[English] 日本語
Yorodumi
- PDB-5lr5: N6-methyladenine is accommodated in a conventional A-U basepair -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lr5
TitleN6-methyladenine is accommodated in a conventional A-U basepair
ComponentsRNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')
KeywordsRNA / N6-methyladenine / RNA folding / Watson-Crick basepairs
Function / homologyRNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsHuang, L. / Lilley, D.M.J.
CitationJournal: EMBO Rep. / Year: 2017
Title: Control of box C/D snoRNP assembly by N(6)-methylation of adenine.
Authors: Huang, L. / Ashraf, S. / Wang, J. / Lilley, D.M.
History
DepositionAug 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Feb 20, 2019Group: Data collection / Derived calculations / Polymer sequence
Category: diffrn_source / entity_poly ...diffrn_source / entity_poly / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_seq_map_depositor_info / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')
B: RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')
C: RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')
D: RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1765
Polymers13,0794
Non-polymers961
Water18010
1
A: RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')
B: RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,5402
Polymers6,5402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint5 kcal/mol
Surface area3230 Å2
MethodPISA
2
C: RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')
D: RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6363
Polymers6,5402
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-12 kcal/mol
Surface area3220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.470, 50.470, 108.625
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: RNA chain
RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')


Mass: 3269.872 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium Sulfate 0.1 M Sodium Acetate trihydrate pH 4.6 25% w/v Polyethylene Glycol 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9193 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9193 Å / Relative weight: 1
ReflectionResolution: 2.27→43.71 Å / Num. obs: 5911 / % possible obs: 98.4 % / Observed criterion σ(I): 1.4 / Redundancy: 41.7 % / CC1/2: 1 / Rmerge(I) obs: 0.143 / Net I/σ(I): 13.3
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 38.7 % / Rmerge(I) obs: 2.7 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.545 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→43.708 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.71
RfactorNum. reflection% reflection
Rfree0.2873 528 4.54 %
Rwork0.2474 --
obs0.249 5910 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→43.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 856 5 10 871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02956
X-RAY DIFFRACTIONf_angle_d4.6911494
X-RAY DIFFRACTIONf_dihedral_angle_d10.504404
X-RAY DIFFRACTIONf_chiral_restr0.053188
X-RAY DIFFRACTIONf_plane_restr0.00340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.64160.43581200.42352802X-RAY DIFFRACTION96
2.6416-3.02370.41421820.38582765X-RAY DIFFRACTION98
3.0237-3.80930.2831050.28472677X-RAY DIFFRACTION92
3.8093-43.71550.21771210.1722865X-RAY DIFFRACTION99

+
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