[English] 日本語
Yorodumi
- PDB-4rcj: Crystal structure of YTHDF1 YTH domain in complex with 5mer m6A RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rcj
TitleCrystal structure of YTHDF1 YTH domain in complex with 5mer m6A RNA
Components
  • RNA (5'-R(*GP*GP*(6MZ)P*CP*U)-3')
  • YTH domain-containing family protein 1
KeywordsRNA BINDING PROTEIN/RNA / Structural Genomics / Structural Genomics Consortium / SGC / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


regulation of axon guidance / organelle assembly / regulation of antigen processing and presentation / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / mRNA destabilization / positive regulation of translational initiation / immune system process / regulation of mRNA stability / stress granule assembly ...regulation of axon guidance / organelle assembly / regulation of antigen processing and presentation / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / mRNA destabilization / positive regulation of translational initiation / immune system process / regulation of mRNA stability / stress granule assembly / positive regulation of translation / learning / P-body / memory / cytoplasmic stress granule / ribosome binding / mRNA binding / RNA binding / cytoplasm
Similarity search - Function
ph1033 like fold / ph1033 like domains / YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
RNA / YTH domain-containing family protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsTempel, W. / Xu, C. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins.
Authors: Xu, C. / Liu, K. / Ahmed, H. / Loppnau, P. / Schapira, M. / Min, J.
History
DepositionSep 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 2.0Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YTH domain-containing family protein 1
B: RNA (5'-R(*GP*GP*(6MZ)P*CP*U)-3')


Theoretical massNumber of molelcules
Total (without water)23,8489
Polymers23,8482
Non-polymers07
Water3,189177
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.648, 40.029, 59.308
Angle α, β, γ (deg.)90.00, 93.41, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein YTH domain-containing family protein 1 / Dermatomyositis associated with cancer putative autoantigen 1 / DACA-1


Mass: 22248.084 Da / Num. of mol.: 1 / Fragment: UNP residues 365-554
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDF1, C20orf21 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q9BYJ9
#2: RNA chain RNA (5'-R(*GP*GP*(6MZ)P*CP*U)-3')


Mass: 1600.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 1.9 Å3/Da / Density % sol: 34.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG-3350, 0.2 M sodium chloride, 0.1 M bis-tris, pH 6.5, vapor diffusion, sitting drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791829 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791829 Å / Relative weight: 1
ReflectionResolution: 1.6→40.03 Å / Num. obs: 23138 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.6-1.6330.6091.83203107393.5
8.79-40.033.20.0352150515897.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
Aimless0.3.6data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4RCI

4rci


Resolution: 1.6→40.03 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.1607 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8468 / SU B: 2.042 / SU ML: 0.071 / SU R Cruickshank DPI: 0.0988 / SU Rfree: 0.0988 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ARP/WARP WAS USED IN DENSITY IMPROVEMENT MODE AFTER MOLECULAR REPLACEMENT. JLIGAND WAS USED FOR PREPARATION OF NUCLEOTIDE LINK RESTRAINT TARGETS. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. ...Details: ARP/WARP WAS USED IN DENSITY IMPROVEMENT MODE AFTER MOLECULAR REPLACEMENT. JLIGAND WAS USED FOR PREPARATION OF NUCLEOTIDE LINK RESTRAINT TARGETS. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS EVALUATED WITH MOLPROBITY. WEAK ELECTRON DENSITY NEAR THE 3'-END OF THE MODELED OLIGONUCLEOTIDE SUGGESTS THE PRESENCE OF AN ADDITIONAL NUCLEOTIDE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2096 1164 5 %RANDOM
Rwork0.1711 ---
obs0.1732 23124 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.76 Å2 / Biso mean: 14.351 Å2 / Biso min: 4 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å2-0.16 Å2
2--0.38 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 91 7 177 1794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191694
X-RAY DIFFRACTIONr_bond_other_d0.0010.021513
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.9092315
X-RAY DIFFRACTIONr_angle_other_deg1.38733491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2765195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.88524.02482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63715279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.6681510
X-RAY DIFFRACTIONr_chiral_restr0.1280.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021864
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02410
X-RAY DIFFRACTIONr_mcbond_it1.8031.19759
X-RAY DIFFRACTIONr_mcbond_other1.771.184758
X-RAY DIFFRACTIONr_mcangle_it2.5761.777949
LS refinement shellResolution: 1.6→1.647 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 68 -
Rwork0.294 1565 -
all-1633 -
obs--95.66 %

+
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