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- PDB-9no2: CryoEM structure of RibD-enolase complex -

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Basic information

Entry
Database: PDB / ID: 9no2
TitleCryoEM structure of RibD-enolase complex
Components
  • Enolase
  • Riboflavin biosynthesis protein RibD
KeywordsSTRUCTURAL PROTEIN / reductase / deaminase / glycolysis
Function / homology
Function and homology information


5-amino-6-(5-phosphoribosylamino)uracil reductase / diaminohydroxyphosphoribosylaminopyrimidine deaminase / diaminohydroxyphosphoribosylaminopyrimidine deaminase activity / 5-amino-6-(5-phosphoribosylamino)uracil reductase activity / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / riboflavin biosynthetic process / glycolytic process / magnesium ion binding ...5-amino-6-(5-phosphoribosylamino)uracil reductase / diaminohydroxyphosphoribosylaminopyrimidine deaminase / diaminohydroxyphosphoribosylaminopyrimidine deaminase activity / 5-amino-6-(5-phosphoribosylamino)uracil reductase activity / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / riboflavin biosynthetic process / glycolytic process / magnesium ion binding / cell surface / extracellular region / zinc ion binding
Similarity search - Function
Riboflavin biosynthesis protein RibD / : / Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain ...Riboflavin biosynthesis protein RibD / : / Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Cytidine and deoxycytidylate deaminase zinc-binding region / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
Riboflavin biosynthesis protein RibD / Enolase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. novicida (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsLiu, X. / Clemens, D. / Lee, B. / Aguirre, R. / Horwitz, M. / Zhou, Z.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI151055 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
CitationJournal: Protein Cell / Year: 2025
Title: Structure, identification and characterization of the RibD-enolase complex in Francisella.
Authors: Xiaoyu Liu / Daniel L Clemens / Bai-Yu Lee / Roman Aguirre / Marcus A Horwitz / Z Hong Zhou /
History
DepositionMar 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enolase
B: Riboflavin biosynthesis protein RibD
C: Enolase
D: Riboflavin biosynthesis protein RibD


Theoretical massNumber of molelcules
Total (without water)178,4034
Polymers178,4034
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Enolase / 2-phospho-D-glycerate hydro-lyase / 2-phosphoglycerate dehydratase


Mass: 49562.883 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Francisella tularensis subsp. novicida (bacteria)
Strain: strain U112 / References: UniProt: A0Q5J9, phosphopyruvate hydratase
#2: Protein Riboflavin biosynthesis protein RibD


Mass: 39638.863 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Francisella tularensis subsp. novicida (bacteria)
Strain: strain U112
References: UniProt: A0Q460, diaminohydroxyphosphoribosylaminopyrimidine deaminase, 5-amino-6-(5-phosphoribosylamino)uracil reductase
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: RibD-enolase complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Francisella tularensis subsp. novicida (bacteria)
Source (recombinant)Organism: Francisella tularensis subsp. novicida (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 356717 / Symmetry type: POINT
RefinementHighest resolution: 3.05 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312204
ELECTRON MICROSCOPYf_angle_d0.60216510
ELECTRON MICROSCOPYf_dihedral_angle_d5.0131648
ELECTRON MICROSCOPYf_chiral_restr0.0461904
ELECTRON MICROSCOPYf_plane_restr0.0042118

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