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- PDB-6kdq: Crystal structure of human NRMT1 in complex with alpha-N-monometh... -

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Basic information

Entry
Database: PDB / ID: 6kdq
TitleCrystal structure of human NRMT1 in complex with alpha-N-monomethylated human CENP-A peptide
Components
  • CENP-A peptide
  • N-terminal Xaa-Pro-Lys N-methyltransferase 1
KeywordsTRANSFERASE / core methyltransferase fold
Function / homology
Function and homology information


N-terminal peptidyl-glycine methylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal peptidyl-proline dimethylation / N-terminal protein N-methyltransferase activity / CENP-A containing chromatin assembly / protein methyltransferase activity / protein localization to chromosome, centromeric region / kinetochore assembly ...N-terminal peptidyl-glycine methylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal peptidyl-proline dimethylation / N-terminal protein N-methyltransferase activity / CENP-A containing chromatin assembly / protein methyltransferase activity / protein localization to chromosome, centromeric region / kinetochore assembly / condensed chromosome, centromeric region / spindle organization / histone methyltransferase activity / establishment of mitotic spindle orientation / chromosome, centromeric region / mitotic cytokinesis / protein localization to CENP-A containing chromatin / pericentric heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / 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 / chromosome segregation / RHO GTPases Activate Formins / structural constituent of chromatin / Separation of Sister Chromatids / nucleosome / protein heterodimerization activity / chromatin binding / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 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

Downloads & links

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Assembly

Deposited unit
A: N-terminal Xaa-Pro-Lys N-methyltransferase 1
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
E: CENP-A peptide
F: CENP-A peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7526
Polymers56,9834
Non-polymers7692
Water11,818656
1
A: N-terminal Xaa-Pro-Lys N-methyltransferase 1
E: CENP-A peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8763
Polymers28,4912
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-3 kcal/mol
Surface area11140 Å2
MethodPISA
2
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
F: CENP-A peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8763
Polymers28,4912
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-3 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.724, 65.790, 69.003
Angle α, β, γ (deg.)90.000, 106.540, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein N-terminal Xaa-Pro-Lys N-methyltransferase 1 / Alpha N-terminal protein methyltransferase 1A / Methyltransferase-like protein 11A / N-terminal ...Alpha N-terminal protein methyltransferase 1A / Methyltransferase-like protein 11A / N-terminal RCC1 methyltransferase / X-Pro-Lys N-terminal protein methyltransferase 1A / NTM1A


Mass: 27589.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTMT1,NRMT1 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9BV86, protein N-terminal methyltransferase
#2: Protein/peptide CENP-A peptide


Mass: 902.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49450*PLUS
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 2.19 Å3/Da / Density % sol: 43.85 % / Mosaicity: 2.315 ° / Mosaicity esd: 0.014 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.7
Details: 0.2M Ammonium acetate, 0.1M Sodium citrate dehydrate pH 5.7, 31% w/v PEG 4000

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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 31, 2015 / 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: 1.499→50 Å / Num. obs: 77499 / % possible obs: 98.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.044 / Rrim(I) all: 0.089 / Χ2: 1.652 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.533.10.36137940.8840.240.4361.14197.3
1.53-1.553.10.3237940.9110.2120.3861.20197.4
1.55-1.583.10.26738590.9370.1760.3221.26997.6
1.58-1.623.10.23538470.9470.1550.2831.33997.6
1.62-1.653.10.20538250.9620.1360.2471.44897.9
1.65-1.693.10.18838590.9620.1250.2271.49198
1.69-1.733.10.1738670.9670.1120.2051.59198.2
1.73-1.783.10.14438400.9770.0950.1731.60598.3
1.78-1.833.10.12538640.9820.0820.1511.75498.4
1.83-1.893.20.11238750.9840.0740.1351.9398.6
1.89-1.963.10.09538560.9880.0630.1151.8898.6
1.96-2.043.10.08239010.9890.0550.0992.02898.8
2.04-2.133.10.07539080.9910.050.0911.87898.9
2.13-2.243.10.06938630.9910.0460.0831.91398.7
2.24-2.383.20.06639130.9910.0440.0791.66298.7
2.38-2.563.40.07138760.9890.0450.0851.79998.5
2.56-2.823.80.0838780.990.0470.0932.05798.3
2.82-3.234.50.0939470.990.0470.1021.80299.7
3.23-4.074.40.06439500.9930.0350.0731.57599
4.07-504.50.06539830.990.0340.0741.53698.1

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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: 1.499→28.229 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.3
RfactorNum. reflection% reflection
Rfree0.1803 3776 4.87 %
Rwork0.1575 --
obs0.1586 77468 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 59.11 Å2 / Biso mean: 20.2055 Å2 / Biso min: 8.1 Å2
Refinement stepCycle: final / Resolution: 1.499→28.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 52 656 4452
Biso mean--12.33 32.51 -
Num. residues----468
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.499-1.5180.26961330.2262253894
1.518-1.5380.24921370.2142275897
1.538-1.55910.21581310.1982267297
1.5591-1.58130.24251410.1886268598
1.5813-1.60490.23941460.1901270198
1.6049-1.630.20661590.1789266198
1.63-1.65670.21221460.171272198
1.6567-1.68530.17671450.1764272498
1.6853-1.71590.19931350.1774266298
1.7159-1.74890.17391260.1726276798
1.7489-1.78460.21241270.1696276398
1.7846-1.82340.20211280.1696271598
1.8234-1.86580.19321320.1662274298
1.8658-1.91250.19291500.167273399
1.9125-1.96420.21411520.1633270799
1.9642-2.0220.16641210.1548276699
2.022-2.08720.17531270.1541277099
2.0872-2.16180.15741650.1514271299
2.1618-2.24830.20081380.1532275499
2.2483-2.35060.19781420.1569273999
2.3506-2.47440.17991480.1592274199
2.4744-2.62940.18691380.1616273898
2.6294-2.83220.16711230.1641277398
2.8322-3.11690.17911600.15812771100
3.1169-3.56710.1951300.1419278899
3.5671-4.49130.13441520.1284277099
4.4913-28.2290.15781440.1543282198
Refinement TLS params.Method: refined / Origin x: 14.4345 Å / Origin y: -1.9531 Å / Origin z: 14.1057 Å
111213212223313233
T0.0706 Å20.011 Å20.0011 Å2-0.1062 Å2-0.0146 Å2--0.0664 Å2
L0.2306 °20.244 °2-0.0872 °2-0.561 °2-0.2628 °2--0.1807 °2
S-0.0196 Å °0.0356 Å °0.0047 Å °-0.0352 Å °0.0225 Å °0.0025 Å °0.0185 Å °-0.0046 Å °-0.0027 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-5 - 223
2X-RAY DIFFRACTION1allB-2 - 223
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allE1 - 6
6X-RAY DIFFRACTION1allF1 - 7
7X-RAY DIFFRACTION1allS1 - 656

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