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- PDB-7ql7: Crystal structure of YTHDF1 YTH domain in complex with the ebsulf... -

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Basic information

Entry
Database: PDB / ID: 7ql7
TitleCrystal structure of YTHDF1 YTH domain in complex with the ebsulfur derivative compound 9
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}-(2-morpholin-4-ylethyl)-2-sulfanyl-benzamide / THIOCYANATE ION / YTH domain-containing family protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsDalle Vedove, A. / Cazzanelli, G. / Quattrone, A. / Provenzani, A. / Lolli, G.
Funding support Italy, 3items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchMFAG 2017 - ID 19882 Italy
Italian Association for Cancer ResearchAIRC IG2018 - ID 21548 Italy
Italian Association for Cancer ResearchAIRC IG2018 - ID 22075 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
DepositionDec 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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)47,0077
Polymers46,2962
Non-polymers7115
Water55831
1
A: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5354
Polymers23,1481
Non-polymers3873
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)23,4733
Polymers23,1481
Non-polymers3242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.854, 119.854, 78.306
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)
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 364 - 558 / Label seq-ID: 5 - 199

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 364 through 558)AA
2chain BBB

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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 (E. coli) / References: UniProt: Q9BYJ9
#2: Chemical ChemComp-E3J / ~{N}-(2-morpholin-4-ylethyl)-2-sulfanyl-benzamide


Mass: 266.359 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H18N2O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.04 Å3/Da / Density % sol: 59.5 % / Mosaicity: 0.18 °
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: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.3→65.55 Å / Num. obs: 25950 / % possible obs: 100 % / Redundancy: 24.3 % / CC1/2: 1 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.017 / Rrim(I) all: 0.083 / Net I/σ(I): 26 / Num. measured all: 630167 / Scaling rejects: 5
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
2.3-2.3921.81.8575808026700.6960.4051.9012100
8.61-65.55180.0291051258510.0070.02986.999.8

