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- PDB-5e2a: Crystal structure of NTMT1 in complex with N-terminally methylate... -

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Basic information

Entry
Database: PDB / ID: 5e2a
TitleCrystal structure of NTMT1 in complex with N-terminally methylated SPKRIA 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-proline dimethylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal protein N-methyltransferase activity / sulfate binding / mitotic nuclear membrane reassembly / protein methyltransferase activity / 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 / sulfate binding / mitotic nuclear membrane reassembly / protein methyltransferase activity / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / regulation of mitotic spindle assembly / Postmitotic nuclear pore complex (NPC) reformation / spindle organization / nucleosomal DNA binding / histone methyltransferase activity / regulation of mitotic nuclear division / viral process / nucleosome binding / spindle assembly / regulation of mitotic cell cycle / guanyl-nucleotide exchange factor activity / condensed nuclear chromosome / mitotic spindle organization / 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 / cytoplasm / cytosol
Similarity search - Function
Regulator of chromosome condensation (RCC1) signature 1. / : / Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / RCC1-like domain / Regulator of chromosome condensation (RCC1) signature 2. / 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 / RCC1-like domain / Regulator of chromosome condensation (RCC1) signature 2. / 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 30, 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 1.3Sep 27, 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

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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)57,15143
Polymers56,0144
Non-polymers1,13739
Water7,674426
1
A: N-terminal Xaa-Pro-Lys N-methyltransferase 1
D: RCC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,66828
Polymers28,0072
Non-polymers66126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 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)28,48315
Polymers28,0072
Non-polymers47713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-4 kcal/mol
Surface area9920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.160, 107.160, 205.589
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: 686.843 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 33 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.98 Å3/Da / Density % sol: 58.79 %
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: Aug 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→29.62 Å / Num. obs: 70896 / % possible obs: 100 % / Redundancy: 20.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.028 / Rrim(I) all: 0.129 / Net I/σ(I): 27.6 / Num. measured all: 1473712
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
1.75-1.7819.81.1393.57568538280.8410.2611.16999.9
9.09-29.6216.30.024108.9998761310.0060.02497.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
Aimless0.5.12data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdbid 2ex4

2ex4


Resolution: 1.75→29.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.161 / WRfactor Rwork: 0.138 / FOM work R set: 0.8996 / SU B: 2.969 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0808 / SU Rfree: 0.0819 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Coot was used for interactive model building. Molprobity was used for geometry validation.
RfactorNum. reflection% reflectionSelection details
Rfree0.184 2626 3.7 %THIN SHELLS (SFTOOLS)
Rwork0.1571 ---
obs0.1581 68176 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.69 Å2 / Biso mean: 17.264 Å2 / Biso min: 7.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.75→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3638 0 110 426 4174
Biso mean--17.85 24.79 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193931
X-RAY DIFFRACTIONr_bond_other_d0.0020.023696
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.9915352
X-RAY DIFFRACTIONr_angle_other_deg1.03438536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2195509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28923.559177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52715674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0331533
X-RAY DIFFRACTIONr_chiral_restr0.1160.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214458
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02887
X-RAY DIFFRACTIONr_mcbond_it0.4920.7761922
X-RAY DIFFRACTIONr_mcbond_other0.4840.7741921
X-RAY DIFFRACTIONr_mcangle_it0.8221.1572409
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 187 -
Rwork0.216 4930 -
all-5117 -
obs--99.92 %
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)
11.0431-0.19920.09460.8462-0.14351.6871-0.0574-0.0221-0.01390.07590.02940.0465-0.0637-0.10310.02790.04010.0160.00670.0128-0.00090.004716.102631.7351-14.4836
21.7781-0.96-0.81731.55750.38651.6349-0.1319-0.1034-0.17060.16820.06820.11960.18320.05890.06380.09860.02770.04170.04790.00840.0341-6.792538.879414.1927
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 223
2X-RAY DIFFRACTION2B-1 - 223

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