[English] 日本語
Yorodumi
- PDB-5z9r: NMNAT as a specific chaperone antagonizing pathological condensat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z9r
TitleNMNAT as a specific chaperone antagonizing pathological condensation of phosphorylated tau
ComponentsNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3
KeywordsTRANSFERASE / antagonizing pathological condensation of phosphorylated tau / CHAPERONE
Function / homology
Function and homology information


Nicotinate metabolism / nicotinamide-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase activity / NAD biosynthetic process / response to tumor necrosis factor / response to wounding / axon / neuronal cell body ...Nicotinate metabolism / nicotinamide-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase activity / NAD biosynthetic process / response to tumor necrosis factor / response to wounding / axon / neuronal cell body / mitochondrion / ATP binding / nucleus
Similarity search - Function
Nicotinate/nicotinamide nucleotide adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDou, S. / Ma, X. / Li, D. / Liu, C.
CitationJournal: Elife / Year: 2020
Title: Nicotinamide mononucleotide adenylyltransferase uses its NAD+substrate-binding site to chaperone phosphorylated Tau.
Authors: Ma, X. / Zhu, Y. / Lu, J. / Xie, J. / Li, C. / Shin, W.S. / Qiang, J. / Liu, J. / Dou, S. / Xiao, Y. / Wang, C. / Jia, C. / Long, H. / Yang, J. / Fang, Y. / Jiang, L. / Zhang, Y. / Zhang, S. ...Authors: Ma, X. / Zhu, Y. / Lu, J. / Xie, J. / Li, C. / Shin, W.S. / Qiang, J. / Liu, J. / Dou, S. / Xiao, Y. / Wang, C. / Jia, C. / Long, H. / Yang, J. / Fang, Y. / Jiang, L. / Zhang, Y. / Zhang, S. / Zhai, R.G. / Liu, C. / Li, D.
History
DepositionFeb 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3
B: Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3


Theoretical massNumber of molelcules
Total (without water)63,1462
Polymers63,1462
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-4 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.650, 80.822, 64.501
Angle α, β, γ (deg.)90.000, 102.220, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 / NMN/NaMN adenylyltransferase 3 / Nicotinamide-nucleotide adenylyltransferase 3 / NMN ...NMN/NaMN adenylyltransferase 3 / Nicotinamide-nucleotide adenylyltransferase 3 / NMN adenylyltransferase 3 / Nicotinate-nucleotide adenylyltransferase 3 / NaMN adenylyltransferase 3


Mass: 31572.975 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nmnat3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q99JR6, nicotinamide-nucleotide adenylyltransferase, nicotinate-nucleotide adenylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.04 M citric acid, 0.06 M Bis-Tris propane, pH 7.0, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 35818 / % possible obs: 98.2 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.051 / Rrim(I) all: 0.114 / Χ2: 1.007 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.075.50.37636450.9690.1730.4151.083100
2.07-2.155.50.27836050.9810.1290.3071.056100
2.15-2.255.50.2136180.9870.0980.2320.981100
2.25-2.375.50.17336190.9860.0820.1910.95100
2.37-2.525.50.15536260.9880.0750.1720.948100
2.52-2.715.50.14336560.9790.0690.1591.047100
2.71-2.995.50.13236650.9770.0650.1471.002100
2.99-3.425.30.10836010.9860.0540.1211.00699.2
3.42-4.3150.08434840.9890.0440.0950.95495.1
4.31-5050.08132990.9880.0410.0911.04488.3

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KQN

1kqn


Resolution: 2→31.52 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.58
RfactorNum. reflection% reflection
Rfree0.2236 1793 5.02 %
Rwork0.1911 --
obs0.1927 35744 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.35 Å2 / Biso mean: 46.0131 Å2 / Biso min: 27.86 Å2
Refinement stepCycle: final / Resolution: 2→31.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3518 0 0 215 3733
Biso mean---48 -
Num. residues----435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083598
X-RAY DIFFRACTIONf_angle_d0.9214882
X-RAY DIFFRACTIONf_chiral_restr0.052549
X-RAY DIFFRACTIONf_plane_restr0.005625
X-RAY DIFFRACTIONf_dihedral_angle_d18.8862168
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.05410.28881420.237126082750100
2.0541-2.11450.27081250.21826752800100
2.1145-2.18270.2891370.210926272764100
2.1827-2.26070.23911340.201726702804100
2.2607-2.35120.22541360.195826592795100
2.3512-2.45820.22811590.199626252784100
2.4582-2.58770.23361390.19526572796100
2.5877-2.74980.25731320.211526402772100
2.7498-2.96190.24371570.206526682825100
2.9619-3.25970.24641350.19762640277599
3.2597-3.73080.21991460.1892616276298
3.7308-4.69790.17891370.16842474261192
4.6979-31.52390.21611140.182392250687

+
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://pdbjlvh1.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