[English] 日本語
Yorodumi
- PDB-5cvd: Crystal structure of human NRMT1 in complex with alpha-N-dimethyl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cvd
TitleCrystal structure of human NRMT1 in complex with alpha-N-dimethylated human CENP-A peptide
Components
  • N-teminal peptide from Histone H3-like centromeric protein A
  • N-terminal Xaa-Pro-Lys N-methyltransferase 1
KeywordsTRANSFERASE/PEPTIDE / Alpha-N-methyltransferase / Histone Methylation / SAM-MTase / CENP-A / TRANSFERASE-PEPTIDE 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 / CENP-A containing chromatin assembly / protein methyltransferase activity / kinetochore assembly / protein localization to chromosome, centromeric region ...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 / CENP-A containing chromatin assembly / protein methyltransferase activity / kinetochore assembly / protein localization to chromosome, centromeric region / condensed chromosome, centromeric region / spindle organization / histone methyltransferase activity / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / pericentric heterochromatin / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / Deposition of new CENPA-containing nucleosomes at the centromere / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / chromosome segregation / RHO GTPases Activate Formins / Separation of Sister Chromatids / structural constituent of chromatin / nucleosome / protein heterodimerization activity / chromatin binding / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / Vaccinia Virus protein VP39 / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / Vaccinia Virus protein VP39 / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone H3-like centromeric protein A / N-terminal Xaa-Pro-Lys N-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsWu, R. / Li, H.
CitationJournal: Genes Dev. / Year: 2015
Title: Molecular basis for histone N-terminal methylation by NRMT1
Authors: Wu, R. / Yue, Y. / Zheng, X. / Li, H.
History
DepositionJul 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Nov 8, 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Mar 20, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-terminal Xaa-Pro-Lys N-methyltransferase 1
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
D: N-teminal peptide from Histone H3-like centromeric protein A
E: N-teminal peptide from Histone H3-like centromeric protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2326
Polymers57,4644
Non-polymers7692
Water13,097727
1
A: N-terminal Xaa-Pro-Lys N-methyltransferase 1
D: N-teminal peptide from Histone H3-like centromeric protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1163
Polymers28,7322
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
E: N-teminal peptide from Histone H3-like centromeric protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1163
Polymers28,7322
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.839, 66.245, 68.998
Angle α, β, γ (deg.)90.000, 106.690, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-541-

HOH

-
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: 27589.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTMT1, NRMT1 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9BV86, protein N-terminal methyltransferase
#2: Protein/peptide N-teminal peptide from Histone H3-like centromeric protein A / Centromere autoantigen A / Centromere protein A / CENP-A


Mass: 1142.382 Da / Num. of mol.: 2 / Fragment: UNP residues 2-10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49450
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 727 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M (NH4)Ac, 0.1 M Sodium citrate tribasic dihydrate, 28%(w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 119380 / % possible obs: 98.3 % / Redundancy: 4.7 % / Biso Wilson estimate: 9.06 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.055 / Rrim(I) all: 0.122 / Χ2: 1.401 / Net I/av σ(I): 16.362 / Net I/σ(I): 8.6 / Num. measured all: 558514
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.3-1.324.60.63158330.7880.3260.7111.24296.7
1.32-1.354.60.57858300.8160.2980.6511.25896.8
1.35-1.374.60.52958620.8430.2720.5961.2996.9
1.37-1.44.60.48558680.8650.250.5461.30697.1
1.4-1.434.70.42559250.8830.2180.4781.31397.4
1.43-1.464.70.37258640.9110.1920.4191.34197.4
1.46-1.54.70.31859260.9350.1630.3581.36697.6
1.5-1.544.70.26459470.9510.1350.2971.3998
1.54-1.594.70.22859110.9630.1170.2571.41198.2
1.59-1.644.70.19859570.9710.1010.2231.41698
1.64-1.74.70.1859890.9750.0920.2021.4698.6
1.7-1.764.70.16159720.9780.0830.1821.45298.6
1.76-1.844.70.13460260.9840.0690.1511.41798.9
1.84-1.944.70.12159850.9860.0620.1361.42599
1.94-2.064.70.11260210.9860.0570.1261.51299.2
2.06-2.224.70.10460520.9870.0530.1171.49599.3
2.22-2.454.70.09960830.9870.0510.1121.68799.7
2.45-2.84.60.08160460.990.0420.0921.53699.7
2.8-3.534.70.0760990.9930.0360.0791.45299.5
3.53-504.70.06861840.9920.0350.0771.23799.1

-
Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EX4

2ex4


Resolution: 1.3→29.612 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.16 3639 3.05 %
Rwork0.1322 115738 -
obs0.1331 119377 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.32 Å2 / Biso mean: 14.1414 Å2 / Biso min: 4.53 Å2
Refinement stepCycle: final / Resolution: 1.3→29.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3758 0 74 734 4566
Biso mean--7.14 25.25 -
Num. residues----470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063980
X-RAY DIFFRACTIONf_angle_d1.1555394
X-RAY DIFFRACTIONf_chiral_restr0.069589
X-RAY DIFFRACTIONf_plane_restr0.005701
X-RAY DIFFRACTIONf_dihedral_angle_d13.0831547
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.31710.2321470.19644229437695
1.3171-1.33520.21291440.17914347449197
1.3352-1.35430.2431440.17624387453197
1.3543-1.37450.2141230.16794360448397
1.3745-1.39590.22141540.16654344449897
1.3959-1.41880.20211420.15644446458897
1.4188-1.44330.18181550.14914353450897
1.4433-1.46950.21941300.14184430456097
1.4695-1.49780.18021190.13724417453698
1.4978-1.52840.18121370.12944428456598
1.5284-1.56160.16671100.12594458456898
1.5616-1.59790.16411350.12084461459698
1.5979-1.63790.16181450.1154414455998
1.6379-1.68220.15171090.11494472458198
1.6822-1.73170.16021350.11914494462999
1.7317-1.78760.16341410.11644471461299
1.7876-1.85140.14311530.11734470462399
1.8514-1.92550.15091630.11894454461799
1.9255-2.01320.13231360.11814511464799
2.0132-2.11930.14231600.11784474463499
2.1193-2.2520.14121560.11714496465299
2.252-2.42580.14611490.125745144663100
2.4258-2.66980.14141460.130145674713100
2.6698-3.05580.14971350.13814515465099
3.0558-3.84860.1461360.131645974733100
3.8486-29.61960.16551350.14274629476499

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more