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- PDB-7yfj: Crystal structure of human WTAP -

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Basic information

Entry
Database: PDB / ID: 7yfj
TitleCrystal structure of human WTAP
ComponentsPre-mRNA-splicing regulator WTAP
KeywordsPROTEIN BINDING / WTAP-VIRMA / m6A writer
Function / homology
Function and homology information


RNA N6-methyladenosine methyltransferase complex / mRNA modification / regulation of alternative mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / RNA splicing / mRNA processing / nuclear membrane / nuclear speck / nucleoplasm / identical protein binding ...RNA N6-methyladenosine methyltransferase complex / mRNA modification / regulation of alternative mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / RNA splicing / mRNA processing / nuclear membrane / nuclear speck / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Pre-mRNA-splicing regulator WTAP / WTAP/Mum2p family
Similarity search - Domain/homology
Pre-mRNA-splicing regulator WTAP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsYan, X.H. / Guan, Z.Y. / Tang, C. / Yin, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2022
Title: AI-empowered integrative structural characterization of mA methyltransferase complex.
Authors: Xuhui Yan / Kai Pei / Zeyuan Guan / Feiqing Liu / Junjun Yan / Xiaohuan Jin / Qiang Wang / Mengjun Hou / Chun Tang / Ping Yin /
History
DepositionJul 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-mRNA-splicing regulator WTAP
B: Pre-mRNA-splicing regulator WTAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9324
Polymers28,7782
Non-polymers1542
Water1,51384
1
B: Pre-mRNA-splicing regulator WTAP
hetero molecules

A: Pre-mRNA-splicing regulator WTAP


Theoretical massNumber of molelcules
Total (without water)28,9324
Polymers28,7782
Non-polymers1542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area2890 Å2
ΔGint-25 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.754, 62.754, 336.345
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-341-

HOH

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Components

#1: Protein Pre-mRNA-splicing regulator WTAP / Female-lethal(2)D homolog / hFL(2)D / WT1-associated protein / Wilms tumor 1-associating protein


Mass: 14389.101 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WTAP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15007
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.32 Å3/Da / Density % sol: 62.97 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: MES, magnesium nitrate, sodium bromide, PEG6000, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.397→48.9 Å / Num. obs: 16547 / % possible obs: 99.5 % / Redundancy: 20 % / Biso Wilson estimate: 55.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.031 / Rrim(I) all: 0.103 / Net I/σ(I): 19.8
Reflection shellResolution: 2.397→2.49 Å / Redundancy: 20.7 % / Rmerge(I) obs: 0.978 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1679 / CC1/2: 0.978 / Rpim(I) all: 0.3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→45.64 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 860 5.24 %
Rwork0.22 --
obs0.221 16410 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.56 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1543 0 10 84 1637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081580
X-RAY DIFFRACTIONf_angle_d0.9252106
X-RAY DIFFRACTIONf_dihedral_angle_d22.483639
X-RAY DIFFRACTIONf_chiral_restr0.046232
X-RAY DIFFRACTIONf_plane_restr0.004281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.54680.28181190.2852506X-RAY DIFFRACTION99
2.5468-2.74340.29751260.26972549X-RAY DIFFRACTION100
2.7434-3.01950.28661450.24382551X-RAY DIFFRACTION100
3.0195-3.45620.27981500.25612566X-RAY DIFFRACTION100
3.4562-4.3540.20451490.19432630X-RAY DIFFRACTION100
4.354-45.640.23071710.20532748X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 24.8693 Å / Origin y: 31.4866 Å / Origin z: 14.2729 Å
111213212223313233
T0.6624 Å20.0113 Å20.0855 Å2-0.4474 Å2-0.0932 Å2--0.4906 Å2
L2.1416 °2-3.3347 °2-3.154 °2-5.6498 °25.472 °2--5.5549 °2
S-0.1545 Å °-0.2317 Å °-0.1168 Å °0.0536 Å °0.1798 Å °0.2614 Å °0.026 Å °0.3326 Å °-0.0167 Å °
Refinement TLS groupSelection details: ALL

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