[English] 日本語
Yorodumi
- PDB-7pcu: Crystal structure of YTHDF1 YTH domain in complex with ebselen -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pcu
TitleCrystal structure of YTHDF1 YTH domain in complex with ebselen
ComponentsYTH domain-containing family protein 1
KeywordsRNA BINDING PROTEIN / mRNA binding and stability
Function / homology
Function and homology information


regulation of antigen processing and presentation / regulation of axon guidance / organelle assembly / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / immune system process / mRNA destabilization / positive regulation of translational initiation / stress granule assembly / regulation of mRNA stability ...regulation of antigen processing and presentation / regulation of axon guidance / organelle assembly / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / immune system process / mRNA destabilization / positive regulation of translational initiation / stress granule assembly / regulation of mRNA stability / learning / positive regulation of translation / P-body / memory / cytoplasmic stress granule / ribosome binding / mRNA binding / RNA binding / cytoplasm
Similarity search - Function
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
N-phenyl-2-selanylbenzamide / YTH domain-containing family protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsDalle Vedove, A. / Cazzanelli, G. / Quattrone, A. / Provenzani, A. / Lolli, G.
Funding support Italy, 2items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchMFAG 2017 - ID. 19882 Italy
Italian Association for Cancer ResearchIG2018 - ID. 21548 Italy
CitationJournal: Acs Pharmacol Transl Sci / Year: 2022
Title: Small-Molecule Ebselen Binds to YTHDF Proteins Interfering with the Recognition of N 6 -Methyladenosine-Modified RNAs.
Authors: Micaelli, M. / Dalle Vedove, A. / Cerofolini, L. / Vigna, J. / Sighel, D. / Zaccara, S. / Bonomo, I. / Poulentzas, G. / Rosatti, E.F. / Cazzanelli, G. / Alunno, L. / Belli, R. / Peroni, D. / ...Authors: Micaelli, M. / Dalle Vedove, A. / Cerofolini, L. / Vigna, J. / Sighel, D. / Zaccara, S. / Bonomo, I. / Poulentzas, G. / Rosatti, E.F. / Cazzanelli, G. / Alunno, L. / Belli, R. / Peroni, D. / Dassi, E. / Murakami, S. / Jaffrey, S.R. / Fragai, M. / Mancini, I. / Lolli, G. / Quattrone, A. / Provenzani, A.
History
DepositionAug 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YTH domain-containing family protein 1
B: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8494
Polymers46,2962
Non-polymers5522
Water32418
1
A: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4242
Polymers23,1481
Non-polymers2761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4242
Polymers23,1481
Non-polymers2761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.260, 120.260, 78.775
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 364 through 558)
21(chain B and (resid 364 through 458 or resid 471 through 558))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYS(chain A and resid 364 through 558)AA364 - 5585 - 199
21SERSERTYRTYR(chain B and (resid 364 through 458 or resid 471 through 558))BB364 - 4585 - 99
22LYSLYSLYSLYS(chain B and (resid 364 through 458 or resid 471 through 558))BB471 - 558112 - 199

-
Components

#1: Protein YTH domain-containing family protein 1 / DF1 / Dermatomyositis associated with cancer putative autoantigen 1 / DACA-1


Mass: 23148.166 Da / Num. of mol.: 2 / Fragment: YTH domain (residues 361-559)
Mutation: First residue G derives from the expression tag: E544A/E545V/E546V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDF1, C20orf21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BYJ9
#2: Chemical ChemComp-9JT / N-phenyl-2-selanylbenzamide / ~{N}-phenyl-2-selanyl-benzamide / Ebselen, bound form


Mass: 276.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11NOSe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.01 % / Mosaicity: 0.15 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 6% PEG3350, 0.2 M KSCN

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9718 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 2.65→47.8 Å / Num. obs: 17368 / % possible obs: 100 % / Redundancy: 24.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.043 / Rrim(I) all: 0.208 / Net I/σ(I): 13.9 / Num. measured all: 423712 / Scaling rejects: 201
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.65-2.7825.91.7165871622640.7850.3411.752.2100
8.79-47.818.20.078101405580.9990.0180.0831.999.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.11.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RCI

