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- PDB-5cvd: Crystal structure of human NRMT1 in complex with alpha-N-dimethyl... -

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Basic information

Entry
Database: PDB / ID: 5cvd
TitleCrystal structure of human NRMT1 in complex with alpha-N-dimethylated human CENP-A peptide
Components
  • N-teminal peptide from Histone H3-like centromeric protein A
  • N-terminal Xaa-Pro-Lys N-methyltransferase 1
KeywordsTRANSFERASE/PEPTIDE / Alpha-N-methyltransferase / Histone Methylation / SAM-MTase / CENP-A / TRANSFERASE-PEPTIDE complex
Function / homology
Function and homology information


N-terminal peptidyl-glycine methylation / N-terminal peptidyl-proline dimethylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal protein N-methyltransferase activity / CENP-A containing chromatin assembly / protein methyltransferase activity / kinetochore assembly / protein localization to chromosome, centromeric region ...N-terminal peptidyl-glycine methylation / N-terminal peptidyl-proline dimethylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal protein N-methyltransferase activity / CENP-A containing chromatin assembly / protein methyltransferase activity / kinetochore assembly / protein localization to chromosome, centromeric region / condensed chromosome, centromeric region / spindle organization / histone methyltransferase activity / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / 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 / Separation of Sister Chromatids / structural constituent of chromatin / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsWu, R. / Li, H.
CitationJournal: Genes Dev. / Year: 2015
Title: Molecular basis for histone N-terminal methylation by NRMT1
Authors: Wu, R. / Yue, Y. / Zheng, X. / Li, H.
History
DepositionJul 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Mar 20, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn

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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
D: N-teminal peptide from Histone H3-like centromeric protein A
E: N-teminal peptide from Histone H3-like centromeric protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2326
Polymers57,4644
Non-polymers7692
Water13,097727
1
A: N-terminal Xaa-Pro-Lys N-methyltransferase 1
D: N-teminal peptide from Histone H3-like centromeric protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1163
Polymers28,7322
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
E: N-teminal peptide from Histone H3-like centromeric protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1163
Polymers28,7322
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.839, 66.245, 68.998
Angle α, β, γ (deg.)90.000, 106.690, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-541-

HOH

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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: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9BV86, protein N-terminal methyltransferase
#2: Protein/peptide N-teminal peptide from Histone H3-like centromeric protein A / Centromere autoantigen A / Centromere protein A / CENP-A


Mass: 1142.382 Da / Num. of mol.: 2 / Fragment: UNP residues 2-10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49450
#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.: 727 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M (NH4)Ac, 0.1 M Sodium citrate tribasic dihydrate, 28%(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 119380 / % possible obs: 98.3 % / Redundancy: 4.7 % / Biso Wilson estimate: 9.06 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.055 / Rrim(I) all: 0.122 / Χ2: 1.401 / Net I/av σ(I): 16.362 / Net I/σ(I): 8.6 / Num. measured all: 558514
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.3-1.324.60.63158330.7880.3260.7111.24296.7
1.32-1.354.60.57858300.8160.2980.6511.25896.8
1.35-1.374.60.52958620.8430.2720.5961.2996.9
1.37-1.44.60.48558680.8650.250.5461.30697.1
1.4-1.434.70.42559250.8830.2180.4781.31397.4
1.43-1.464.70.37258640.9110.1920.4191.34197.4
1.46-1.54.70.31859260.9350.1630.3581.36697.6
1.5-1.544.70.26459470.9510.1350.2971.3998
1.54-1.594.70.22859110.9630.1170.2571.41198.2
1.59-1.644.70.19859570.9710.1010.2231.41698
1.64-1.74.70.1859890.9750.0920.2021.4698.6
1.7-1.764.70.16159720.9780.0830.1821.45298.6
1.76-1.844.70.13460260.9840.0690.1511.41798.9
1.84-1.944.70.12159850.9860.0620.1361.42599
1.94-2.064.70.11260210.9860.0570.1261.51299.2
2.06-2.224.70.10460520.9870.0530.1171.49599.3
2.22-2.454.70.09960830.9870.0510.1121.68799.7
2.45-2.84.60.08160460.990.0420.0921.53699.7
2.8-3.534.70.0760990.9930.0360.0791.45299.5
3.53-504.70.06861840.9920.0350.0771.23799.1

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EX4

2ex4


Resolution: 1.3→29.612 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.16 3639 3.05 %
Rwork0.1322 115738 -
obs0.1331 119377 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.32 Å2 / Biso mean: 14.1414 Å2 / Biso min: 4.53 Å2
Refinement stepCycle: final / Resolution: 1.3→29.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3758 0 74 734 4566
Biso mean--7.14 25.25 -
Num. residues----470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063980
X-RAY DIFFRACTIONf_angle_d1.1555394
X-RAY DIFFRACTIONf_chiral_restr0.069589
X-RAY DIFFRACTIONf_plane_restr0.005701
X-RAY DIFFRACTIONf_dihedral_angle_d13.0831547
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.31710.2321470.19644229437695
1.3171-1.33520.21291440.17914347449197
1.3352-1.35430.2431440.17624387453197
1.3543-1.37450.2141230.16794360448397
1.3745-1.39590.22141540.16654344449897
1.3959-1.41880.20211420.15644446458897
1.4188-1.44330.18181550.14914353450897
1.4433-1.46950.21941300.14184430456097
1.4695-1.49780.18021190.13724417453698
1.4978-1.52840.18121370.12944428456598
1.5284-1.56160.16671100.12594458456898
1.5616-1.59790.16411350.12084461459698
1.5979-1.63790.16181450.1154414455998
1.6379-1.68220.15171090.11494472458198
1.6822-1.73170.16021350.11914494462999
1.7317-1.78760.16341410.11644471461299
1.7876-1.85140.14311530.11734470462399
1.8514-1.92550.15091630.11894454461799
1.9255-2.01320.13231360.11814511464799
2.0132-2.11930.14231600.11784474463499
2.1193-2.2520.14121560.11714496465299
2.252-2.42580.14611490.125745144663100
2.4258-2.66980.14141460.130145674713100
2.6698-3.05580.14971350.13814515465099
3.0558-3.84860.1461360.131645974733100
3.8486-29.61960.16551350.14274629476499

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