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- PDB-8qsu: Crystal structure of SPOUT1/CENP-32 bound to SAH -

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Basic information

Entry
Database: PDB / ID: 8qsu
TitleCrystal structure of SPOUT1/CENP-32 bound to SAH
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-ADENOSYL-L-HOMOCYSTEINE / Putative methyltransferase C9orf114
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.38 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: To Be Published
Title: Bi-allelic variants of SPOUT1, a novel RNA methyltransferase, cause chromosome missegregation and a rare neurodevelopmental disease
Authors: Jeyaprakash, A.A. / Abad, M.A.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative methyltransferase C9orf114
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1632
Polymers33,7791
Non-polymers3841
Water00
1
A: Putative methyltransferase C9orf114
hetero molecules

A: Putative methyltransferase C9orf114
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3264
Polymers67,5572
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area3100 Å2
ΔGint-12 kcal/mol
Surface area25630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.020, 81.170, 135.500
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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
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: 3.08 Å3/Da / Density % sol: 60.02 %
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: 0.97957 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2.38→25.52 Å / Num. obs: 16700 / % possible obs: 98.55 % / Redundancy: 12.9 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07095 / Rpim(I) all: 0.0209 / Rrim(I) all: 0.07407 / Net I/σ(I): 21.2
Reflection shellResolution: 2.38→2.53 Å / Rmerge(I) obs: 0.6979 / Num. unique obs: 2678 / CC1/2: 0.971 / CC star: 0.993 / Rpim(I) all: 0.1975 / Rrim(I) all: 0.7258 / % possible all: 96.23

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Processing

Software
NameVersionClassification
PHENIX(dev_4694: ???)refinement
XDSdata reduction
xia2data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.38→25.52 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 846 5.07 %RANDOM
Rwork0.2245 ---
obs0.2263 16697 98.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→25.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2175 0 26 0 2201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.921
X-RAY DIFFRACTIONf_dihedral_angle_d20.314830
X-RAY DIFFRACTIONf_chiral_restr0.052342
X-RAY DIFFRACTIONf_plane_restr0.009404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.530.3861560.30842522X-RAY DIFFRACTION96
2.53-2.720.36621420.28242564X-RAY DIFFRACTION97
2.72-30.31491390.27562615X-RAY DIFFRACTION99
3-3.430.25771300.25622664X-RAY DIFFRACTION99
3.43-4.320.2371370.2292681X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.2142-1.4212-0.70593.3262-1.12815.688-0.1290.1646-0.4056-0.44180.2420.30740.6857-0.3785-0.14330.6249-0.0719-0.00680.5485-0.02740.5811.60737.927855.5847
25.0026-2.03980.43712.5507-2.4487.16010.19160.13340.24590.59840.42010.7921-0.4584-1.0335-0.53790.82280.03280.0910.93130.1530.83086.115752.408752.4703
34.1140.293-0.86014.6431-1.97427.5641-0.26231.28520.3976-0.08630.66450.6174-0.9099-0.4222-0.38991.0296-0.2051-0.01581.19480.25390.878810.220161.355436.1209
46.085-0.4791.03911.3159-1.24536.0689-0.09980.92791.0753-0.2086-0.2651-0.5844-1.38841.05240.29311.0317-0.17690.00770.92940.14060.857218.746961.547542.5192
53.5444-0.59151.19112.9275-0.18916.69370.01930.5574-0.4632-0.63720.0859-0.35641.24010.8807-0.07320.77850.16580.07310.6827-0.15020.651324.507328.926855.2924
68.49072.1110.07718.1333-0.75636.85570.15740.0401-1.092-0.21540.1252-0.86150.30011.2091-0.07090.50290.04370.01190.739-0.13430.541526.360339.413361.8619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 72 through 150 )
2X-RAY DIFFRACTION2chain 'A' and (resid 151 through 186 )
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 225 )
4X-RAY DIFFRACTION4chain 'A' and (resid 226 through 262 )
5X-RAY DIFFRACTION5chain 'A' and (resid 263 through 352 )
6X-RAY DIFFRACTION6chain 'A' and (resid 353 through 376 )

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