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- PDB-5e1m: Crystal structure of NTMT1 in complex with PPKRIA peptide -

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Basic information

Entry
Database: PDB / ID: 5e1m
TitleCrystal structure of NTMT1 in complex with PPKRIA peptide
Components
  • N-terminal Xaa-Pro-Lys N-methyltransferase 1
  • RCC1
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC
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 / mitotic nuclear membrane reassembly / protein methyltransferase activity / sulfate binding / Rev-mediated nuclear export of HIV RNA ...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 / mitotic nuclear membrane reassembly / protein methyltransferase activity / sulfate binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / spindle organization / regulation of mitotic nuclear division / histone methyltransferase activity / nucleosome binding / spindle assembly / viral process / nucleosomal DNA binding / mitotic spindle organization / guanyl-nucleotide exchange factor activity / condensed nuclear chromosome / chromosome segregation / small GTPase binding / G1/S transition of mitotic cell cycle / chromosome / histone binding / protein heterodimerization activity / cell division / chromatin binding / chromatin / protein-containing complex / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Regulator of chromosome condensation (RCC1) signature 1. / Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Vaccinia Virus protein VP39 ...: / Regulator of chromosome condensation (RCC1) signature 1. / Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Regulator of chromosome condensation / N-terminal Xaa-Pro-Lys N-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsDong, C. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Genes Dev. / Year: 2015
Title: Structural basis for substrate recognition by the human N-terminal methyltransferase 1.
Authors: Dong, C. / Mao, Y. / Tempel, W. / Qin, S. / Li, L. / Loppnau, P. / Huang, R. / Min, J.
History
DepositionSep 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / 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

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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: RCC1
E: RCC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,05152
Polymers56,0064
Non-polymers1,04548
Water7,512417
1
A: N-terminal Xaa-Pro-Lys N-methyltransferase 1
D: RCC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,57228
Polymers28,0032
Non-polymers56926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-4 kcal/mol
Surface area10480 Å2
MethodPISA
2
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
E: RCC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,47924
Polymers28,0032
Non-polymers47722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-4 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.406, 107.406, 205.604
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABDE

#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: 27320.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTMT1, C9orf32, METTL11A, NRMT, NRMT1, AD-003 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V3R
References: UniProt: Q9BV86, protein N-terminal methyltransferase
#2: Protein/peptide RCC1


Mass: 682.854 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P18754*PLUS

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Non-polymers , 4 types, 465 molecules

#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 43 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 26% PEG3350, 16% tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→29.68 Å / Num. obs: 71201 / % possible obs: 100 % / Redundancy: 20.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.024 / Rrim(I) all: 0.111 / Net I/σ(I): 27 / Num. measured all: 1466692
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
1.75-1.7820.40.9424.37847538480.910.210.96699.9
9.09-29.68150.03182.7925661710.0080.03297.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
Aimless0.5.9data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: isomorphous crystal structure of same protein.

Resolution: 1.75→29.68 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.1683 / WRfactor Rwork: 0.1449 / FOM work R set: 0.8978 / SU B: 3.001 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0828 / SU Rfree: 0.0837 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Coot was used for interactive model building. Molprobity was used for geometry validation.
RfactorNum. reflection% reflectionSelection details
Rfree0.1882 2625 3.7 %THIN SHELLS (SFTOOLS)
Rwork0.1611 ---
obs0.1621 68505 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.35 Å2 / Biso mean: 18.374 Å2 / Biso min: 7.73 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.75→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 0 113 417 4174
Biso mean--18.08 26.02 -
Num. residues----465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193942
X-RAY DIFFRACTIONr_bond_other_d0.0020.023734
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.9895363
X-RAY DIFFRACTIONr_angle_other_deg1.06138624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2445502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97823.446177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33215684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8951537
X-RAY DIFFRACTIONr_chiral_restr0.1150.2601
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214446
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02899
X-RAY DIFFRACTIONr_mcbond_it0.5480.8191917
X-RAY DIFFRACTIONr_mcbond_other0.540.8171916
X-RAY DIFFRACTIONr_mcangle_it0.9071.222401
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 4 -
Rwork0.211 5156 -
all-5160 -
obs--99.75 %
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)
10.9909-0.16350.08530.9579-0.15841.8284-0.0543-0.0303-0.01450.08630.02890.0559-0.0702-0.12980.02540.04130.01960.00910.01580.00080.005216.160131.6899-14.5184
22.0269-1.0728-0.9771.5540.45651.7607-0.1542-0.1214-0.19190.17820.08340.10860.20230.06940.07090.10970.03310.04640.05210.00970.0367-6.805338.975214.2489
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 223
2X-RAY DIFFRACTION2B-2 - 223

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