[English] 日本語
Yorodumi
- PDB-6is0: Crystal structure of the zebrafish cap-specific adenosine methylt... -

+
Open data


ID or keywords:

Loading...

-
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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
Non-polymers , 5 types, 320 molecules

#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / 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 / 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 / Bis-tris propane


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


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more