0.2162 37449 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 177.43 Å2 / Biso mean: 62.1116 Å2 / Biso min: 23.89 Å2
Refinement stepCycle: final / Resolution: 2.7→48.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8017 0 0 64 8081
Biso mean---43.52 -
Num. residues----988
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 (%)
2.7-2.7730.3781410.319226732814100
2.773-2.85460.33881440.289127172861100
2.8546-2.94670.34911470.274226922839100
2.9467-3.0520.2641300.255427122842100
3.052-3.17420.35981440.255127072851100
3.1742-3.31860.29921490.253726812830100
3.3186-3.49360.25911230.221227392862100
3.4936-3.71240.24171610.201327192880100
3.7124-3.99890.2441690.196727112880100
3.9989-4.4010.20741520.188127362888100
4.401-5.03730.20121260.169127842910100
5.0373-6.34420.23591490.207727882937100
6.3442-48.13230.22821410.20252914305599
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)
11.90340.3665-0.4172.102-0.59671.50320.10970.0691-0.02920.1421-0.0708-0.00370.0755-0.2408-0.0830.32520.0206-0.05090.322-0.09760.2393-38.5342-1.5242-43.5379
21.29230.7048-0.55252.08550.33112.01030.0164-0.44010.01040.26780.2193-0.0138-0.2438-0.0405-0.1180.53390.0177-0.0880.52740.01590.4263-24.48481.269-18.1712
32.2811-0.7348-1.21245.50262.09465.14760.1410.24550.26080.42320.3647-0.227-0.7316-0.0145-0.64730.8529-0.00670.00850.6933-0.07330.523-23.816622.1616-1.4093
42.0182-0.0316-0.83791.40321.3272.4256-0.0450.67640.83020.04860.7058-1.7325-0.86030.3249-0.62671.2284-0.31160.3690.6666-0.32451.1365-19.738929.4723-1.7311
51.0466-0.2536-0.68210.9490.22751.77410.0254-0.1101-0.30450.34720.1233-0.03790.34260.1739-0.28690.46530.0415-0.11670.2797-0.01960.5605-23.0752-11.8726-30.6425
62.21050.5282-0.2571.9503-0.63571.43350.0436-0.01890.04790.1720.0840.0051-0.1336-0.2786-0.10630.31150.0612-0.03010.3549-0.07570.2936-33.80482.5504-38.1858
72.3202-0.55720.13660.69610.51142.33220.1354-0.13370.3230.0723-0.047-0.1259-0.2337-0.2076-0.15190.47050.06590.02710.3072-0.05060.508-34.954518.8551-42.2947
81.1878-0.9394-0.78561.32430.16250.8078-0.0028-0.01480.0979-0.00130.0632-0.00570.22370.2393-0.06350.304-0.0067-0.04520.51160.10080.3295-32.1271-1.755620.7707
91.116-1.1743-0.11081.296-0.45371.94280.05990.3299-0.1355-0.2821-0.10830.0341-0.1316-0.1167-0.05120.5487-0.0342-0.08390.7031-0.07480.4181-46.18541.1308-4.6837
102.44790.5704-1.3513.936-1.90263.0278-0.141-0.7553-0.5142-0.0322-0.3065-0.4841-0.6049-0.28770.17820.65280.2235-0.06280.6659-0.12450.2868-44.648422.988-21.3066
110.8083-0.61590.14580.8458-1.36583.47530.1450.1148-0.0688-0.42250.26760.2824-0.2786-0.8873-0.26910.64420.1906-0.04280.7387-0.10510.4839-51.540212.8059-14.1856
120.9184-1.8012-1.51323.81593.08774.8317-0.1499-0.1077-0.30230.20520.0705-0.19230.51180.010.04810.39820.0115-0.06780.34260.0610.547-45.2571-14.870821.0112
133.7740.6581.10992.3451-0.02471.92950.0340.2784-0.6209-0.22010.0615-0.27470.32260.3478-0.05640.37040.0618-0.01060.3411-0.00020.3915-26.651-9.315911.3558
140.4653-0.1363-0.50412.53280.24821.24590.0135-0.0341-0.1556-0.2171-0.0890.0612-0.002-0.04270.0620.32260.02-0.0730.40710.04380.3673-40.99286.155618.1563
152.76790.0143-0.10323.04440.48620.07650.00090.35510.5182-0.4737-0.00480.1852-0.1749-0.0034-0.03390.4178-0.0178-0.04770.44050.04590.3937-47.504317.023216.2963
162.94250.3143-0.45191.8118-0.57842.380.23180.23470.3324-0.0856-0.0705-0.0608-0.19050.1712-0.08760.35180.0282-0.03750.29290.02740.3508-36.246118.858119.54
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 165 through 198 )A165 - 198
2X-RAY DIFFRACTION2chain 'A' and (resid 199 through 270 )A199 - 270
3X-RAY DIFFRACTION3chain 'A' and (resid 271 through 307 )A271 - 307
4X-RAY DIFFRACTION4chain 'A' and (resid 308 through 353 )A308 - 353
5X-RAY DIFFRACTION5chain 'A' and (resid 354 through 418 )A354 - 418
6X-RAY DIFFRACTION6chain 'A' and (resid 419 through 601 )A419 - 601
7X-RAY DIFFRACTION7chain 'A' and (resid 602 through 668 )A602 - 668
8X-RAY DIFFRACTION8chain 'B' and (resid 165 through 198 )B165 - 198
9X-RAY DIFFRACTION9chain 'B' and (resid 199 through 270 )B199 - 270
10X-RAY DIFFRACTION10chain 'B' and (resid 271 through 301 )B271 - 301
11X-RAY DIFFRACTION11chain 'B' and (resid 302 through 386 )B302 - 386
12X-RAY DIFFRACTION12chain 'B' and (resid 387 through 418 )B387 - 418
13X-RAY DIFFRACTION13chain 'B' and (resid 419 through 477 )B419 - 477
14X-RAY DIFFRACTION14chain 'B' and (resid 478 through 573 )B478 - 573
15X-RAY DIFFRACTION15chain 'B' and (resid 574 through 600 )B574 - 600
16X-RAY DIFFRACTION16chain 'B' and (resid 601 through 668 )B601 - 668

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