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- PDB-8x7f: CryoEM structure of the trifunctional NAD biosynthesis/regulator ... -

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Basic information

Entry
Database: PDB / ID: 8x7f
TitleCryoEM structure of the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD
ComponentsTrifunctional NAD biosynthesis/regulator protein NadR
KeywordsCELL INVASION / the trifunctional NAD biosynthesis/regulator protein NadR
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Trifunctional NAD biosynthesis/regulator protein NadR
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsJiang, W.X. / Dong, X. / Cheng, X.Q. / Ma, L.X. / Xing, Q.
Funding support China, 1items
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, W.X. / Dong, X. / Cheng, X.Q. / Ma, L.X. / Xing, Q.
History
DepositionNov 24, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trifunctional NAD biosynthesis/regulator protein NadR
D: Trifunctional NAD biosynthesis/regulator protein NadR
G: Trifunctional NAD biosynthesis/regulator protein NadR
J: Trifunctional NAD biosynthesis/regulator protein NadR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,60812
Polymers161,5744
Non-polymers3,0348
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Trifunctional NAD biosynthesis/regulator protein NadR


Mass: 40393.555 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: nadR, nadI, b4390, JW5800 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P27278, nicotinamide-nucleotide adenylyltransferase, ribosylnicotinamide kinase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.2
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 38 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 484976 / Algorithm: FOURIER SPACE / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 52.79 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002511896
ELECTRON MICROSCOPYf_angle_d0.506516140
ELECTRON MICROSCOPYf_chiral_restr0.04361704
ELECTRON MICROSCOPYf_plane_restr0.00442072
ELECTRON MICROSCOPYf_dihedral_angle_d4.98411568

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