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- PDB-8qsw: Crystal structure of SPOUT1/CENP-32 | A356N catalytic site mutant -

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Basic information

Entry
Database: PDB / ID: 8qsw
TitleCrystal structure of SPOUT1/CENP-32 | A356N catalytic site mutant
ComponentsPutative methyltransferase C9orf114
KeywordsCELL CYCLE / SPOUT RNA Methyltransferase Spindle organisation Chromosome missegregation Cell viability Cell Cycle
Function / homology
Function and homology information


rRNA (uridine-N3-)-methyltransferase activity / maintenance of centrosome location / miRNA processing / spindle pole centrosome / rRNA base methylation / S-adenosyl-L-methionine binding / miRNA binding / post-transcriptional regulation of gene expression / Transferases; Transferring one-carbon groups; Methyltransferases / kinetochore ...rRNA (uridine-N3-)-methyltransferase activity / maintenance of centrosome location / miRNA processing / spindle pole centrosome / rRNA base methylation / S-adenosyl-L-methionine binding / miRNA binding / post-transcriptional regulation of gene expression / Transferases; Transferring one-carbon groups; Methyltransferases / kinetochore / mitotic spindle / cell division / RNA binding / cytoplasm
Similarity search - Function
Putative RNA methyltransferase / Putative RNA methyltransferase / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
28S rRNA (uridine-N(3))-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJeyaprakash, A.A. / Abad, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/X001245/1 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS.
Authors: Dharmadhikari, A.V. / Abad, M.A. / Khan, S. / Maroofian, R. / Sands, T.T. / Ullah, F. / Samejima, I. / Shen, Y. / Wear, M.A. / Moore, K.E. / Kondakova, E. / Mitina, N. / Schaub, T. / Lee, G. ...Authors: Dharmadhikari, A.V. / Abad, M.A. / Khan, S. / Maroofian, R. / Sands, T.T. / Ullah, F. / Samejima, I. / Shen, Y. / Wear, M.A. / Moore, K.E. / Kondakova, E. / Mitina, N. / Schaub, T. / Lee, G.K. / Umandap, C.H. / Berger, S.M. / Iglesias, A.D. / Popp, B. / Abou Jamra, R. / Gabriel, H. / Rentas, S. / Rippert, A.L. / Gray, C. / Izumi, K. / Conlin, L.K. / Koboldt, D.C. / Mosher, T.M. / Hickey, S.E. / Albert, D.V.F. / Norwood, H. / Lewanda, A.F. / Dai, H. / Liu, P. / Mitani, T. / Marafi, D. / Eker, H.K. / Pehlivan, D. / Posey, J.E. / Lippa, N.C. / Vena, N. / Heinzen, E.L. / Goldstein, D.B. / Mignot, C. / de Sainte Agathe, J.M. / Al-Sannaa, N.A. / Zamani, M. / Sadeghian, S. / Azizimalamiri, R. / Seifia, T. / Zaki, M.S. / Abdel-Salam, G.M.H. / Abdel-Hamid, M.S. / Alabdi, L. / Alkuraya, F.S. / Dawoud, H. / Lofty, A. / Bauer, P. / Zifarelli, G. / Afzal, E. / Zafar, F. / Efthymiou, S. / Gossett, D. / Towne, M.C. / Yeneabat, R. / Perez-Duenas, B. / Cazurro-Gutierrez, A. / Verdura, E. / Cantarin-Extremera, V. / Marques, A.D.V. / Helwak, A. / Tollervey, D. / Wontakal, S.N. / Aggarwal, V.S. / Rosenfeld, J.A. / Tarabykin, V. / Ohta, S. / Lupski, J.R. / Houlden, H. / Earnshaw, W.C. / Davis, E.E. / Jeyaprakash, A.A. / Liao, J.
History
DepositionOct 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2May 28, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative methyltransferase C9orf114


Theoretical massNumber of molelcules
Total (without water)33,6811
Polymers33,6811
Non-polymers00
Water181
1
A: Putative methyltransferase C9orf114

A: Putative methyltransferase C9orf114


Theoretical massNumber of molelcules
Total (without water)67,3622
Polymers67,3622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3130 Å2
ΔGint-9 kcal/mol
Surface area26770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.240, 80.694, 136.363
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Putative methyltransferase C9orf114


Mass: 33681.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPOUT1 / Plasmid: pEC-K-His-3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold / References: UniProt: Q5T280
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.09 M NaF, NaBr, NaI; 0.1 M Sodium HEPES, MOPS (acid) pH 7.5 and 30 % Ethylene glycol, PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.5→37.62 Å / Num. obs: 14321 / % possible obs: 97.33 % / Redundancy: 4.5 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06425 / Rpim(I) all: 0.03278 / Rrim(I) all: 0.07257 / Net I/σ(I): 11.22
Reflection shellResolution: 2.5→2.69 Å / Rmerge(I) obs: 0.4695 / Mean I/σ(I) obs: 2.72 / Num. unique obs: 2840 / CC1/2: 0.963 / CC star: 0.991 / Rpim(I) all: 0.2461 / Rrim(I) all: 0.5331

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→37.62 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 27.116 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 711 5 %RANDOM
Rwork0.20275 ---
obs0.20546 13609 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.116 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20 Å2-0 Å2
2--5.58 Å20 Å2
3----7.41 Å2
Refinement stepCycle: 1 / Resolution: 2.5→37.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 0 1 2205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122250
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162115
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.6483056
X-RAY DIFFRACTIONr_angle_other_deg0.5751.5684865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1635284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.49517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.19810360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022705
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02523
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.8195.0641142
X-RAY DIFFRACTIONr_mcbond_other4.8165.0631142
X-RAY DIFFRACTIONr_mcangle_it7.1049.0941424
X-RAY DIFFRACTIONr_mcangle_other7.1019.0931425
X-RAY DIFFRACTIONr_scbond_it5.5135.6041108
X-RAY DIFFRACTIONr_scbond_other5.515.6031109
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.09410.0561633
X-RAY DIFFRACTIONr_long_range_B_refined10.35348.82385
X-RAY DIFFRACTIONr_long_range_B_other10.35148.792386
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 52 -
Rwork0.367 975 -
obs--98.56 %
Refinement TLS params.Method: refined / Origin x: -16.5668 Å / Origin y: -3.0888 Å / Origin z: -16.9173 Å
111213212223313233
T0.0724 Å2-0.0924 Å2-0.0187 Å2-0.1399 Å20.0153 Å2--0.0504 Å2
L3.1262 °2-1.0129 °2-0.8437 °2-4.0946 °22.3887 °2--5.3945 °2
S-0.1456 Å °0.4024 Å °-0.073 Å °-0.3347 Å °0.3006 Å °-0.0937 Å °-0.1195 Å °0.1973 Å °-0.155 Å °

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