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- PDB-5e1b: Crystal structure of NRMT1 in complex with SPKRIA peptide -

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Basic information

Entry
Database: PDB / ID: 5e1b
TitleCrystal structure of NRMT1 in complex with SPKRIA 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 / regulation of mitotic spindle assembly / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / spindle organization / nucleosomal DNA binding / regulation of mitotic nuclear division / histone methyltransferase activity / viral process / spindle assembly / nucleosome binding / mitotic spindle organization / regulation of mitotic cell cycle / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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 1.3Sep 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)57,12364
Polymers55,9864
Non-polymers1,13760
Water7,855436
1
A: N-terminal Xaa-Pro-Lys N-methyltransferase 1
D: RCC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,65431
Polymers27,9932
Non-polymers66129
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-3 kcal/mol
Surface area10320 Å2
MethodPISA
2
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
E: RCC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,46933
Polymers27,9932
Non-polymers47731
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-3 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.259, 107.259, 205.416
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: 672.817 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, 496 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.: 54 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 3.05 Å3/Da / Density % sol: 59.62 %
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: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.6→50.01 Å / Num. obs: 92380 / % possible obs: 100 % / Redundancy: 21.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.029 / Rrim(I) all: 0.137 / Net I/σ(I): 21.7 / Num. measured all: 2000468
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
1.6-1.6321.81.2133.29769244880.8690.2651.241100
8.76-47.5416.40.04459.6116277070.9990.0110.04599.5

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Phasing

PhasingMethod: molecular replacement

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Processing

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

2ex4


Resolution: 1.65→47.54 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1635 / WRfactor Rwork: 0.1405 / FOM work R set: 0.9009 / SU B: 2.274 / SU ML: 0.043 / SU R Cruickshank DPI: 0.0661 / SU Rfree: 0.0683 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Coot was used for interactive model building. Molprobity was used for geometry validation.
RfactorNum. reflection% reflectionSelection details
Rfree0.1759 3324 3.9 %THIN SHELLS (SFTOOLS)
Rwork0.1507 ---
obs0.1517 80997 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.18 Å2 / Biso mean: 16.708 Å2 / Biso min: 6.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å2-0 Å2
2--0.04 Å20 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 1.65→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3652 0 130 436 4218
Biso mean--18.17 25.03 -
Num. residues----465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193974
X-RAY DIFFRACTIONr_bond_other_d0.0020.023775
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.9895409
X-RAY DIFFRACTIONr_angle_other_deg1.0438717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1825510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7423.187182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.08815693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5221539
X-RAY DIFFRACTIONr_chiral_restr0.1190.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214487
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02907
X-RAY DIFFRACTIONr_mcbond_it0.5170.6821925
X-RAY DIFFRACTIONr_mcbond_other0.5120.681924
X-RAY DIFFRACTIONr_mcangle_it0.8781.0182412
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 236 -
Rwork0.18 5866 -
all-6102 -
obs--100 %
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)
10.9712-0.20870.08490.8877-0.09111.6274-0.0492-0.0271-0.01410.07310.02170.0433-0.0605-0.10270.02750.04330.01680.00750.0139-0.00090.004316.145131.6356-14.466
21.7626-0.9721-0.76471.50690.35761.601-0.1351-0.107-0.1810.17070.06790.12780.18550.05520.06720.10390.02770.04130.05310.01040.0365-6.835738.811714.2247
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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