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- EMDB-67660: DPR epimerase complex, substrate-bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-67660
TitleDPR epimerase complex, substrate-bound state
Map data
Sample
  • Complex: DPR epimerase complex
    • Protein or peptide: Decaprenylphosphoryl-beta-D-ribose oxidase
    • Protein or peptide: Decaprenylphosphoryl-2-keto-beta-D-erythro-pentose reductase
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: [(2~{E})-3,7-dimethylocta-2,6-dienyl] [(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate
  • Ligand: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
  • Ligand: water
KeywordsEpimerase complex / OXIDOREDUCTASE / ISOMERASE
Function / homology
Function and homology information


decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose 2-reductase / arabinan biosynthetic process / cell wall polysaccharide biosynthetic process / decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / oxidoreductase activity ...decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose 2-reductase / arabinan biosynthetic process / cell wall polysaccharide biosynthetic process / decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / oxidoreductase activity / response to antibiotic / plasma membrane
Similarity search - Function
D-arabinono-1,4-lactone oxidase, C-terminal domain / D-arabinono-1,4-lactone oxidase / L-gulonolactone/D-arabinono-1,4-lactone oxidase / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / short chain dehydrogenase ...D-arabinono-1,4-lactone oxidase, C-terminal domain / D-arabinono-1,4-lactone oxidase / L-gulonolactone/D-arabinono-1,4-lactone oxidase / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Decaprenylphosphoryl-2-keto-beta-D-erythro-pentose reductase / Decaprenylphosphoryl-beta-D-ribose oxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsWu F / Gao S / Rao Z / Zhang L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32394011 China
CitationJournal: To Be Published
Title: DPR epimerase complex, substrate-bound state
Authors: Wu F / Gao S / Rao Z / Zhang L
History
DepositionDec 11, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67660.png

Downloads & links

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Map

FileDownload / File: emd_67660.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 340 pix.
= 282.88 Å		0.83 Å/pix.
x 340 pix.
= 282.88 Å		0.83 Å/pix.
x 340 pix.
= 282.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.991988 - 5.520064
Average (Standard dev.)0.0012155612 (±0.08661586)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 282.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67660_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67660_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DPR epimerase complex

EntireName: DPR epimerase complex
Components
  • Complex: DPR epimerase complex
    • Protein or peptide: Decaprenylphosphoryl-beta-D-ribose oxidase
    • Protein or peptide: Decaprenylphosphoryl-2-keto-beta-D-erythro-pentose reductase
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: [(2~{E})-3,7-dimethylocta-2,6-dienyl] [(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate
  • Ligand: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
  • Ligand: water

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Supramolecule #1: DPR epimerase complex

SupramoleculeName: DPR epimerase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 155 KDa

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Macromolecule #1: Decaprenylphosphoryl-beta-D-ribose oxidase

MacromoleculeName: Decaprenylphosphoryl-beta-D-ribose oxidase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria) / Strain: ATCC 25618 / H37Rv
Molecular weightTheoretical: 50.161875 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MLSVGATTTA TRLTGWGRTA PSVANVLRTP DAEMIVKAVA RVAESGGGRG AIARGLGRSY GDNAQNGGGL VIDMTPLNTI HSIDADTKL VDIDAGVNLD QLMKAALPFG LWVPVLPGTR QVTVGGAIAC DIHGKNHHSA GSFGNHVRSM DLLTADGEIR H LTPTGEDA ...String:
MLSVGATTTA TRLTGWGRTA PSVANVLRTP DAEMIVKAVA RVAESGGGRG AIARGLGRSY GDNAQNGGGL VIDMTPLNTI HSIDADTKL VDIDAGVNLD QLMKAALPFG LWVPVLPGTR QVTVGGAIAC DIHGKNHHSA GSFGNHVRSM DLLTADGEIR H LTPTGEDA ELFWATVGGN GLTGIIMRAT IEMTPTSTAY FIADGDVTAS LDETIALHSD GSEARYTYSS AWFDAISAPP KL GRAAVSR GRLATVEQLP AKLRSEPLKF DAPQLLTLPD VFPNGLANKY TFGPIGELWY RKSGTYRGKV QNLTQFYHPL DMF GEWNRA YGPAGFLQYQ FVIPTEAVDE FKKIIGVIQA SGHYSFLNVF KLFGPRNQAP LSFPIPGWNI CVDFPIKDGL GKFV SELDR RVLEFGGRLY TAADSRTTAE TFHAMYPRVD EWISVRRKVD PLRVFASDMA RRLELL

UniProtKB: Decaprenylphosphoryl-beta-D-ribose oxidase

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Macromolecule #2: Decaprenylphosphoryl-2-keto-beta-D-erythro-pentose reductase

MacromoleculeName: Decaprenylphosphoryl-2-keto-beta-D-erythro-pentose reductase
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
EC number: decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose 2-reductase
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 27.501812 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MVLDAVGNPQ TVLLLGGTSE IGLAICERYL HNSAARIVLA CLPDDPRRED AAAAMKQAGA RSVELIDFDA LDTDSHPKMI EAAFSGGDV DVAIVAFGLL GDAEELWQNQ RKAVQIAEIN YTAAVSVGVL LAEKMRAQGF GQIIAMSSAA GERVRRANFV Y GSTKAGLD ...String:
MVLDAVGNPQ TVLLLGGTSE IGLAICERYL HNSAARIVLA CLPDDPRRED AAAAMKQAGA RSVELIDFDA LDTDSHPKMI EAAFSGGDV DVAIVAFGLL GDAEELWQNQ RKAVQIAEIN YTAAVSVGVL LAEKMRAQGF GQIIAMSSAA GERVRRANFV Y GSTKAGLD GFYLGLSEAL REYGVRVLVI RPGQVRTRMS AHLKEAPLTV DKEYVANLAV TASAKGKELV WAPAAFRYVM MV LRHIPRS IFRKLPI

UniProtKB: Decaprenylphosphoryl-2-keto-beta-D-erythro-pentose reductase

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Macromolecule #3: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 2 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #4: [(2~{E})-3,7-dimethylocta-2,6-dienyl] [(2~{S},3~{R},4~{S},5~{R})-...

MacromoleculeName: [(2~{E})-3,7-dimethylocta-2,6-dienyl] [(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate
type: ligand / ID: 4 / Number of copies: 2 / Formula: A1L5J
Molecular weightTheoretical: 366.344 Da

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Macromolecule #5: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

MacromoleculeName: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / type: ligand / ID: 5 / Number of copies: 2 / Formula: NAI
Molecular weightTheoretical: 665.441 Da
Chemical component information

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.5 mg/mL
BufferpH: 7.5 / Details: 150mM NaCl, 20mM Hepes
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 312548
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5

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