[English] 日本語
Yorodumi
- PDB-6l7y: Crystal structure of Cet1 from Trypanosoma cruzi in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l7y
TitleCrystal structure of Cet1 from Trypanosoma cruzi in complex with #466 ligand.
ComponentsmRNA_triPase domain-containing protein
KeywordsHYDROLASE / mRNA capping / RNA triphosphatase
Function / homology
Function and homology information


mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / mRNA processing / metal ion binding / nucleus
Similarity search - Function
RNA 5'-triphosphatase Cet1/Ctl1 / mRNA capping enzyme, beta chain / mRNA triphosphatase Cet1-like / mRNA triphosphatase Cet1-like superfamily / CYTH-like domain superfamily
Similarity search - Domain/homology
3,4,6,7-tetrahydroacridine-1,8(2H,5H)-dione / mRNA 5'-phosphatase
Similarity search - Component
Biological speciesTrypanosoma cruzi strain CL Brener (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsKuwabara, N. / Ho, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16H05180 Japan
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystal structures of the RNA triphosphatase fromTrypanosoma cruziprovide insights into how it recognizes the 5'-end of the RNA substrate.
Authors: Takagi, Y. / Kuwabara, N. / Dang, T.T. / Furukawa, K. / Ho, C.K.
History
DepositionNov 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: mRNA_triPase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3976
Polymers23,7971
Non-polymers6005
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-16 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.943, 115.943, 56.749
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

#1: Protein mRNA_triPase domain-containing protein


Mass: 23797.006 Da / Num. of mol.: 1 / Mutation: D126N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi strain CL Brener (eukaryote)
Strain: CL Brener / Gene: Tc00.1047053508479.390 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4E2I1
#2: Chemical ChemComp-JJY / 3,4,6,7-tetrahydroacridine-1,8(2H,5H)-dione


Mass: 215.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.63 Å3/Da / Density % sol: 73.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES-NaOH (pH 7.5), ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.51→49.4 Å / Num. obs: 15320 / % possible obs: 99.7 % / Redundancy: 9.7 % / Biso Wilson estimate: 64.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.087 / Net I/σ(I): 16.6
Reflection shellResolution: 2.51→2.61 Å / Rmerge(I) obs: 1.208 / Num. unique obs: 1683 / CC1/2: 0.927 / Rrim(I) all: 1.273

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L7V

6l7v


Resolution: 2.51→49.4 Å / SU ML: 0.3203 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.4353
RfactorNum. reflection% reflection
Rfree0.2402 730 4.8 %
Rwork0.2014 --
obs0.2032 15215 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 81.39 Å2
Refinement stepCycle: LAST / Resolution: 2.51→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1606 0 36 8 1650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331677
X-RAY DIFFRACTIONf_angle_d0.6272271
X-RAY DIFFRACTIONf_chiral_restr0.0429251
X-RAY DIFFRACTIONf_plane_restr0.0034291
X-RAY DIFFRACTIONf_dihedral_angle_d8.99451386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.70.42331240.34582840X-RAY DIFFRACTION97.69
2.7-2.970.31021570.28882854X-RAY DIFFRACTION98.95
2.97-3.40.29171410.24612881X-RAY DIFFRACTION99.34
3.4-4.290.23521540.18712906X-RAY DIFFRACTION99.84
4.29-49.40.20011540.16523004X-RAY DIFFRACTION99.84
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)
11.435196694450.646145281659-0.800914382836.768589614713.6121536156.428519338020.3213516786781.40920383078-0.399261227346-0.694169284806-0.4950197620070.190885743090.1097729395280.6217299543440.1778175280471.17932512816-0.0831219984016-0.08087506387290.814190025047-0.02784892687650.4515425711198.1338823969104.111387585-11.8223408704
23.85874105704-5.026157819470.9173612530947.79932525613-4.042242066723.709910499460.0379871981123-0.08255862943160.111657247695-0.381717449159-0.09624121560010.0313187364674-0.639182062803-0.3533537972470.129989265790.6926095183550.031254353107-0.0143726932920.652598324415-0.03928323830660.4603734049884.37089240927117.343251449-4.82920052279
37.613059031284.81590677735-1.916657513248.02456135934-1.937685683055.1588798149-0.254263988807-0.17173656653-0.2567395679180.2895551908840.0983846633217-0.5359563696180.1976557215680.1884008615230.1053784859520.6956338419360.0385094541593-0.07838409077870.577127974441-0.0876053785350.60267496529519.1308923873110.1007291489.20800649649
44.75594331108-1.98270117902-2.953972333993.315962303680.2943688201625.302236428110.5115242635670.4175840190560.0586027172447-0.833558269816-0.406183472615-0.964033644049-0.7033996985020.817704723148-0.1234762575570.864128955441-0.1610175534520.142407294080.780922406133-0.04500857627060.81895414349419.0843990983125.8538063144.69944649366
53.071355377162.925437337914.458315511619.145174060711.338031219527.400799916420.06754288665050.264556661442-0.03366129536660.06181619050730.441085292662-0.994785702006-0.2824725770320.639169059234-0.5566193519760.714154055182-0.01427783634730.1001074156530.525175725413-0.1076665446110.64429961571110.2614373862132.85984090812.8748802554
61.26381725607-0.350260363705-0.1923652022162.2054792049-0.3213024879530.9291911976680.171736765150.326602380906-0.241291084753-0.223166071546-0.1513317295450.2804247416950.0950082475810.0889424182004-0.001403909394580.626044098602-0.03843082824630.01777259762980.591502626556-0.0118575826850.5031957674046.52219355779114.2766286821.88226257951
72.70450865091-1.45122140639-2.217043082632.59967458637-0.7510442279494.84626305443-0.282634833395-0.3128437159820.0568285687669-0.3125841725530.368170341294-0.200279206537-0.3807405993180.212652863146-0.03117665699580.654283397418-0.1944382322540.001804092416680.581641567638-0.07254587562710.4965422937199.50254438256129.05233269.9327624932
83.4967075771-2.28560348442-2.722863958385.826276335274.224421161293.43769262938-0.1800282022650.5314245706840.831959167557-0.2263987776990.1006063607-0.4844690620030.8251871169410.122616524968-0.2280146689430.579620881851-0.2019017856760.032395314570.6253174261140.0658208785810.65418278064417.6527494268119.5153135133.42408233534
94.2204561140.225794241261-0.6078818545952.791669240491.187683341164.17366773208-0.1230728098090.009246488823320.37588160507-0.1625809133730.4384845316370.172328296569-1.06342746269-0.341614632765-0.3822987272140.741701967879-0.02001569800450.03978692698140.5718581426250.03612420010580.62462132909912.1536997975118.91777818-0.839351941601
107.48975855614-2.340117998653.98056300784.67779078657-2.710889781552.65197898164-0.1828329119821.1253275214-0.12746815157-0.7370850426380.0967429176196-0.499066418270.8063080313730.7477479400220.03502467971260.7374056837580.01057729757390.1447487146120.659461605594-0.0704371618130.51088653602617.709649116108.216398712-6.57268140005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 98 )
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 114 )
5X-RAY DIFFRACTION5chain 'A' and (resid 115 through 131 )
6X-RAY DIFFRACTION6chain 'A' and (resid 132 through 164 )
7X-RAY DIFFRACTION7chain 'A' and (resid 165 through 189 )
8X-RAY DIFFRACTION8chain 'A' and (resid 190 through 201 )
9X-RAY DIFFRACTION9chain 'A' and (resid 202 through 223 )
10X-RAY DIFFRACTION10chain 'A' and (resid 224 through 241 )

+
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