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- PDB-6wj7: The structure of NTMT1 in complex with compound C2A -

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Basic information

Entry
Database: PDB / ID: 6wj7
TitleThe structure of NTMT1 in complex with compound C2A
Components
  • GLY-PRO-LYS-ARG-ILE-ALA-NH2
  • N-terminal Xaa-Pro-Lys N-methyltransferase 1
KeywordsTRANSFERASE / methyltransferase / enzyme / inhibitor complex / transferase-transferase-inhibitor 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 / protein methyltransferase activity / spindle organization / histone methyltransferase activity / chromosome segregation ...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 / protein methyltransferase activity / spindle organization / histone methyltransferase activity / chromosome segregation / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-AN6 / N-terminal Xaa-Pro-Lys N-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å
AuthorsSrinivasan, K. / Chen, D. / Huang, R. / Noinaj, N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM117275 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127896 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA023168 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Probing the Plasticity in the Active Site of Protein N-terminal Methyltransferase 1 Using Bisubstrate Analogues.
Authors: Chen, D. / Dong, C. / Dong, G. / Srinivasan, K. / Min, J. / Noinaj, N. / Huang, R.
History
DepositionApr 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Feb 22, 2023Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / pdbx_entity_instance_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_validate_rmsd_bond / refine / refine_hist / refine_ls_shell / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.group_PDB / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][3] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_validate_rmsd_bond.auth_comp_id_1 / _pdbx_validate_rmsd_bond.auth_comp_id_2 / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_percent_reflns_obs / _refine_hist.cycle_id / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used
Revision 2.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 3.0Apr 24, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
A: GLY-PRO-LYS-ARG-ILE-ALA-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3563
Polymers27,9612
Non-polymers3951
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-4 kcal/mol
Surface area10110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.804, 72.804, 80.131
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-510-

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: 27320.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTMT1, C9orf32, METTL11A, NRMT, NRMT1, AD-003 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9BV86, protein N-terminal methyltransferase
#2: Protein/peptide GLY-PRO-LYS-ARG-ILE-ALA-NH2


Mass: 640.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-AN6 / 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine


Type: L-peptide linking / Mass: 395.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N7O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.8 M Lithium Chloride 0.1 M Tris: HCl, pH 8.5 32 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. obs: 46403 / % possible obs: 99.93 % / Redundancy: 6.5 % / Biso Wilson estimate: 16.51 Å2 / CC1/2: 0.99 / Rsym value: 0.12 / Net I/σ(I): 20.4
Reflection shellResolution: 1.42→1.44 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4545 / CC1/2: 0.46 / Rsym value: 1.3 / % possible all: 99.78

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DTN

6dtn


Resolution: 1.42→24.59 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.188 1996 4.3 %
Rwork0.165 --
obs0.166 46403 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.95 Å2
Refinement stepCycle: LAST / Resolution: 1.42→24.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 0 233 2049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.460.27231410.26083119X-RAY DIFFRACTION100
1.46-1.50.25321410.22843093X-RAY DIFFRACTION100
1.5-1.540.26111410.2283176X-RAY DIFFRACTION100
1.54-1.590.24611430.18993131X-RAY DIFFRACTION100
1.59-1.650.22651380.18333121X-RAY DIFFRACTION100
1.65-1.720.19411390.17453166X-RAY DIFFRACTION100
1.72-1.790.17791380.17053141X-RAY DIFFRACTION100
1.79-1.890.17191460.15793161X-RAY DIFFRACTION100
1.89-2.010.17021430.1653182X-RAY DIFFRACTION100
2.01-2.160.17051390.1523163X-RAY DIFFRACTION100
2.16-2.380.17461450.1683167X-RAY DIFFRACTION100
2.38-2.720.21821450.17093216X-RAY DIFFRACTION100
2.72-3.430.1931450.16633227X-RAY DIFFRACTION100
3.43-24.590.16251520.13983344X-RAY DIFFRACTION100
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)
10.249-0.06920.03620.3159-0.46320.78670.00490.03790.0006-0.0530.01120.5760.0037-0.56320.23220.12760.01120.02020.27190.00630.268815.4601-12.52137.5017
20.06990.0648-0.01350.0649-0.0379-0.00550.06640.02520.007-0.1135-0.02030.14580.13180.01680.00010.1818-0.015-0.0180.14380.01360.141827.7149-19.6259-3.2834
30.4886-0.11220.45030.6969-0.15710.137-0.08080.37930.0153-0.2329-0.004-0.2338-0.0570.3621-0.0330.1432-0.01930.00730.18230.03360.147142.1666-7.9671-2.4774
40.2399-0.04480.15690.49310.16370.3107-0.0338-0.02990.10090.0453-0.092-0.1279-0.00890.0666-0.0440.1227-0.0147-0.03450.13290.03080.177744.4108-7.44499.7232
50.4070.02120.5370.9065-0.37130.73420.01580.0065-0.0365-0.0109-0.0483-0.10460.06660.0198-00.12080.0056-0.00180.11860.00480.13738.2816-19.71618.1004
60.233-0.1722-0.05560.4192-0.44750.50960.0334-0.2406-0.04140.2526-0.0724-0.0281-0.0457-0.0796-00.1673-0.0009-0.01450.1555-0.0120.12733.9759-11.984217.8061
70.31250.2616-0.00081.1661-0.78280.977-0.0402-0.01850.16330.0460.03110.1051-0.2421-0.0893-0.00060.15490.0202-0.01170.1119-0.02670.134528.5265-3.33987.6185
80.38710.03760.4630.0769-0.20920.4458-0.1380.08870.2797-0.06690.02830.189-0.3186-0.0758-0.00460.24410.0279-0.03980.1173-0.01560.212829.58044.46163.7092
90.13040.1183-0.04760.6389-0.22960.2415-0.02340.02610.0268-0.08930.0453-0.1531-0.15440.01990.00250.1766-0.0136-0.0170.12040.01270.129233.0393-2.3136-5.4214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESID 5 THROUGH 22 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 23 THROUGH 34 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 35 THROUGH 53 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 54 THROUGH 73 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 74 THROUGH 110 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 111 THROUGH 130 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 131 THROUGH 181 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 182 THROUGH 206 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 207 THROUGH 223 )

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