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- PDB-8k2e: Crystal structure of YTHDC1 and Y3 complex -

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Basic information

Entry
Database: PDB / ID: 8k2e
TitleCrystal structure of YTHDC1 and Y3 complex
ComponentsYTH domain-containing protein 1
KeywordsRNA BINDING PROTEIN / Inhibitor / complex
Function / homology
Function and homology information


primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / dosage compensation by inactivation of X chromosome / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / mRNA export from nucleus / mRNA splicing, via spliceosome ...primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / dosage compensation by inactivation of X chromosome / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / mRNA export from nucleus / mRNA splicing, via spliceosome / spermatogenesis / in utero embryonic development / nuclear speck / mRNA binding / RNA binding / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
: / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhang, H.L. / Yang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat. Mach. Intell. / Year: 2024
Title: PocketFlow is a data-and-knowledge-driven structure-based molecular generative model
Authors: Jiang, Y. / Zhang, G. / You, J. / Zhang, H. / Yao, R. / Xie, H. / Zhang, L. / Xia, Z. / Dai, M. / Wu, Y. / Li, L. / Yang, S.
History
DepositionJul 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,9576
Polymers37,2312
Non-polymers7254
Water4,954275
1
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9783
Polymers18,6161
Non-polymers3632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area8520 Å2
MethodPISA
2
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9783
Polymers18,6161
Non-polymers3632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-10 kcal/mol
Surface area8520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.644, 103.515, 41.815
Angle α, β, γ (deg.)90.000, 102.425, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 343 through 377 or resid 379...
d_2ens_1(chain "B" and (resid 343 through 377 or resid 379...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLYGLYTRPTRPAB343 - 3771 - 35
d_12THRTHRGLYGLYAB379 - 42237 - 80
d_13SERSERTRPTRPAB424 - 44782 - 105
d_14CYSCYSASNASNAB449 - 466107 - 124
d_15HISHISMETMETAB468 - 507126 - 165
d_21GLYGLYTRPTRPBA343 - 3771 - 35
d_22THRTHRALAALABA379 - 43237 - 90
d_23METMETTRPTRPBA434 - 44792 - 105
d_24CYSCYSASNASNBA449 - 466107 - 124
d_25HISHISMETMETBA468 - 507126 - 165

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Components

#1: Protein YTH domain-containing protein 1 / Splicing factor YT521 / YT521-B


Mass: 18615.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDC1, KIAA1966, YT521 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96MU7
#2: Chemical ChemComp-VIM / 2-chloranyl-6-(4-fluoranylphenoxy)benzoic acid


Mass: 266.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H8ClFO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-Tris at pH 6.5, 0.2M ammonium sulfate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 43363 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 12.52 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.039 / Rrim(I) all: 0.102 / Χ2: 0.969 / Net I/σ(I): 10.5 / Num. measured all: 291216
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.6-1.635.90.44921270.8830.9680.20.4940.939100
1.63-1.666.30.41421770.9180.9780.1780.4520.942100
1.66-1.696.80.36421400.9410.9850.1510.3950.971100
1.69-1.726.50.30921820.950.9870.1310.3360.973100
1.72-1.766.80.26621770.9620.990.1090.2880.979100
1.76-1.86.90.23521700.970.9920.0960.2541.001100
1.8-1.856.80.20521330.9740.9930.0840.2221.004100
1.85-1.96.70.17521900.9760.9940.0730.191.013100
1.9-1.956.60.15321320.9810.9950.0640.1671.046100
1.95-2.026.70.1421550.9840.9960.0580.1521.018100
2.02-2.096.70.12422130.9850.9960.0510.1351.056100
2.09-2.1770.11521330.9870.9970.0470.1241.02100
2.17-2.276.80.10921650.9860.9970.0450.1181.043100
2.27-2.396.50.10221560.9850.9960.0430.1110.998100
2.39-2.546.80.121910.9860.9960.0410.1080.962100
2.54-2.7470.09421580.9890.9970.0380.1020.924100
2.74-3.0170.08922020.990.9980.0360.0960.887100
3.01-3.456.70.08421560.9890.9970.0350.0910.862100
3.45-4.3470.08221860.9910.9980.0330.0890.845100
4.34-506.70.08122200.9920.9980.0340.0880.91199.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-30007.21data scaling
PHASER2.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→31.71 Å / SU ML: 0.1812 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.4875
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2239 2136 4.94 %
Rwork0.1855 41062 -
obs0.1875 43198 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.83 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 46 275 2876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01492688
X-RAY DIFFRACTIONf_angle_d1.33153643
X-RAY DIFFRACTIONf_chiral_restr0.0826397
X-RAY DIFFRACTIONf_plane_restr0.01459
X-RAY DIFFRACTIONf_dihedral_angle_d6.3447353
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.968831611012 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.2531380.21092599X-RAY DIFFRACTION95.7
1.64-1.680.24811290.21032743X-RAY DIFFRACTION99.65
1.68-1.720.25181370.20452747X-RAY DIFFRACTION99.86
1.72-1.770.23131430.19622722X-RAY DIFFRACTION99.97
1.77-1.830.23221540.19482745X-RAY DIFFRACTION100
1.83-1.90.22121250.18982780X-RAY DIFFRACTION99.93
1.9-1.970.2421310.19812738X-RAY DIFFRACTION100
1.97-2.060.25321450.19432729X-RAY DIFFRACTION100
2.06-2.170.21661440.19292737X-RAY DIFFRACTION100
2.17-2.310.21891490.18112751X-RAY DIFFRACTION100
2.31-2.490.22241400.18882754X-RAY DIFFRACTION100
2.49-2.730.2441670.20172711X-RAY DIFFRACTION100
2.74-3.130.2211400.19822764X-RAY DIFFRACTION99.97
3.13-3.940.23741360.16812779X-RAY DIFFRACTION100
3.94-31.710.17731580.15862763X-RAY DIFFRACTION99.76
Refinement TLS params.Method: refined / Origin x: 11.922301416 Å / Origin y: 9.43863791641 Å / Origin z: 8.174750024 Å
111213212223313233
T0.0461836233711 Å20.000778095049528 Å2-0.00407424123539 Å2-0.0555654105963 Å20.00269744773242 Å2--0.0489934141353 Å2
L0.161673240843 °20.203665616305 °2-0.103361898257 °2-0.586605810962 °2-0.191789549305 °2--0.136387535279 °2
S-0.0200003926128 Å °0.0511732025673 Å °0.00668334792649 Å °-0.0276753811377 Å °0.0426701411503 Å °0.0836169163549 Å °-0.0277717613082 Å °-0.00157040832244 Å °0.00782749665256 Å °
Refinement TLS groupSelection details: all

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