[English] 日本語
Yorodumi
- PDB-9h4z: NNMT-SAM IN COMPLEX WITH 3b -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9h4z
TitleNNMT-SAM IN COMPLEX WITH 3b
ComponentsNicotinamide N-methyltransferase
KeywordsTRANSFERASE / NNMT SAH SAM
Function / homology
Function and homology information


pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide N-methyltransferase activity / nicotinamide metabolic process / positive regulation of protein deacetylation / Metabolism of ingested SeMet, Sec, MeSec into H2Se / Methylation / : / positive regulation of gluconeogenesis / methylation / cytosol
Similarity search - Function
Methyltransferase, NNMT/PNMT/TEMT / Methyltransferase NNMT/PNMT/TEMT, conserved site / : / NNMT/PNMT/TEMT family / NNMT/PNMT/TEMT family of methyltransferases signature. / SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / S-ADENOSYLMETHIONINE / Nicotinamide N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsJohansson, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Mechanism and kinetics of turnover inhibitors of nicotinamide N-methyl transferase in vitro and in vivo.
Authors: Akerud, T. / De Fusco, C. / Brandt, P. / Bergstrom, F. / Johansson, P. / Ek, M. / Borjesson, U. / Johansson, A. / Danielsson, J. / Bauer, M. / Arnaud, B. / Castaldo, M. / Stromstedt, M. / ...Authors: Akerud, T. / De Fusco, C. / Brandt, P. / Bergstrom, F. / Johansson, P. / Ek, M. / Borjesson, U. / Johansson, A. / Danielsson, J. / Bauer, M. / Arnaud, B. / Castaldo, M. / Stromstedt, M. / Rosengren, B. / Jansen, F. / Fredlund, L.
History
DepositionOct 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Nicotinamide N-methyltransferase
D: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8026
Polymers62,6532
Non-polymers1,1494
Water7,422412
1
B: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9013
Polymers31,3271
Non-polymers5752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9013
Polymers31,3271
Non-polymers5752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.01, 69.72, 115.19
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Nicotinamide N-methyltransferase


Mass: 31326.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NNMT
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P40261, nicotinamide N-methyltransferase
#2: Chemical ChemComp-A1ISI / 8-methoxychromen-4-one


Mass: 176.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 32% PEG3350, 0.2 M NaAc, and 0.1 M Hepes pH 6.8-7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.41→46.3 Å / Num. obs: 95503 / % possible obs: 98.9 % / Redundancy: 5.6 % / CC1/2: 1 / Net I/σ(I): 11.7
Reflection shellResolution: 1.41→1.46 Å / Num. unique obs: 1851 / CC1/2: 0.44

-
Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
autoPROCdata reduction
XSCALEdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→46.34 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU R Cruickshank DPI: 0.065 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.068 / SU Rfree Cruickshank DPI: 0.067
RfactorNum. reflection% reflectionSelection details
Rfree0.217 4727 -RANDOM
Rwork0.19 ---
obs0.191 95503 98.7 %-
Displacement parametersBiso mean: 32.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.1288 Å20 Å20 Å2
2--2.2134 Å20 Å2
3----2.0846 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.41→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3997 0 80 412 4489
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014222HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.085731HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1456SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes96HARMONIC2
X-RAY DIFFRACTIONt_gen_planes637HARMONIC5
X-RAY DIFFRACTIONt_it4222HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion536SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5337SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.04
X-RAY DIFFRACTIONt_other_torsion15.89
LS refinement shellResolution: 1.41→1.45 Å
RfactorNum. reflection% reflection
Rfree0.263 305 -
Rwork0.2556 --
obs0.256 6069 86.04 %
Refinement TLS params.

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)
10.7591-0.4515-0.15592.30720.08140.54410.073-0.2352-0.0785-0.2352-0.0523-0.0616-0.0785-0.0616-0.0206-0.10340.00760.0069-0.1138-0.00590.12652.601-24.625972.9641
21.0639-0.2216-0.35471.3099-0.16970.95580.0675-0.10590.0358-0.1059-0.0140.04230.03580.0423-0.0535-0.10440.0048-0.0046-0.0827-0.00850.084327.826-47.153572.8847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ B|* }
2X-RAY DIFFRACTION2{ D|* }

+
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