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

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Basic information

Entry
Database: PDB / ID: 6irw
TitleCrystal structure of the human cap-specific adenosine methyltransferase bound to SAH
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
S-ADENOSYL-L-HOMOCYSTEINE / mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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: Phosphorylated CTD-interacting factor 1
B: Phosphorylated CTD-interacting factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,5554
Polymers118,7862
Non-polymers7692
Water34219
1
A: Phosphorylated CTD-interacting factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7772
Polymers59,3931
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphorylated CTD-interacting factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7772
Polymers59,3931
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.215, 120.379, 156.946
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: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.79 Å3/Da / Density % sol: 55.94 % / Mosaicity: 0.04 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 9% PEG 3350, 0.2M 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: Jun 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→47.99 Å / Num. obs: 30286 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 59.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.049 / Rrim(I) all: 0.127 / Net I/σ(I): 10.6 / Num. measured all: 202713 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.9-3.066.80.68243380.9120.2820.738100
9.17-47.995.90.0410770.9980.0180.04399.5

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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: 2.9→47.989 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.41
RfactorNum. reflection% reflection
Rfree0.2361 1443 4.78 %
Rwork0.2077 --
obs0.209 30176 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 168.61 Å2 / Biso mean: 65.126 Å2 / Biso min: 23.71 Å2
Refinement stepCycle: final / Resolution: 2.9→47.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7993 0 52 19 8064
Biso mean--38.53 35 -
Num. residues----985
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.00370.29411610.300928042965100
3.0037-3.12390.29091510.257428072958100
3.1239-3.2660.27311350.242528492984100
3.266-3.43820.26831330.238628482981100
3.4382-3.65350.2541600.215128423002100
3.6535-3.93550.22661170.200828612978100
3.9355-4.33130.20391360.185328753011100
4.3313-4.95750.21741280.172929183046100
4.9575-6.24380.24431630.201628973060100
6.2438-47.99530.20541590.19833032319199
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)
12.7937-0.9031.02071.333-0.44331.34030.05310.01170.1552-0.0234-0.12570.169-0.171-0.3150.08460.40890.01960.06590.4904-0.12830.3292-38.75511.792620.7387
20.4861-1.00150.34892.59320.29881.67490.00990.2840.247-0.2646-0.0102-0.09510.155-0.0271-0.00680.5503-0.04520.15570.73560.09020.4897-24.3952-0.8995-4.3714
34.29171.45891.64835.33372.12063.1591-0.0073-0.41180.41050.0109-0.35650.47540.56680.39690.02120.84990.21340.01890.59080.16810.2998-25.8785-22.7888-20.8777
40.8241-1.13190.0071.51091.76254.04120.17160.09210.0976-0.07750.363-0.35370.48170.8975-0.3930.61150.11360.05580.7550.12940.5034-18.9616-13.3945-14.0797
51.0302-2.19631.99755.5961-4.89866.6445-0.09210.09330.54430.3946-0.0940.0435-0.78950.09920.20110.46120.02290.10020.4359-0.09440.7338-25.777915.343420.7957
65.03810.9578-0.37442.8664-0.53633.5367-0.15420.3370.7004-0.17730.17770.1882-0.6217-0.57260.01860.46130.07330.01680.4037-0.00790.4849-44.05939.476111.2526
72.3119-0.14810.76483.0368-0.21591.40410.04250.02630.1309-0.1249-0.0468-0.14080.0689-0.02880.00630.29880.00290.09870.4075-0.05870.3506-28.3847-8.760717.7434
82.90891.22290.77371.49750.43662.7503-0.1062-0.0514-0.2133-0.09450.11210.26460.3119-0.44620.01560.4549-0.01050.140.3648-0.06550.4038-37.2219-16.976813.8843
93.95920.68320.68593.32490.52934.96160.1808-0.0033-0.78710.1394-0.1669-0.10880.3608-0.1231-0.01430.35980.0035-0.01290.328-0.05250.3929-31.6667-20.814225.3523
101.0824-0.3456-0.13430.6304-0.76222.25170.0892-0.35310.13560.29760.09130.14020.0092-0.0837-0.16130.5278-0.02320.07160.49310.00650.4616-41.3978-1.2815-25.3991
112.46970.60511.06575.2723-2.86514.82390.18580.353-0.89070.30190.60250.71751.0177-0.8148-0.85240.9744-0.2224-0.05290.90830.05310.7189-49.7173-26.6421-1.8231
120.6596-0.00540.62852.78960.09521.22380.0779-0.21220.21790.3680.0660.0793-0.4769-0.0685-0.18310.33390.05190.11750.36650.01460.6277-47.109812.023-30.9038
132.65040.98760.22223.36940.90042.01570.1135-0.14940.01570.3046-0.0424-0.00660.03220.1808-0.06840.30520.06040.02340.37920.08490.3335-36.115-2.2379-38.2883
143.3261-0.98191.19651.490.363.68830.2258-0.009-0.45860.16060.00990.20870.48570.3746-0.2650.53440.0292-0.03450.35280.06520.5168-35.4957-18.9234-42.3252
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 301 )A271 - 301
4X-RAY DIFFRACTION4chain 'A' and (resid 302 through 385 )A302 - 385
5X-RAY DIFFRACTION5chain 'A' and (resid 386 through 418 )A386 - 418
6X-RAY DIFFRACTION6chain 'A' and (resid 419 through 477 )A419 - 477
7X-RAY DIFFRACTION7chain 'A' and (resid 478 through 600 )A478 - 600
8X-RAY DIFFRACTION8chain 'A' and (resid 601 through 634 )A601 - 634
9X-RAY DIFFRACTION9chain 'A' and (resid 635 through 668 )A635 - 668
10X-RAY DIFFRACTION10chain 'B' and (resid 165 through 280 )B165 - 280
11X-RAY DIFFRACTION11chain 'B' and (resid 281 through 353 )B281 - 353
12X-RAY DIFFRACTION12chain 'B' and (resid 354 through 418 )B354 - 418
13X-RAY DIFFRACTION13chain 'B' and (resid 419 through 600 )B419 - 600
14X-RAY DIFFRACTION14chain 'B' and (resid 601 through 668 )B601 - 668

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