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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: 2.3→44.231 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 1275 4.92 %
Rwork0.1914 24620 -
obs0.1935 25895 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.85 Å2 / Biso mean: 74.3636 Å2 / Biso min: 40.64 Å2
Refinement stepCycle: final / Resolution: 2.3→44.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 46 31 3092
Biso mean--88.6 60 -
Num. residues----367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083132
X-RAY DIFFRACTIONf_angle_d1.0194200
X-RAY DIFFRACTIONf_chiral_restr0.066435
X-RAY DIFFRACTIONf_plane_restr0.006536
X-RAY DIFFRACTIONf_dihedral_angle_d21.6661895
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1774X-RAY DIFFRACTION12.476TORSIONAL
12B1774X-RAY DIFFRACTION12.476TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3001-2.39210.2991560.26182656
2.3921-2.5010.29581490.24912669
2.501-2.63290.30661120.23732724
2.6329-2.79780.29081440.23782690
2.7978-3.01380.25171420.24252713
3.0138-3.3170.27851400.22792719
3.317-3.79670.25881460.20532737
3.7967-4.78250.20981310.1612796
4.7825-44.2310.19691550.16432916
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)
12.97793.4536-0.54776.00282.95336.70980.4214-0.2576-0.864-0.3702-0.67190.16771.7359-0.46350.42960.6282-0.0537-0.05260.56920.0010.57983.2308-55.27311.7495
25.90422.0833-0.69356.2745-0.05033.1812-0.09220.51420.3024-0.54840.11060.0585-0.15530.7267-0.04070.4848-0.0016-0.02830.51630.09260.461419.7317-41.2737-0.2962
34.34620.9766-0.24775.2221-1.68563.77360.210.0108-0.04930.79650.07360.0575-0.5923-0.133-0.18570.5409-0.0046-0.02980.4555-0.01950.49357.5178-41.536810.0474
47.2212-0.79790.53095.1178-0.53883.9637-0.27880.0030.7855-0.11180.14980.2246-0.79920.23980.11020.5217-0.0914-0.08340.44870.02080.507214.3973-32.94585.119
54.11350.0440.63956.37830.14532.4941-0.05970.05470.00760.0286-0.1298-0.806-0.18640.53190.15660.4245-0.0544-0.00020.54860.06280.469426.3637-42.17016.3424
68.7094-1.8401-5.70082.27323.39766.29190.1414-0.4196-0.0267-0.1409-0.24440.3687-0.29410.05670.00070.5364-0.0479-0.04270.5986-0.00320.5774-1.5022-48.101118.7718
76.1023-0.57071.93017.63631.99311.96340.3982-1.1875-0.5760.7188-0.49810.3739-0.3156-0.55630.12810.6851-0.03930.12910.62080.08350.50262.963-51.490741.8421
83.37030.66931.13128.8851.16572.10.353-0.89440.18811.587-0.42160.3497-0.5133-0.0127-0.06551.1377-0.16130.20290.8415-0.16520.74461.3432-30.251547.2114
94.59174.73655.60066.42476.52727.18940.6241-0.25320.411-1.56870.1114-1.1328-1.74440.8438-0.34221.0036-0.22450.21730.537-0.07750.72718.1099-29.624530.3656
102.17420.5275-1.75838.4649-2.35277.2425-0.2167-0.0242-0.4871-0.74330.02390.1845-0.61260.91060.18230.5741-0.17770.0150.53940.01310.438610.2757-41.53231.7417
117.96661.43621.29832.09272.41968.29710.7816-1.15830.5324-0.3793-0.2164-0.6966-1.08971.241-0.57351.1317-0.49390.14750.9635-0.03950.93219.151-26.358634.0663
125.6205-0.9727-4.23332.61682.29996.61950.4011-1.06140.35280.7825-0.4692-0.1204-0.54420.6241-0.07541.0446-0.18950.09950.7996-0.07410.69889.3259-28.331739.1695
136.41960.1485-1.20664.76871.13965.62240.3974-0.20560.70810.0149-0.3346-0.4151-0.93510.7333-0.11560.7812-0.11870.00840.52990.01030.59111.8988-34.491934.0658
146.45051.4289-0.73814.44510.46593.67440.46830.17211.0661-0.3722-0.30940.6824-1.2774-0.1435-0.08990.96880.02040.15170.4933-0.07570.85-0.9898-26.037134.1285
154.9213-2.62-2.67035.34112.41365.1936-0.28720.02260.09340.31240.0294-0.08360.33790.19710.25640.51970.0182-0.01140.4970.03290.52339.941-53.237224.1312
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 363 through 374 )A363 - 374
2X-RAY DIFFRACTION2chain 'A' and (resid 375 through 398 )A375 - 398
3X-RAY DIFFRACTION3chain 'A' and (resid 399 through 414 )A399 - 414
4X-RAY DIFFRACTION4chain 'A' and (resid 415 through 475 )A415 - 475
5X-RAY DIFFRACTION5chain 'A' and (resid 476 through 531 )A476 - 531
6X-RAY DIFFRACTION6chain 'A' and (resid 532 through 558 )A532 - 558
7X-RAY DIFFRACTION7chain 'B' and (resid 364 through 374 )B364 - 374
8X-RAY DIFFRACTION8chain 'B' and (resid 375 through 389 )B375 - 389
9X-RAY DIFFRACTION9chain 'B' and (resid 390 through 398 )B390 - 398
10X-RAY DIFFRACTION10chain 'B' and (resid 399 through 414 )B399 - 414
11X-RAY DIFFRACTION11chain 'B' and (resid 415 through 428 )B415 - 428
12X-RAY DIFFRACTION12chain 'B' and (resid 429 through 440 )B429 - 440
13X-RAY DIFFRACTION13chain 'B' and (resid 441 through 475 )B441 - 475
14X-RAY DIFFRACTION14chain 'B' and (resid 476 through 531 )B476 - 531
15X-RAY DIFFRACTION15chain 'B' and (resid 532 through 558 )B532 - 558

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