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- PDB-7pcu: Crystal structure of YTHDF1 YTH domain in complex with ebselen -

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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 / positive regulation of translation / learning / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Water


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

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Experimental details

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Experiment

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

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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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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