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- PDB-5e1o: Crystal structure of NTMT1 in complex with RPKRIA peptide -

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Basic information

Entry
Database: PDB / ID: 5e1o
TitleCrystal structure of NTMT1 in complex with RPKRIA peptide
Components
  • N-terminal Xaa-Pro-Lys N-methyltransferase 1
  • RCC1
KeywordsTRANSFERASE / methyl transferase / Structural Genomics / Structural Genomics Consortium / SGC
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 / mitotic nuclear membrane reassembly / protein methyltransferase activity / sulfate binding / Rev-mediated nuclear export of HIV RNA ...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 / 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 / nucleosomal DNA binding / regulation of mitotic nuclear division / spindle organization / histone methyltransferase activity / nucleosome binding / spindle assembly / viral process / guanyl-nucleotide exchange factor activity / mitotic spindle organization / condensed nuclear chromosome / chromosome segregation / G1/S transition of mitotic cell cycle / small GTPase binding / 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 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)57,07944
Polymers56,1264
Non-polymers95340
Water6,954386
1
A: N-terminal Xaa-Pro-Lys N-methyltransferase 1
D: RCC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,54024
Polymers28,0632
Non-polymers47722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-3 kcal/mol
Surface area10340 Å2
MethodPISA
2
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
E: RCC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,54020
Polymers28,0632
Non-polymers47718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-2 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.450, 107.450, 206.388
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: 742.933 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, 426 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 36 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 59.86 %
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: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2→84.83 Å / Num. obs: 48256 / % possible obs: 99.9 % / Redundancy: 21.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.037 / Rrim(I) all: 0.175 / Net I/σ(I): 23 / Num. measured all: 1038174
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
2-2.0522.10.8857638434610.9390.1890.90199.7
8.94-84.8316.90.04662.1112936670.9990.0110.04899.5

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Processing

Software
NameVersionClassification
Aimless0.5.12data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: isomorphous crystal structure of same protein

Resolution: 2→84.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.1735 / WRfactor Rwork: 0.1404 / FOM work R set: 0.8921 / SU B: 4.789 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1161 / SU Rfree: 0.1155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Coot was used for interactive model building. Molprobity was used for geometry validation.
RfactorNum. reflection% reflectionSelection details
Rfree0.1888 1857 3.9 %THIN SHELLS (SFTOOLS)
Rwork0.1512 ---
obs0.1526 46342 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.75 Å2 / Biso mean: 21.142 Å2 / Biso min: 8.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 2→84.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 100 387 4135
Biso mean--18.9 28.34 -
Num. residues----465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193885
X-RAY DIFFRACTIONr_bond_other_d0.0020.023652
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.9875281
X-RAY DIFFRACTIONr_angle_other_deg1.05838419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2575490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89823.427178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33415665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1951534
X-RAY DIFFRACTIONr_chiral_restr0.1220.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214390
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02884
X-RAY DIFFRACTIONr_mcbond_it0.6710.9691899
X-RAY DIFFRACTIONr_mcbond_other0.6670.9671898
X-RAY DIFFRACTIONr_mcangle_it1.0841.442373
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 165 -
Rwork0.174 3293 -
all-3458 -
obs--99.48 %
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)
11.1574-0.23970.1431.0892-0.14082.1173-0.0569-0.0319-0.01480.14440.03060.0857-0.0378-0.13660.02620.05090.01020.02510.01020.00210.013916.114731.7416-14.6004
22.2718-1.1476-0.97751.72080.29441.9396-0.1655-0.1399-0.20490.14880.09470.09860.2580.09220.07080.13040.03830.0540.0420.01180.0428-6.809139.020114.3296
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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