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- PDB-4rg1: Methyltransferase domain of C9orf114 -

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Basic information

Entry
Database: PDB / ID: 4rg1
TitleMethyltransferase domain of C9orf114
ComponentsC9orf114
KeywordsTRANSFERASE / C9orf114 / Methyltransferase / SAH / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


kinetochore => GO:0000776 / 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 / mitotic spindle / kinetochore ...kinetochore => GO:0000776 / 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 / mitotic spindle / kinetochore / methylation / cell cycle / cell division / RNA binding / cytoplasm
Similarity search - Function
Putative RNA methyltransferase / Putative RNA methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel ...Putative RNA methyltransferase / Putative RNA methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-1,2-PROPANEDIOL / S-ADENOSYL-L-HOMOCYSTEINE / Putative methyltransferase C9orf114
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å
AuthorsDong, A. / Zeng, H. / Walker, J.R. / Li, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of Human C9orf114 in complex with S-adenosyl-homocysteine
Authors: Zeng, H. / Dong, A. / Walker, J.R. / Li, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C9orf114
B: C9orf114
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,52911
Polymers68,5652
Non-polymers6,9649
Water10,593588
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-4 kcal/mol
Surface area24150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.509, 67.816, 85.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-596-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein C9orf114


Mass: 34282.582 Da / Num. of mol.: 2 / Fragment: methyltransferase domain (UNP residues 64-376)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C9orf114 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) Codon Plus RIL / References: UniProt: Q5T280

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Non-polymers , 5 types, 597 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 / Polyethylene glycol


Mass: 1529.829 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#5: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 588 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 28% PEG3350, 0.2 M diammonium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2014
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 64378 / Num. obs: 64378 / % possible obs: 100 % / Redundancy: 8.4 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.099 / Χ2: 1.077 / Net I/σ(I): 24
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.86-1.898.20.96231230.715199.7
1.89-1.938.30.82731620.756199.8
1.93-1.968.40.69932100.7981100
1.96-28.60.59831770.7661100
2-2.058.60.48731610.7921100
2.05-2.098.60.39731770.8571100
2.09-2.158.60.31432140.8261100
2.15-2.218.60.2731770.8631100
2.21-2.278.60.25331900.9371100
2.27-2.348.60.20932020.9241100
2.34-2.438.60.16431940.8961100
2.43-2.528.60.14632170.941100
2.52-2.648.50.12831930.9551100
2.64-2.788.50.09832081.0621100
2.78-2.958.50.08532321.1921100
2.95-3.188.40.07432411.6121100
3.18-3.58.30.06632422.0441100
3.5-4.018.20.05232791.9921100
4.01-5.0580.03533161.3781100
5.05-5080.03234631.236199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.65 Å49.12 Å
Translation3.65 Å49.12 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
SBC-Collectdata collection
HKL-3000data reduction
Coot0.7.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K3R

1k3r


Resolution: 1.86→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.1577 / FOM work R set: 0.8236 / SU B: 2.747 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1153 / SU Rfree: 0.1137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 888 1.4 %RANDOM
Rwork0.1716 ---
obs0.1722 61911 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.46 Å2 / Biso mean: 24.781 Å2 / Biso min: 12.07 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å2-0 Å20 Å2
2--2.3 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.86→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4235 0 112 588 4935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194786
X-RAY DIFFRACTIONr_bond_other_d0.0020.024520
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9946531
X-RAY DIFFRACTIONr_angle_other_deg0.7973.00110392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3765631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79423.623207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66415724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8871537
X-RAY DIFFRACTIONr_chiral_restr0.0790.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215505
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021086
X-RAY DIFFRACTIONr_mcbond_it1.7752.4422420
X-RAY DIFFRACTIONr_mcbond_other1.772.4422419
X-RAY DIFFRACTIONr_mcangle_it2.8433.6353028
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 67 -
Rwork0.253 4503 -
all-4570 -
obs--99.85 %

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