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- EMDB-62540: E. coli MaeB holo form -

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Basic information

Entry
Database: EMDB / ID: EMD-62540
TitleE. coli MaeB holo form
Map data
Sample
  • Complex: Malic enzyme B from Escherichia coli holo form
    • Protein or peptide: NADP-dependent malic enzyme
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsoxidoreductase / cryo-EM / allostery / STRUCTURAL PROTEIN
Function / homology
Function and homology information


malolactic enzyme activity / malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / malate dehydrogenase (decarboxylating) (NADP+) activity / oxaloacetate decarboxylase activity / malate metabolic process / acyltransferase activity / NAD binding / manganese ion binding / identical protein binding / cytosol
Similarity search - Function
NAD(P)-dependent malic enzyme / Malic enzyme, NAD-binding domain, bacterial type / : / Phosphate acetyltransferase, domain 2 / Phosphate acetyltransferase, domain 1 / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / Malic enzyme, conserved site / Malic enzymes signature. / Malic enzyme, N-terminal domain ...NAD(P)-dependent malic enzyme / Malic enzyme, NAD-binding domain, bacterial type / : / Phosphate acetyltransferase, domain 2 / Phosphate acetyltransferase, domain 1 / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / Malic enzyme, conserved site / Malic enzymes signature. / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain / Malic enzyme, NAD binding domain / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP-dependent malic enzyme
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsSassa M / Yamato H / Tanino H / Fukuda Y / Inoue T
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Malic enzymes from different bacteria evolved distinct effector binding sites showing the same allosteric regulation mechanism
Authors: Sassa M / Yamato H / Tanino H / Fukuda Y / Inoue T
History
DepositionNov 28, 2024-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62540.png

Downloads & links

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Map

FileDownload / File: emd_62540.map.gz / Format: CCP4 / Size: 512 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 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.2039464 - 1.935817
Average (Standard dev.)-0.0000908331 (±0.03269267)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62540_msk_1.map
Projections & Slices
AxesZYX

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Mask #2

Fileemd_62540_msk_2.map
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Mask #3

Fileemd_62540_msk_3.map
Projections & Slices
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Half map: #2

Fileemd_62540_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_62540_half_map_2.map
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Sample components

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Entire : Malic enzyme B from Escherichia coli holo form

EntireName: Malic enzyme B from Escherichia coli holo form
Components
  • Complex: Malic enzyme B from Escherichia coli holo form
    • Protein or peptide: NADP-dependent malic enzyme
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Malic enzyme B from Escherichia coli holo form

SupramoleculeName: Malic enzyme B from Escherichia coli holo form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: NADP-dependent malic enzyme

MacromoleculeName: NADP-dependent malic enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 82.507266 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDDQLKQSAL DFHEFPVPGK IQVSPTKPLA TQRDLALAYS PGVAAPCLEI EKDPLKAYKY TARGNLVAVI SNGTAVLGLG NIGALAGKP VMEGKGVLFK KFAGIDVFDI EVDELDPDKF IEVVAALEPT FGGINLEDIK APECFYIEQK LRERMNIPVF H DDQHGTAI ...String:
MDDQLKQSAL DFHEFPVPGK IQVSPTKPLA TQRDLALAYS PGVAAPCLEI EKDPLKAYKY TARGNLVAVI SNGTAVLGLG NIGALAGKP VMEGKGVLFK KFAGIDVFDI EVDELDPDKF IEVVAALEPT FGGINLEDIK APECFYIEQK LRERMNIPVF H DDQHGTAI ISTAAILNGL RVVEKNISDV RMVVSGAGAA AIACMNLLVA LGLQKHNIVV CDSKGVIYQG REPNMAETKA AY AVVDDGK RTLDDVIEGA DIFLGCSGPK VLTQEMVKKM ARAPMILALA NPEPEILPPL AKEVRPDAII CTGRSDYPNQ VNN VLCFPF IFRGALDVGA TAINEEMKLA AVRAIAELAH AEQSEVVASA YGDQDLSFGP EYIIPKPFDP RLIVKIAPAV AKAA MESGV ATRPIADFDV YIDKLTEFVY KTNLFMKPIF SQARKAPKRV VLPEGEEARV LHATQELVTL GLAKPILIGR PNVIE MRIQ KLGLQIKAGV DFEIVNNESD PRFKEYWTEY FQIMKRRGVT QEQAQRALIS NPTVIGAIMV QRGEADAMIC GTVGDY HEH FSVVKNVFGY RDGVHTAGAM NALLLPSGNT FIADTYVNDE PDAEELAEIT LMAAETVRRF GIEPRVALLS HSNFGSS DC PSSSKMRQAL ELVRERAPEL MIDGEMHGDA ALVEAIRNDR MPDSSLKGSA NILVMPNMEA ARISYNLLRV SSSEGVTV G PVLMGVAKPV HVLTPIASVR RIVNMVALAV VEAQTQPL

UniProtKB: NADP-dependent malic enzyme

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Macromolecule #2: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: NAP
Molecular weightTheoretical: 743.405 Da
Chemical component information

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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
Component:
ConcentrationFormulaName
1.0 mMMgCl2sodium magnesium
3.0 mMNADP+nicotinamide adenine dinucleotide phosphate
20.0 mMHEPES
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.007 kPa / Details: 20 mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: 3 microliters droplet, 3 seconds delay before blotting, 3 seconds blot, 0 second delay before plunging..

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7099 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: OTHER
Details: The crystal structure of E. coli MaeB apo form was used as a startup model.
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 125475
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: UCSF Chimera
Output model

PDB-9krt:
E. coli MaeB holo form

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