4rci


Resolution: 2.65→47.797 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2522 884 5.1 %
Rwork0.2024 16437 -
obs0.205 17321 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.33 Å2 / Biso mean: 79.6504 Å2 / Biso min: 36.98 Å2
Refinement stepCycle: final / Resolution: 2.65→47.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 32 18 3083
Biso mean--102.19 61.24 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053141
X-RAY DIFFRACTIONf_angle_d0.9074220
X-RAY DIFFRACTIONf_chiral_restr0.051436
X-RAY DIFFRACTIONf_plane_restr0.006541
X-RAY DIFFRACTIONf_dihedral_angle_d19.4181886
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1756X-RAY DIFFRACTION14.936TORSIONAL
12B1756X-RAY DIFFRACTION14.936TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.6501-2.81610.34411480.27692691
2.8161-3.03350.30661390.25812686
3.0335-3.33870.28541500.22172701
3.3387-3.82160.26551370.20442702
3.8216-4.81410.24031550.1822762
4.8141-47.7970.22671550.19132895
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)
16.70520.81321.1993.92422.11524.6286-0.23690.9903-0.4065-0.7025-0.0009-0.34120.30240.1336-0.01030.56530.03720.02020.5970.03240.40613.4654-49.007-3.8191
25.78531.21650.55.4454-0.46563.0069-0.12320.03160.52870.0362-0.0106-0.1927-0.43760.29510.11290.5429-0.0778-0.06480.52490.03460.407719.207-38.75915.9975
37.0973-0.602-3.25214.83491.52688.3342-0.2197-0.34190.24520.16680.09490.9188-0.1892-0.91850.03240.48310.0175-0.03630.6583-0.00770.6245-1.3741-48.239318.2668
43.9798-1.015-0.92023.95423.86533.84670.5405-1.3296-0.05991.9904-1.06661.52640.7935-0.46790.34561.0173-0.14240.23840.82780.04750.61482.8394-51.768541.4555
52.6962-0.92632.23524.7494-0.74231.84820.202-1.52040.70021.37580.66470.0245-1.2038-0.49-0.57461.4091-0.3390.42841.2702-0.30490.80981.9556-30.92447.1632
64.6631.37840.50375.5027-0.10922.7190.4118-0.36160.549-0.4929-0.095-0.4997-0.91030.8444-0.26360.9146-0.29980.21980.7478-0.11190.535913.2838-34.61331.674
72.17970.6263-0.62394.76860.57790.15130.8356-0.05730.4843-0.0515-0.1185-0.3389-1.19831.16950.10371.1013-0.26020.28350.7997-0.10270.70668.073-30.015636.461
81.6296-1.21120.54872.8743-1.31010.56780.3252-0.10950.6032-0.35730.2419-0.6670.34931.2114-0.36460.7616-0.38250.09961.2578-0.18150.90522.1896-36.784834.6892
95.58481.77250.34025.392.09244.4250.3769-0.00441.2021-0.6108-0.37330.9761-1.6929-0.1132-0.00621.17280.0110.23960.6366-0.07540.93-0.1054-26.214333.8231
105.8785-0.5467-3.48635.32331.31796.53950.0215-0.1611-0.7251-0.044-0.4035-0.2470.01850.49390.42740.55980.00780.0160.51820.07890.659110.0778-53.535623.481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 363 through 389 )A363 - 389
2X-RAY DIFFRACTION2chain 'A' and (resid 390 through 531 )A390 - 531
3X-RAY DIFFRACTION3chain 'A' and (resid 532 through 558 )A532 - 558
4X-RAY DIFFRACTION4chain 'B' and (resid 364 through 374 )B364 - 374
5X-RAY DIFFRACTION5chain 'B' and (resid 375 through 389 )B375 - 389
6X-RAY DIFFRACTION6chain 'B' and (resid 390 through 426 )B390 - 426
7X-RAY DIFFRACTION7chain 'B' and (resid 427 through 452 )B427 - 452
8X-RAY DIFFRACTION8chain 'B' and (resid 453 through 475 )B453 - 475
9X-RAY DIFFRACTION9chain 'B' and (resid 476 through 531 )B476 - 531
10X-RAY DIFFRACTION10chain 'B' and (resid 532 through 558 )B532 - 558

+
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