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- PDB-6is0: Crystal structure of the zebrafish cap-specific adenosine methylt... -

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Basic information

Entry
Database: PDB / ID: 6is0
TitleCrystal structure of the zebrafish cap-specific adenosine methyltransferase bound to SAH and m7G-capped RNA
Components
  • PDX1 C-terminal-inhibiting factor 1
  • m7G-capped RNA
KeywordsTRANSFERASE/RNA / RNA METHYLATION / METHYLTRANSFERASE / M6A / N6-METHYLADENOSINE / TRANSFERASE-RNA complex
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 / RNA / mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
synthetic construct (others)
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 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
Revision 2.0Mar 6, 2024Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

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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
C: m7G-capped RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0289
Polymers58,6542
Non-polymers1,3737
Water5,639313
1
A: PDX1 C-terminal-inhibiting factor 1
hetero molecules

C: m7G-capped RNA


Theoretical massNumber of molelcules
Total (without water)60,0289
Polymers58,6542
Non-polymers1,3737
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area2510 Å2
ΔGint7 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.219, 84.035, 92.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / RNA chain , 2 types, 2 molecules AC

#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: RNA chain m7G-capped RNA


Mass: 1083.701 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 320 molecules

#3: 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
#4: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 458.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O11P2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.48 Å3/Da / Density % sol: 50.36 % / Mosaicity: 0.04 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 9% PEG 3350, 0.1M potassium thiocyanate, 0.05M 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: Jan 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47.74 Å / Num. obs: 54004 / % possible obs: 99.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 31.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.021 / Rrim(I) all: 0.054 / Net I/σ(I): 19 / Num. measured all: 364594 / Scaling rejects: 130
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.846.90.57631280.9110.2340.62298.3
9-47.746.10.0395210.9980.0160.04299.6

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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: 1.8→47.736 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.54
RfactorNum. reflection% reflection
Rfree0.2145 2657 4.93 %
Rwork0.1771 --
obs0.1789 53942 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.87 Å2 / Biso mean: 40.4453 Å2 / Biso min: 18.15 Å2
Refinement stepCycle: final / Resolution: 1.8→47.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 75 90 313 4286
Biso mean--44.01 42.7 -
Num. residues----470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.83270.28411280.23282631275998
1.8327-1.8680.25681340.21482675280998
1.868-1.90610.25741540.20422618277298
1.9061-1.94760.22441360.20032615275198
1.9476-1.99290.23221410.1892657279898
1.9929-2.04270.21781180.17872672279099
2.0427-2.09790.2341420.18112646278899
2.0979-2.15970.18161400.17382699283998
2.1597-2.22940.21991170.17472649276699
2.2294-2.30910.21061370.17062707284499
2.3091-2.40150.20911360.17742692282899
2.4015-2.51080.21391450.17182685283099
2.5108-2.64320.20351560.17532695285199
2.6432-2.80880.22831420.18462700284299
2.8088-3.02560.23571380.18492719285799
3.0256-3.330.21151380.181527472885100
3.33-3.81170.23311400.173127752915100
3.8117-4.80160.19311540.154227802934100
4.8016-47.75290.20471610.185129233084100
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)
10.7330.1604-0.82512.7317-0.34960.97670.1453-0.00020.1232-0.1688-0.1392-0.2167-0.17460.2187-0.01860.25350.00530.00330.31370.00980.283168.109113.79274.6215
22.2231-0.5099-1.94411.52891.30552.6225-0.0371-0.0641-0.01250.1461-0.03380.11520.0696-0.09220.06380.21680.04360.0080.25850.0240.188149.3376.086223.8386
33.5351-0.628-0.24763.5594-0.58773.17680.03960.6005-0.5051-0.8484-0.21340.4986-0.0751-0.8430.14370.47140.16590.0350.521-0.02320.362124.887615.023528.4802
44.079-1.0590.1273.1167-0.82291.5205-0.2395-0.27280.12820.29790.23990.631-0.453-0.77570.10540.50990.19750.07790.5511-0.04840.452921.689519.931338.96
51.3227-0.1655-1.29450.28320.85412.24270.0687-0.2633-0.0592-0.0992-0.0890.1599-0.25730.05330.05510.37030.03470.00240.238-0.00760.259245.07248.986928.5191
61.10420.7481-1.14633.591-0.24261.55830.0911-0.26820.02470.2519-0.1062-0.4192-0.03230.51880.00190.21430.0387-0.04220.35680.03940.325775.13014.65078.9885
73.0902-0.25550.89172.82560.25483.61990.09760.4651-0.2358-0.4839-0.05530.28320.1857-0.4159-0.01040.2660.0327-0.03510.2987-0.03690.222455.28930.6995-3.6783
81.80330.7867-0.8091.8398-0.3482.34010.10740.05330.07720.0706-0.10820.0453-0.0796-0.06180.00180.19440.032-0.01080.22080.0090.204861.43041.07293.1576
91.3283-0.97150.14241.92880.42562.34320.16110.14270.1732-0.3977-0.14450.1605-0.3967-0.0015-0.02920.330.0444-0.01420.25570.01720.278858.560521.16282.4404
101.8636-0.0748-0.412.45970.47052.6350.0703-0.16740.38870.10360.01820.0538-0.48370.0539-0.08240.28820.01440.0010.2168-0.00660.268660.027624.31914.7414
112.6959-0.96940.04581.86240.80282.76230.18590.29360.4114-0.4043-0.16940.3519-0.7018-0.4182-0.04170.63350.08880.02910.30250.01580.573754.955134.1565.4565
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 178 through 202 )A178 - 202
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 274 )A203 - 274
3X-RAY DIFFRACTION3chain 'A' and (resid 275 through 305 )A275 - 305
4X-RAY DIFFRACTION4chain 'A' and (resid 306 through 334 )A306 - 334
5X-RAY DIFFRACTION5chain 'A' and (resid 335 through 389 )A335 - 389
6X-RAY DIFFRACTION6chain 'A' and (resid 390 through 423 )A390 - 423
7X-RAY DIFFRACTION7chain 'A' and (resid 424 through 459 )A424 - 459
8X-RAY DIFFRACTION8chain 'A' and (resid 460 through 484 )A460 - 484
9X-RAY DIFFRACTION9chain 'A' and (resid 485 through 532 )A485 - 532
10X-RAY DIFFRACTION10chain 'A' and (resid 533 through 605 )A533 - 605
11X-RAY DIFFRACTION11chain 'A' and (resid 606 through 673 )A606 - 673

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