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- PDB-7d8d: The crystal structure of ScNTM1 in complex with SAH and Rps25a he... -

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Basic information

Entry
Database: PDB / ID: 7d8d
TitleThe crystal structure of ScNTM1 in complex with SAH and Rps25a hexapeptide
Components
  • Alpha N-terminal protein methyltransferase 1
  • Rps25A-peptide
KeywordsTRANSFERASE / ScNTM1 / N-terminal methylation / methyltransferase / Saccharomyces cerevisiae / substrate binding pocket
Function / homology
Function and homology information


N-terminal protein amino acid methylation / protein N-terminal methyltransferase / N-terminal peptidyl-proline dimethylation / N-terminal protein N-methyltransferase activity / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit ...N-terminal protein amino acid methylation / protein N-terminal methyltransferase / N-terminal peptidyl-proline dimethylation / N-terminal protein N-methyltransferase activity / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / methyltransferase activity / cytosolic small ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / cytosol / cytoplasm
Similarity search - Function
Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / Ribosomal protein S25 / S25 ribosomal protein / Winged helix DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Alpha N-terminal protein methyltransferase 1 / Small ribosomal subunit protein eS25A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsZhang, H.Y. / Yue, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U1632124 to L.N. China
Ministry of Science and Technology (MoST, China)2017YFA0503600 to L.N. China
CitationJournal: Crystallography Reports / Year: 2021
Title: Structural Basis for Peptide Binding of Alpha-N Terminal Methyltransferase from Saccharomyces cerevisiae
Authors: Zhang, H.Y. / Kuang, Z. / Xue, L. / Yue, J. / Khan, M.H. / Zhu, Z. / Niu, L.
History
DepositionOct 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha N-terminal protein methyltransferase 1
D: Rps25A-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1943
Polymers26,8102
Non-polymers3841
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-4 kcal/mol
Surface area10780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.692, 52.014, 127.723
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Alpha N-terminal protein methyltransferase 1 / Translation associated element 1 / X-Pro-Lys N-terminal protein methyltransferase 1 / NTM1


Mass: 26098.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TAE1, NTM1, YBR261C, YBR1729 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P38340, protein N-terminal methyltransferase
#2: Protein/peptide Rps25A-peptide


Mass: 710.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E792
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M magnesium chloride hexahydrate,0.1M Bis-Tris(pH 6.5) and 25% PEG3350
PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97891 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 0.999→50 Å / Num. obs: 130264 / % possible obs: 93 % / Redundancy: 8.6 % / Biso Wilson estimate: 6.32 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.031 / Rrim(I) all: 0.094 / Net I/σ(I): 38.8
Reflection shellResolution: 1→1.02 Å / Num. unique obs: 3404 / CC1/2: 0.032 / % possible all: 49

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Processing

Software
NameVersionClassification
HKL-20001.18.2_3874data collection
PHENIX1.18.2_3874refinement
HKL-20001.18.2_3874, 1.10.1_2155data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EX4

2ex4


Resolution: 1.05→27.21 Å / SU ML: 0.0649 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.4271
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1357 6044 5.09 %
Rwork0.1177 112714 -
obs0.1187 118874 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.37 Å2
Refinement stepCycle: LAST / Resolution: 1.05→27.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 26 327 2233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662034
X-RAY DIFFRACTIONf_angle_d1.11032777
X-RAY DIFFRACTIONf_chiral_restr0.0803304
X-RAY DIFFRACTIONf_plane_restr0.0077362
X-RAY DIFFRACTIONf_dihedral_angle_d22.828797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.070.23472380.20944595X-RAY DIFFRACTION80.81
1.07-1.090.18262890.17785002X-RAY DIFFRACTION88.83
1.09-1.110.17752900.14765373X-RAY DIFFRACTION93.8
1.11-1.130.13962930.12045621X-RAY DIFFRACTION99.19
1.13-1.160.12563140.10925681X-RAY DIFFRACTION100
1.16-1.180.12593200.1025684X-RAY DIFFRACTION100
1.18-1.210.12082780.09975728X-RAY DIFFRACTION100
1.21-1.240.12193120.09955705X-RAY DIFFRACTION100
1.24-1.280.1143200.10015623X-RAY DIFFRACTION100
1.28-1.320.13342810.1035748X-RAY DIFFRACTION100
1.32-1.370.11552930.09765747X-RAY DIFFRACTION100
1.37-1.420.10882780.09945731X-RAY DIFFRACTION100
1.42-1.490.11142950.09715770X-RAY DIFFRACTION100
1.49-1.570.11412980.09275740X-RAY DIFFRACTION100
1.57-1.670.11033430.09825719X-RAY DIFFRACTION100
1.67-1.790.13383140.10975770X-RAY DIFFRACTION100
1.8-1.980.13213340.1155724X-RAY DIFFRACTION99.62
1.98-2.260.13133350.11125833X-RAY DIFFRACTION99.9
2.26-2.850.13323050.12385854X-RAY DIFFRACTION99.82
2.85-27.210.1643140.14316066X-RAY DIFFRACTION98.76

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