[English] 日本語
Yorodumi
- EMDB-38098: CryoEM structure of the trifunctional NAD biosynthesis/regulator ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38098
TitleCryoEM structure of the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD
Map data
Sample
  • Complex: the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD
    • Protein or peptide: Trifunctional NAD biosynthesis/regulator protein NadR
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: PHOSPHATE ION
Keywordsthe trifunctional NAD biosynthesis/regulator protein NadR / CELL INVASION
Function / homology
Function and homology information


response to alkaline pH / adenylyltransferase complex / ribosylnicotinamide kinase / ribosylnicotinamide kinase activity / nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / cellular response to metal ion / NAD+ biosynthetic process / catalytic complex / cis-regulatory region sequence-specific DNA binding ...response to alkaline pH / adenylyltransferase complex / ribosylnicotinamide kinase / ribosylnicotinamide kinase activity / nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / cellular response to metal ion / NAD+ biosynthetic process / catalytic complex / cis-regulatory region sequence-specific DNA binding / protein homotetramerization / magnesium ion binding / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / Nicotinamide-nucleotide adenylyltransferase / NAD biosynthesis/regulator protein NadR / NadR/Ttd14, AAA domain / NadR, nicotinamide/nicotinate mononucleotide adenylyltransferase domain / AAA domain / Helix-turn-helix / Cytidyltransferase-like domain / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. ...: / Nicotinamide-nucleotide adenylyltransferase / NAD biosynthesis/regulator protein NadR / NadR/Ttd14, AAA domain / NadR, nicotinamide/nicotinate mononucleotide adenylyltransferase domain / AAA domain / Helix-turn-helix / Cytidyltransferase-like domain / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Trifunctional NAD biosynthesis/regulator protein NadR
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsJiang WX / Dong X / Cheng XQ / Ma LX / Xing Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2100100 China
CitationJournal: To Be Published
Title: CryoEM structure of the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD
Authors: Jiang WX / Dong X / Cheng XQ / Ma LX / Xing Q
History
DepositionNov 24, 2023-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_38098.png

Downloads & links

-
Map

FileDownload / File: emd_38098.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 360 pix.
= 203.76 Å		0.57 Å/pix.
x 360 pix.
= 203.76 Å		0.57 Å/pix.
x 360 pix.
= 203.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.566 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0408
Minimum - Maximum-0.09234191 - 0.19109856
Average (Standard dev.)0.00015232326 (±0.010201069)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 203.76 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_38098_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_38098_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : the trifunctional NAD biosynthesis/regulator protein NadR in comp...

EntireName: the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD
Components
  • Complex: the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD
    • Protein or peptide: Trifunctional NAD biosynthesis/regulator protein NadR
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: PHOSPHATE ION

-
Supramolecule #1: the trifunctional NAD biosynthesis/regulator protein NadR in comp...

SupramoleculeName: the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)

-
Macromolecule #1: Trifunctional NAD biosynthesis/regulator protein NadR

MacromoleculeName: Trifunctional NAD biosynthesis/regulator protein NadR / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: nicotinamide-nucleotide adenylyltransferase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 40.393555 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: KTIGVVFGKF YPLHTGHIYL IQRACSQVDE LHIIMGFDDT RDRALFEDSA MSQQPTVPDR LRWLLQTFKY QKNIRIHAFN EEGMEPYPH GWDVWSNGIK KFMAEKGIQP DLIYTSEEAD APQYMEHLGI ETVLVDPKRT FMSISGAQIR ENPFRYWEYI P TEVKPFFV ...String:
KTIGVVFGKF YPLHTGHIYL IQRACSQVDE LHIIMGFDDT RDRALFEDSA MSQQPTVPDR LRWLLQTFKY QKNIRIHAFN EEGMEPYPH GWDVWSNGIK KFMAEKGIQP DLIYTSEEAD APQYMEHLGI ETVLVDPKRT FMSISGAQIR ENPFRYWEYI P TEVKPFFV RTVAILGGES SGKSTLVNKL ANIFNTTSAW EYGRDYVFSH LGGDEIALQY SDYDKIALGH AQYIDFAVKY AN KVAFIDT DFVTTQAFCK KYEGREHPFV QALIDEYRFD LVILLENNTP WVADGLRSLG SSVDRKEFQN LLVEMLEENN IEF VRVEEE DYDSRFLRCV ELVREMMGEQ R

UniProtKB: Trifunctional NAD biosynthesis/regulator protein NadR

-
Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

-
Macromolecule #3: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.5 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 484976
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
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