[English] 日本語
Yorodumi
- PDB-7yx6: Crystal structure of YTHDF2 with compound YLI_DF_027 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yx6
TitleCrystal structure of YTHDF2 with compound YLI_DF_027
ComponentsYTH domain-containing family protein 2
KeywordsRNA BINDING PROTEIN / epitranscriptomic reader / m6A reader
Function / homology
Function and homology information


C5-methylcytidine-containing RNA reader activity / organelle assembly / spermatogonial cell division / regulation of meiotic cell cycle process involved in oocyte maturation / positive regulation of cap-independent translational initiation / regulation of rRNA processing / gamete generation / endothelial to hematopoietic transition / embryonic morphogenesis / N6-methyladenosine-containing RNA reader activity ...C5-methylcytidine-containing RNA reader activity / organelle assembly / spermatogonial cell division / regulation of meiotic cell cycle process involved in oocyte maturation / positive regulation of cap-independent translational initiation / regulation of rRNA processing / gamete generation / endothelial to hematopoietic transition / embryonic morphogenesis / N6-methyladenosine-containing RNA reader activity / negative regulation of stem cell differentiation / oocyte maturation / regulation of hematopoietic stem cell differentiation / negative regulation of type I interferon-mediated signaling pathway / hematopoietic stem cell proliferation / mRNA destabilization / mRNA catabolic process / humoral immune response / negative regulation of Notch signaling pathway / regulation of neurogenesis / regulation of cell adhesion / regulation of mRNA stability / stress granule assembly / P-body / centriolar satellite / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / innate immune response / mRNA binding / RNA binding / nucleus / cytoplasm / cytosol
Similarity search - Function
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
6-ethyl-1H-pyrimidine-2,4-dione / YTH domain-containing family protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNai, F. / Li, Y. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B-189363 Switzerland
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Fragment Ligands of the m 6 A-RNA Reader YTHDF2.
Authors: Nai, F. / Nachawati, R. / Zalesak, F. / Wang, X. / Li, Y. / Caflisch, A.
History
DepositionFeb 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 2.0Mar 16, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / pdbx_contact_author ...atom_site / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_shell / software
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine_ls_restr.dev_ideal / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.version
Description: Model orientation/position / Details: The LOI binding pose needed correction / Provider: author / Type: Coordinate replacement
Revision 2.1Jul 6, 2022Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.2Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 2.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YTH domain-containing family protein 2
B: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4889
Polymers38,7362
Non-polymers7537
Water2,378132
1
A: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7925
Polymers19,3681
Non-polymers4244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6964
Polymers19,3681
Non-polymers3283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.570, 80.570, 114.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

-
Components

#1: Protein YTH domain-containing family protein 2 / CLL-associated antigen KW-14 / High-glucose-regulated protein 8 / Renal carcinoma antigen NY-REN-2


Mass: 19367.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDF2, HGRG8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5A9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-I6R / 6-ethyl-1H-pyrimidine-2,4-dione


Mass: 140.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 2.05 M Ammonium sulfate, 0.1 M Sodium citrate tribasic pH 4.9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→44.15 Å / Num. obs: 39068 / % possible obs: 99.9 % / Redundancy: 12.3 % / CC1/2: 0.999 / Net I/σ(I): 20.43
Reflection shellResolution: 1.8→1.91 Å / Num. unique obs: 6299 / CC1/2: 0.909

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RDN

4rdn


Resolution: 1.8→44.15 Å / Cross valid method: FREE R-VALUE / σ(F): 1.69 / Phase error: 29.077
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1968 1952 5 %
Rwork0.1842 37061 -
obs0.1872 39013 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.71 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 47 132 2506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092463
X-RAY DIFFRACTIONf_angle_d0.86563332
X-RAY DIFFRACTIONf_chiral_restr0.0601342
X-RAY DIFFRACTIONf_plane_restr0.0081424
X-RAY DIFFRACTIONf_dihedral_angle_d7.287331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.34261400.28592642X-RAY DIFFRACTION94.46
1.84-1.890.28861380.27822648X-RAY DIFFRACTION94.98
1.89-1.950.31421370.25482612X-RAY DIFFRACTION94.98
1.95-2.010.27791400.25512652X-RAY DIFFRACTION94.95
2.01-2.080.25031400.23432653X-RAY DIFFRACTION94.99
2.08-2.170.2441390.23012632X-RAY DIFFRACTION94.98
2.17-2.260.22851380.21612627X-RAY DIFFRACTION95.01
2.26-2.380.21471400.21412651X-RAY DIFFRACTION94.98
2.38-2.530.22971390.2122655X-RAY DIFFRACTION95.03
2.53-2.730.23281400.20662641X-RAY DIFFRACTION94.97
2.73-30.19431400.19382659X-RAY DIFFRACTION95
3-3.440.18141380.17342630X-RAY DIFFRACTION95.01
3.44-4.330.16821410.13782661X-RAY DIFFRACTION94.97
4.33-44.150.15561420.14512698X-RAY DIFFRACTION95

+
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