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- PDB-8qsv: Crystal structure of SPOUT1/CENP-32 bound to SAM -

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Basic information

Entry
Database: PDB / ID: 8qsv
TitleCrystal structure of SPOUT1/CENP-32 bound to SAM
ComponentsPutative methyltransferase C9orf114
KeywordsCELL CYCLE / SPOUT RNA Methyltransferase Spindle Organisation Chromosome missegregation Cell viability
Function / homology
Function and homology information


maintenance of centrosome location / miRNA processing / spindle pole centrosome / miRNA binding / post-transcriptional regulation of gene expression / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / kinetochore / mitotic spindle / methylation ...maintenance of centrosome location / miRNA processing / spindle pole centrosome / miRNA binding / post-transcriptional regulation of gene expression / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / kinetochore / mitotic spindle / methylation / 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
S-ADENOSYLMETHIONINE / Putative methyltransferase C9orf114
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1772
Polymers33,7791
Non-polymers3981
Water362
1
A: Putative methyltransferase C9orf114
hetero molecules

A: Putative methyltransferase C9orf114
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3544
Polymers67,5572
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3080 Å2
ΔGint-11 kcal/mol
Surface area25470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.070, 80.830, 135.690
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: 33778.699 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: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.06 M MgCl2, CaCl2 or 0.09 M NaF, NaBr, NaI with 0.1 M Imidazole, MES (acid) pH 6.5 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: I03 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.62→55.01 Å / Num. obs: 12626 / % possible obs: 99.08 % / Redundancy: 6.5 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.08553 / Rpim(I) all: 0.0365 / Rrim(I) all: 0.0932 / Net I/σ(I): 16.11
Reflection shellResolution: 2.62→2.88 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.6634 / Mean I/σ(I) obs: 3.81 / Num. unique obs: 3066 / CC1/2: 0.947 / CC star: 0.986 / Rpim(I) all: 0.2761 / Rrim(I) all: 0.7196 / % possible all: 98.02

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→55.01 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.911 / SU B: 30.153 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R: 0.442 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2802 628 5 %RANDOM
Rwork0.2028 ---
obs0.20662 12000 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.661 Å2
Baniso -1Baniso -2Baniso -3
1-4.02 Å20 Å2-0 Å2
2--3.72 Å20 Å2
3----7.74 Å2
Refinement stepCycle: 1 / Resolution: 2.62→55.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 27 2 2180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122226
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162081
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.6493029
X-RAY DIFFRACTIONr_angle_other_deg0.5241.5664785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8865280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.633516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.50110336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022648
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02509
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_it4.3754.7541129
X-RAY DIFFRACTIONr_mcbond_other4.3764.7541129
X-RAY DIFFRACTIONr_mcangle_it6.5738.5491406
X-RAY DIFFRACTIONr_mcangle_other6.5718.5511407
X-RAY DIFFRACTIONr_scbond_it4.7835.1441097
X-RAY DIFFRACTIONr_scbond_other4.7815.1451097
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1669.3061624
X-RAY DIFFRACTIONr_long_range_B_refined9.33245.872391
X-RAY DIFFRACTIONr_long_range_B_other9.3345.92392
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.62→2.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 45 -
Rwork0.385 829 -
obs--97 %
Refinement TLS params.Method: refined / Origin x: -16.3715 Å / Origin y: -3.2246 Å / Origin z: -16.7293 Å
111213212223313233
T0.0624 Å2-0.0851 Å2-0.0122 Å2-0.2876 Å20.0695 Å2--0.0925 Å2
L2.6462 °2-0.8051 °2-0.8135 °2-4.3836 °23.2325 °2--6.3294 °2
S-0.1092 Å °0.4997 Å °-0.1831 Å °-0.3404 Å °0.254 Å °0.0039 Å °-0.0462 Å °-0.0811 Å °-0.1449 Å °

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