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- PDB-6kds: Crystal structure of human NRMT2 in complex with alpha-N-monometh... -

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Basic information

Entry
Database: PDB / ID: 6kds
TitleCrystal structure of human NRMT2 in complex with alpha-N-monomethylated human CENP-A peptide
Components
  • Alpha N-terminal protein methyltransferase 1B
  • CENP-A peptide
KeywordsTRANSFERASE / core methyltransferase fold
Function / homology
Function and homology information


protein N-terminal monomethyltransferase / N-terminal protein amino acid methylation / N-terminal protein N-methyltransferase activity / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / kinetochore assembly / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region ...protein N-terminal monomethyltransferase / N-terminal protein amino acid methylation / N-terminal protein N-methyltransferase activity / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / kinetochore assembly / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / protein localization to CENP-A containing chromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / pericentric heterochromatin / CENP-A containing nucleosome / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Deposition of new CENPA-containing nucleosomes at the centromere / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / structural constituent of chromatin / Separation of Sister Chromatids / nucleosome / protein heterodimerization activity / chromatin binding / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / Vaccinia Virus protein VP39 / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / Vaccinia Virus protein VP39 / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone H3-like centromeric protein A / N-terminal Xaa-Pro-Lys N-methyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.844 Å
AuthorsYue, Y. / Li, H.
CitationJournal: To be published
Title: Substrate engagement regulates state-specific alpha-N methylation of CENP-A by NRMT2
Authors: Wu, R. / Yue, Y. / Zheng, X. / Li, H.
History
DepositionJul 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha N-terminal protein methyltransferase 1B
E: CENP-A peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6493
Polymers28,2642
Non-polymers3841
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-4 kcal/mol
Surface area10300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.603, 108.191, 38.799
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Alpha N-terminal protein methyltransferase 1B / Methyltransferase-like protein 11B / X-Pro-Lys N-terminal protein methyltransferase 1B / NTM1B


Mass: 27519.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL11B, C1orf184, NRMT2 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5VVY1, protein N-terminal monomethyltransferase
#2: Protein/peptide CENP-A peptide


Mass: 744.867 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49450*PLUS
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.08 % / Mosaicity: 0.886 ° / Mosaicity esd: 0.007 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.1 / Details: 0.1M Tris pH 8.1, 14% w/v Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2014 / Details: mirrors
RadiationMonochromator: 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: 1.8→50 Å / Num. obs: 47754 / % possible obs: 98.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.06 / Rrim(I) all: 0.107 / Χ2: 2.722 / Net I/σ(I): 10.8 / Num. measured all: 154647
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.8-1.833.40.89423910.4080.5721.16299.7
1.83-1.863.30.69424370.5680.4461.23199.80.828
1.86-1.93.40.64423890.6090.4081.34899.50.765
1.9-1.943.40.48924320.7220.311.52999.90.581
1.94-1.983.40.44323730.7590.281.66999.60.526
1.98-2.033.40.36224350.8280.2311.95199.20.431
2.03-2.083.40.31623960.8610.22.22499.50.375
2.08-2.133.30.26724150.8860.172.37799.40.318
2.13-2.23.30.22523900.9290.1442.52399.40.268
2.2-2.273.30.20924330.930.1342.8298.60.25
2.27-2.353.30.17823710.9510.1152.90598.70.213
2.35-2.443.20.15924040.9620.1022.913980.189
2.44-2.553.20.14223550.9680.0923.16797.60.169
2.55-2.693.20.11823720.9790.0773.28897.70.141
2.69-2.863.10.10223580.980.0673.60996.20.123
2.86-3.083.10.08723340.9850.0584.16995.90.105
3.08-3.3930.07123050.9890.0494.52394.10.086
3.39-3.882.90.05923360.990.0414.38594.90.073
3.88-4.8830.05123930.9930.0354.224970.062
4.88-503.20.04924350.9940.0323.82897.10.059

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
PHENIX1.14rc3_3206refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CVD

5cvd


Resolution: 1.844→32.979 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.04
RfactorNum. reflection% reflection
Rfree0.2047 1113 4.87 %
Rwork0.1783 --
obs0.1796 22847 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.3 Å2 / Biso mean: 31.1282 Å2 / Biso min: 12.25 Å2
Refinement stepCycle: final / Resolution: 1.844→32.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 26 167 1995
Biso mean--20.03 38.43 -
Num. residues----227
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8444-1.92830.28211260.2277234187
1.9283-2.030.22941370.19772730100
2.03-2.15710.2451530.18272751100
2.1571-2.32370.22461390.1731271899
2.3237-2.55740.19291340.1781275599
2.5574-2.92730.22191160.1856275698
2.9273-3.68730.21261460.1785278799
3.6873-32.9790.17471620.1677289698
Refinement TLS params.Method: refined / Origin x: 20.7037 Å / Origin y: 17.6994 Å / Origin z: 17.7445 Å
111213212223313233
T0.0902 Å20.0162 Å20.0194 Å2-0.1007 Å20.0096 Å2--0.0869 Å2
L1.8297 °2-1.0487 °20.2423 °2-2.3396 °2-0.4702 °2--1.1102 °2
S0.0253 Å °-0.0304 Å °-0.0964 Å °-0.096 Å °0.0087 Å °0.1187 Å °0.0224 Å °-0.0321 Å °0.0077 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA58 - 501
2X-RAY DIFFRACTION1allE1 - 6
3X-RAY DIFFRACTION1allS1 - 167

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