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- PDB-9v84: Crystal structure of complex Hit-1 with YTHDC1 -

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Basic information

Entry
Database: PDB / ID: 9v84
TitleCrystal structure of complex Hit-1 with YTHDC1
ComponentsYTH domain-containing protein 1
KeywordsRNA BINDING PROTEIN / RNA-binding proteins / RNA
Function / homology
Function and homology information


primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / Nuclear RNA decay / N6-methyladenosine-containing RNA reader activity / dosage compensation by inactivation of X chromosome / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / molecular sequestering activity ...primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / Nuclear RNA decay / N6-methyladenosine-containing RNA reader activity / dosage compensation by inactivation of X chromosome / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / molecular sequestering activity / mRNA export from nucleus / brown fat cell differentiation / 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
Chem-9N8 / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZhang, H. / Yang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of YTHDC1 with compound Hit-1
Authors: Zhang, H.
History
DepositionMay 29, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 24, 2025Provider: 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
C: YTH domain-containing protein 1
D: YTH domain-containing protein 1
E: YTH domain-containing protein 1
F: YTH domain-containing protein 1
G: YTH domain-containing protein 1
H: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,18240
Polymers147,7718
Non-polymers5,41132
Water3,963220
1
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1485
Polymers18,4711
Non-polymers6764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8060 Å2
MethodPISA
2
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3407
Polymers18,4711
Non-polymers8696
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area8120 Å2
MethodPISA
3
C: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1485
Polymers18,4711
Non-polymers6764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-12 kcal/mol
Surface area8060 Å2
MethodPISA
4
D: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1485
Polymers18,4711
Non-polymers6764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7870 Å2
MethodPISA
5
E: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2446
Polymers18,4711
Non-polymers7725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7920 Å2
MethodPISA
6
F: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1485
Polymers18,4711
Non-polymers6764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8050 Å2
MethodPISA
7
G: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0524
Polymers18,4711
Non-polymers5803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7940 Å2
MethodPISA
8
H: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9563
Polymers18,4711
Non-polymers4842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.160, 77.375, 105.238
Angle α, β, γ (deg.)112.720, 93.180, 104.430
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 18471.432 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDC1, KIAA1966, YT521 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96MU7
#2: Chemical
ChemComp-9N8 / 4-(2-bromanyl-6-fluoranyl-phenyl)carbonyl-~{N}-pyridin-3-yl-1~{H}-pyrrole-2-carboxamide


Mass: 388.191 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H11BrFN3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.64 Å3/Da / Density % sol: 53.41 %
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: Nov 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 71126 / % possible obs: 98.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 29.93 Å2 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.044 / Rrim(I) all: 0.085 / Χ2: 0.929 / Net I/σ(I): 6.5 / Num. measured all: 250352
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.293.60.54335430.7710.3320.6380.99597.5
2.29-2.333.60.49134900.8120.2990.5761.02697.4
2.33-2.383.60.44135440.8450.2690.5181.01897.1
2.38-2.423.50.3835500.8920.2320.4461.03197.7
2.42-2.483.60.33935730.9110.2060.3971.03597.8
2.48-2.533.60.31234840.910.1920.3671.0197.8
2.53-2.63.50.27536270.9350.170.3241.03198.1
2.6-2.673.50.2434610.9470.1470.2821.00797.5
2.67-2.753.40.1935670.9610.1190.2251.02197.6
2.75-2.833.20.15234500.9680.1020.1840.97395.6
2.83-2.943.50.13635710.9790.0860.1611.03798.3
2.94-3.053.70.10835950.9880.0650.1260.96898.6
3.05-3.193.70.0935710.9910.0540.1051.00398.6
3.19-3.363.60.07535640.9920.0460.0880.91598.7
3.36-3.573.60.05835750.9950.0350.0680.85998.8
3.57-3.853.50.04835700.9960.030.0570.79398.8
3.85-4.233.10.04136040.9950.0270.050.78998.8
4.23-4.853.70.03935930.9960.0240.0460.67399.1
4.85-6.13.60.0436010.9960.0240.0470.63499.2
6.1-503.40.04135930.9940.0250.0480.77999.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.468 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 30.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 2871 4.99 %
Rwork0.2283 54608 -
obs0.2303 57479 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.55 Å2 / Biso mean: 30.0362 Å2 / Biso min: 18.93 Å2
Refinement stepCycle: final / Resolution: 2.4→29.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9887 0 400 220 10507
Biso mean--33.26 26.99 -
Num. residues----1294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210456
X-RAY DIFFRACTIONf_angle_d0.56114209
X-RAY DIFFRACTIONf_chiral_restr0.0421540
X-RAY DIFFRACTIONf_plane_restr0.0031789
X-RAY DIFFRACTIONf_dihedral_angle_d13.9436019
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.43940.33281160.2751253893
2.4394-2.48140.34711300.2711258097
2.4814-2.52650.33011280.2775257797
2.5265-2.57510.35531370.2786262797
2.5751-2.62760.32171390.2723254797
2.6276-2.68470.3071750.2786256897
2.6847-2.74710.33191350.2789257298
2.7471-2.81580.29921180.2834254795
2.8158-2.89180.35041360.2742260498
2.8918-2.97680.30291420.2735263598
2.9768-3.07280.31451510.2676259199
3.0728-3.18250.27971350.251267399
3.1825-3.30980.28121330.2589258199
3.3098-3.46020.29361200.2382264999
3.4602-3.64230.26891380.2241264599
3.6423-3.87010.2511470.2117266199
3.8701-4.16810.18711380.184259799
4.1681-4.58620.2381210.1654263699
4.5862-5.24650.21181320.1717263799
5.2465-6.59780.22551640.2046258999
6.5978-29.460.20251360.1984255496
Refinement TLS params.Method: refined / Origin x: 22.6707 Å / Origin y: 28.6677 Å / Origin z: 8.2453 Å
111213212223313233
T0.2506 Å20.0229 Å20.0001 Å2-0.231 Å2-0.017 Å2--0.2599 Å2
L0.0966 °20.0205 °20.0423 °2-0.0334 °2-0.1038 °2--0.3025 °2
S0.0093 Å °-0.026 Å °0.0197 Å °0.0283 Å °-0.0003 Å °-0.014 Å °-0.0088 Å °0.0097 Å °-0.0092 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB348 - 507
2X-RAY DIFFRACTION1allA346 - 507
3X-RAY DIFFRACTION1allC346 - 507
4X-RAY DIFFRACTION1allD346 - 507
5X-RAY DIFFRACTION1allE346 - 507
6X-RAY DIFFRACTION1allF346 - 507
7X-RAY DIFFRACTION1allG346 - 507
8X-RAY DIFFRACTION1allH345 - 507
9X-RAY DIFFRACTION1allI1 - 9
10X-RAY DIFFRACTION1allJ1 - 25
11X-RAY DIFFRACTION1allJ26
12X-RAY DIFFRACTION1allS1 - 721

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