[English] 日本語
Yorodumi
- PDB-6wy2: Crystal structure of RNA-10mer: CCGG(N4-methyl-C)GCCGG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wy2
TitleCrystal structure of RNA-10mer: CCGG(N4-methyl-C)GCCGG
ComponentsRNA-10mer: CCGG(4-methyl-C)GCCGG
KeywordsRNA / RNA DUPLEX
Function / homology: / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.928 Å
AuthorsSekula, B. / Ruszkowski, M. / Mao, S. / Haruehanroengra, P. / Sheng, J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1845486 United States
National Science Foundation (NSF, United States)MCB-1715234 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Base pairing, structural and functional insights into N4-methylcytidine (m4C) and N4,N4-dimethylcytidine (m42C) modified RNA.
Authors: Mao, S. / Sekula, B. / Ruszkowski, M. / Ranganathan, S.V. / Haruehanroengra, P. / Wu, Y. / Shen, F. / Sheng, J.
History
DepositionMay 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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: RNA-10mer: CCGG(4-methyl-C)GCCGG
B: RNA-10mer: CCGG(4-methyl-C)GCCGG
C: RNA-10mer: CCGG(4-methyl-C)GCCGG
D: RNA-10mer: CCGG(4-methyl-C)GCCGG
E: RNA-10mer: CCGG(4-methyl-C)GCCGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,29012
Polymers16,1055
Non-polymers1857
Water2,504139
1
A: RNA-10mer: CCGG(4-methyl-C)GCCGG
hetero molecules

A: RNA-10mer: CCGG(4-methyl-C)GCCGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4914
Polymers6,4422
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1220 Å2
ΔGint-13 kcal/mol
Surface area3860 Å2
MethodPISA
2
B: RNA-10mer: CCGG(4-methyl-C)GCCGG
C: RNA-10mer: CCGG(4-methyl-C)GCCGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5546
Polymers6,4422
Non-polymers1124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-18 kcal/mol
Surface area3840 Å2
MethodPISA
3
D: RNA-10mer: CCGG(4-methyl-C)GCCGG
E: RNA-10mer: CCGG(4-methyl-C)GCCGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4914
Polymers6,4422
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-14 kcal/mol
Surface area3940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.740, 30.425, 58.511
Angle α, β, γ (deg.)90.00, 106.49, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: RNA chain
RNA-10mer: CCGG(4-methyl-C)GCCGG


Mass: 3221.007 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% v/v (+/-)-2-Methyl-2,4-pentanediol (MPD), 0.040 M Sodium cacodylate trihydrate pH 7.0, 0.012 M Spermine tetrahydrochloride, 0.08 M Potassium chloride, 0.02 M Magnesium chloride hexahydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2019
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.928→28.052 Å / Num. obs: 10372 / % possible obs: 88.9 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.037 / Rrim(I) all: 0.061 / Net I/σ(I): 9.9
Reflection shellResolution: 1.929→1.998 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 518 / CC1/2: 0.645 / Rpim(I) all: 0.515 / Rrim(I) all: 0.908 / % possible all: 64.4

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MS9

4ms9


Resolution: 1.928→28.052 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2184 504 4.86 %
Rwork0.1871 --
obs0.1886 10370 83.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.928→28.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1065 7 139 1211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041185
X-RAY DIFFRACTIONf_angle_d0.8441840
X-RAY DIFFRACTIONf_dihedral_angle_d8.974585
X-RAY DIFFRACTIONf_chiral_restr0.029240
X-RAY DIFFRACTIONf_plane_restr0.00550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9283-2.12230.2871950.26721610X-RAY DIFFRACTION56
2.1223-2.42920.28661300.26062658X-RAY DIFFRACTION91
2.4292-3.05990.28031460.22882770X-RAY DIFFRACTION95
3.0599-28.0550.17131330.14772828X-RAY DIFFRACTION93
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)
14.5501-1.18983.58380.6738-0.40163.3326-0.21540.22930.8454-0.0540.0202-0.1438-0.25890.28270.17950.2911-0.01160.05790.22710.02360.4568-6.153315.192626.8359
24.12722.48471.13627.20210.38822.6872-0.15410.27340.2177-0.2546-0.1930.2086-0.0626-0.28060.28520.2701-0.04510.03570.3748-0.06060.255611.91814.863319.1354
35.82426.06880.22239.01760.28232.665-0.40110.62440.2119-0.68970.28310.0587-0.1611-0.1280.08340.22910.04570.00230.36480.00230.286316.154615.102716.8932
42.83841.8813-4.31253.3399-1.08817.5729-0.55580.5752-0.0501-0.54160.24950.03220.51570.23850.37260.51820.01160.07910.60610.03950.401738.570118.49395.0283
57.08236.1984-4.42957.5357-5.66397.4857-0.4931.11530.172-0.49280.72490.65860.3169-0.7499-0.24940.49980.01430.05330.5863-0.00740.498634.565918.22417.2896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 10 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 10 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 10 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 10 )

+
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