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- EMDB-49592: CryoEM structure of RibD-enolase complex -

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Basic information

Entry
Database: EMDB / ID: EMD-49592
TitleCryoEM structure of RibD-enolase complex
Map datacryoEM map
Sample
  • Complex: RibD-enolase complex
    • Protein or peptide: Enolase
    • Protein or peptide: Riboflavin biosynthesis protein RibD
Keywordsreductase / deaminase / glycolysis / STRUCTURAL PROTEIN
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 / cell surface ...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 / cell surface / magnesium ion binding / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsLiu X / Clemens D / Lee B / Aguirre R / Horwitz M / Zhou ZH
Funding support United States, 2 items
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, 2025-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49592.png

Downloads & links

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Map

FileDownload / File: emd_49592.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcryoEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-4.030287 - 5.48025
Average (Standard dev.)-0.00020853446 (±0.10625714)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49592_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_49592_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_49592_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RibD-enolase complex

EntireName: RibD-enolase complex
Components
  • Complex: RibD-enolase complex
    • Protein or peptide: Enolase
    • Protein or peptide: Riboflavin biosynthesis protein RibD

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Supramolecule #1: RibD-enolase complex

SupramoleculeName: RibD-enolase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Francisella tularensis subsp. novicida (bacteria)

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Macromolecule #1: Enolase

MacromoleculeName: Enolase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: phosphopyruvate hydratase
Source (natural)Organism: Francisella tularensis subsp. novicida (bacteria) / Strain: strain U112
Molecular weightTheoretical: 49.562883 KDa
SequenceString: MSSQIKQVFA RQILDSRGNP TVEVDVVLES GAFGRAAVPS GASTGIREAL ELRDGNKALF LGKSVYKAVE NVNTKIAQAV KGLDALDQR LIDKTMIELD GSENKKNLGA NAILGVSLAT ARAAASHLRK PFYRYLMDVK EYLMPVPMMN VINGGSHADN N VDMQEFMI ...String:
MSSQIKQVFA RQILDSRGNP TVEVDVVLES GAFGRAAVPS GASTGIREAL ELRDGNKALF LGKSVYKAVE NVNTKIAQAV KGLDALDQR LIDKTMIELD GSENKKNLGA NAILGVSLAT ARAAASHLRK PFYRYLMDVK EYLMPVPMMN VINGGSHADN N VDMQEFMI VPAGFDTFSE ALRCGTEVFH TLKKVLIADG YSVAGVGDEG GYAPDLPSNE AAIEAILKAV KEAGYEPGKH VF IALDPAS SEFYKDGKYE LKSENKSLTS EEMIDYYAAW VEKYPIVSIE DGLAEEDWAG WKLLTEKLGN KVQLVGDDLF VTN PSILAK GIEKGIANSI LIKLNQIGTL TETFEAMAMA GQAGYTCVVS HRSGETSDTI IADLAVATCS GQIKTGSLSR SDRI AKYNQ LLRIEEELGE NAIYPGIKAF VFNSDEEVEE DVQEIIVEDS EAEKVVVQVE E

UniProtKB: Enolase

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Macromolecule #2: Riboflavin biosynthesis protein RibD

MacromoleculeName: Riboflavin biosynthesis protein RibD / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
EC number: diaminohydroxyphosphoribosylaminopyrimidine deaminase
Source (natural)Organism: Francisella tularensis subsp. novicida (bacteria) / Strain: strain U112
Molecular weightTheoretical: 39.638863 KDa
SequenceString: MKNIDKYYMQ QALTLANRGR LTVSPNPMVG CIIVKNGAII SEGWHETVGE AHAEVHALIK VGDKAKGATA YVTLEPCCHH GRTPPCTDT IIKAGIKKVI IATLDPNPKV AGKGVERLKN AGITVEVGLL EKQAQELNKI FFHYQTTKKP FVYAKWAMSL D GKIAVNDG ...String:
MKNIDKYYMQ QALTLANRGR LTVSPNPMVG CIIVKNGAII SEGWHETVGE AHAEVHALIK VGDKAKGATA YVTLEPCCHH GRTPPCTDT IIKAGIKKVI IATLDPNPKV AGKGVERLKN AGITVEVGLL EKQAQELNKI FFHYQTTKKP FVYAKWAMSL D GKIAVNDG DSKKISSHQA FVNTHELRNI CDAILIGKQT LIDDNPSLDV RININKIKHP TRFILANHLT TINHNWRVLD QR HAKTIFV CSKISAQVAT KLNQLGIEYW LLPQSQHQVC LDTLLEKMGK IGITSLLVEG GNKTLNSFIN QKLVNEFYTY LAP VIIADY NPKQQLSFNQ ISVREDIIIN SCFKENSNV

UniProtKB: Riboflavin biosynthesis protein RibD

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 356717
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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