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- PDB-7u1m: Crystal structure of NTMT1 in complex with compound YD206 -

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Basic information

Entry
Database: PDB / ID: 7u1m
TitleCrystal structure of NTMT1 in complex with compound YD206
ComponentsN-terminal Xaa-Pro-Lys N-methyltransferase 1
KeywordsTRANSFERASE/INHIBITOR / Methyltransferase / Enzyme / Inhibitor complex / TRANSFERASE / TRANSFERASE-INHIBITOR complex
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 / protein methyltransferase activity / spindle organization / histone methyltransferase activity / chromosome segregation ...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 / 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-KYF / S-ADENOSYL-L-HOMOCYSTEINE / N-terminal Xaa-Pro-Lys N-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.17 Å
AuthorsYadav, R. / Noinaj, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)U01CA214649 United States
CitationJournal: J.Med.Chem. / Year: 2022
Title: Venglustat Inhibits Protein N-Terminal Methyltransferase 1 in a Substrate-Competitive Manner.
Authors: Dong, G. / Deng, Y. / Yasgar, A. / Yadav, R. / Talley, D. / Zakharov, A.V. / Jain, S. / Rai, G. / Noinaj, N. / Simeonov, A. / Huang, R.
History
DepositionFeb 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1886
Polymers54,6402
Non-polymers1,5484
Water0
1
A: N-terminal Xaa-Pro-Lys N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0943
Polymers27,3201
Non-polymers7742
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0943
Polymers27,3201
Non-polymers7742
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.609, 89.609, 141.502
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 3 through 5 and (name N...
21(chain B and (resid 3 through 9 or (resid 10...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERVALVAL(chain A and ((resid 3 through 5 and (name N...AA3 - 521 - 23
12SERSERSAHSAH(chain A and ((resid 3 through 5 and (name N...AA - C3 - 30121
13SERSERSAHSAH(chain A and ((resid 3 through 5 and (name N...AA - C3 - 30121
14SERSERSAHSAH(chain A and ((resid 3 through 5 and (name N...AA - C3 - 30121
15SERSERSAHSAH(chain A and ((resid 3 through 5 and (name N...AA - C3 - 30121
21SERSERGLUGLU(chain B and (resid 3 through 9 or (resid 10...BB3 - 921 - 27
22LYSLYSLYSLYS(chain B and (resid 3 through 9 or (resid 10...BB1028
23SERSERSAHSAH(chain B and (resid 3 through 9 or (resid 10...BB - E3 - 30121
24SERSERSAHSAH(chain B and (resid 3 through 9 or (resid 10...BB - E3 - 30121
25SERSERSAHSAH(chain B and (resid 3 through 9 or (resid 10...BB - E3 - 30121

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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.: 2
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: 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
#3: Chemical ChemComp-KYF / (1R,3S,4R)-1-azabicyclo[2.2.2]octan-3-yl {2-[2-(4-fluorophenyl)-1,3-thiazol-4-yl]propan-2-yl}carbamate


Mass: 389.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24FN3O2S / Feature type: SUBJECT OF INVESTIGATION
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: 3 Å3/Da / Density % sol: 59.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CHES:NaOH, pH 9.5 10% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 11983 / % possible obs: 99.5 % / Redundancy: 6.9 % / CC1/2: 1 / CC star: 1 / Rpim(I) all: 0.072 / Net I/σ(I): 29.8
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1196 / CC1/2: 0.426 / CC star: 0.773 / Rpim(I) all: 0.927 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX1.18rc1_3777refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PVA

6pva


Resolution: 3.17→44.8 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2828 1057 10.04 %
Rwork0.2507 9473 -
obs0.2538 10530 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 236.85 Å2 / Biso mean: 148.173 Å2 / Biso min: 104.49 Å2
Refinement stepCycle: final / Resolution: 3.17→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 106 0 3564
Biso mean--159.9 --
Num. residues----442
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1947X-RAY DIFFRACTION19.054TORSIONAL
12B1947X-RAY DIFFRACTION19.054TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.17-3.320.46941030.4702941104477
3.32-3.490.48461340.421412321366100
3.49-3.710.41831390.397512171356100
3.71-40.39231350.37151205134099
4-4.40.35571390.28051214135399
4.4-5.030.27481330.24251213134699
5.03-6.340.26371410.24691225136699
6.34-44.80.19941330.17111226135998

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