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- EMDB-33147: Cryo-EM structures of human mitochondrial NAD(P)+-dependent malic... -

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Basic information

Entry
Database: EMDB / ID: EMD-33147
TitleCryo-EM structures of human mitochondrial NAD(P)+-dependent malic enzyme in a ternary complex with NAD+ and allosteric inhibitor MDSA
Map dataME2-MDSA Full Map
Sample
  • Complex: human mitochondrial NAD(P)+-dependent malic enzyme in apo form
    • Protein or peptide: NAD-dependent malic enzyme, mitochondrial
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: 5-[(3-carboxy-4-oxidanyl-phenyl)methyl]-2-oxidanyl-benzoic acid
KeywordsHuman mitochondrial NAD(P)+-dependent malic enzyme (ME2) / inhibitor / HYDROLASE
Function / homology
Function and homology information


malate dehydrogenase (oxaloacetate-decarboxylating) / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NAD+) activity / malic enzyme activity / malate dehydrogenase (decarboxylating) (NADP+) activity / oxaloacetate decarboxylase activity / malate metabolic process / pyruvate metabolic process / Pyruvate metabolism / Mitochondrial protein degradation ...malate dehydrogenase (oxaloacetate-decarboxylating) / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NAD+) activity / malic enzyme activity / malate dehydrogenase (decarboxylating) (NADP+) activity / oxaloacetate decarboxylase activity / malate metabolic process / pyruvate metabolic process / Pyruvate metabolism / Mitochondrial protein degradation / NAD binding / electron transfer activity / mitochondrial matrix / intracellular membrane-bounded organelle / mitochondrion / metal ion binding
Similarity search - Function
Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / 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 ...Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / 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
NAD-dependent malic enzyme, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsWang CH / Hsieh JT / Ho MC / Hung HC
Funding support Taiwan, 2 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Commun Biol / Year: 2023
Title: Suppression of the human malic enzyme 2 modifies energy metabolism and inhibits cellular respiration
Authors: Hsieh JY / Chen KC / Wang CH / Liu GY / Ye JA / Chou YT / Lin YC / Lyu CJ / Chang RY / Liu YL / Li YH / Lee MR / Ho MC / Hung HC
History
DepositionMar 27, 2022-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33147.png

Downloads & links

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Map

FileDownload / File: emd_33147.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationME2-MDSA Full Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.5470989 - 2.6386578
Average (Standard dev.)0.0018817984 (±0.064114206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: ME2-MDSA Half Map 1

Fileemd_33147_half_map_1.map
AnnotationME2-MDSA Half Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ME2-MDSA Half Map 2

Fileemd_33147_half_map_2.map
AnnotationME2-MDSA Half Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human mitochondrial NAD(P)+-dependent malic enzyme in apo form

EntireName: human mitochondrial NAD(P)+-dependent malic enzyme in apo form
Components
  • Complex: human mitochondrial NAD(P)+-dependent malic enzyme in apo form
    • Protein or peptide: NAD-dependent malic enzyme, mitochondrial
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: 5-[(3-carboxy-4-oxidanyl-phenyl)methyl]-2-oxidanyl-benzoic acid

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Supramolecule #1: human mitochondrial NAD(P)+-dependent malic enzyme in apo form

SupramoleculeName: human mitochondrial NAD(P)+-dependent malic enzyme in apo form
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: NAD-dependent malic enzyme, mitochondrial

MacromoleculeName: NAD-dependent malic enzyme, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: malate dehydrogenase (oxaloacetate-decarboxylating)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.521434 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLSRLRVVST TCTLACRHLH IKEKGKPLML NPRTNKGMAF TLQERQMLGL QGLLPPKIET QDIQALRFHR NLKKMTSPLE KYIYIMGIQ ERNEKLFYRI LQDDIESLMP IVYTPTVGLA CSQYGHIFRR PKGLFISISD RGHVRSIVDN WPENHVKAVV V TDGERILG ...String:
MLSRLRVVST TCTLACRHLH IKEKGKPLML NPRTNKGMAF TLQERQMLGL QGLLPPKIET QDIQALRFHR NLKKMTSPLE KYIYIMGIQ ERNEKLFYRI LQDDIESLMP IVYTPTVGLA CSQYGHIFRR PKGLFISISD RGHVRSIVDN WPENHVKAVV V TDGERILG LGDLGVYGMG IPVGKLCLYT ACAGIRPDRC LPVCIDVGTD NIALLKDPFY MGLYQKRDRT QQYDDLIDEF MK AITDRYG RNTLIQFEDF GNHNAFRFLR KYREKYCTFN DDIQGTAAVA LAGLLAAQKV ISKPISEHKI LFLGAGEAAL GIA NLIVMS MVENGLSEQE AQKKIWMFDK YGLLVKGRKA KIDSYQEPFT HSAPESIPDT FEDAVNILKP STIIGVAGAG RLFT PDVIR AMASINERPV IFALSNPTAQ AECTAEEAYT LTEGRCLFAS GSPFGPVKLT DGRVFTPGQG NNVYIFPGVA LAVIL CNTR HISDSVFLEA AKALTSQLTD EELAQGRLYP PLANIQEVSI NIAIKVTEYL YANKMAFRYP EPEDKAKYVK ERTWRS EYD SLLPDVYEWP ESASSPPVIT E

UniProtKB: NAD-dependent malic enzyme, mitochondrial

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Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 8 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

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Macromolecule #3: 5-[(3-carboxy-4-oxidanyl-phenyl)methyl]-2-oxidanyl-benzoic acid

MacromoleculeName: 5-[(3-carboxy-4-oxidanyl-phenyl)methyl]-2-oxidanyl-benzoic acid
type: ligand / ID: 3 / Number of copies: 4 / Formula: D5S
Molecular weightTheoretical: 288.252 Da
Chemical component information

ChemComp-D5S:
5-[(3-carboxy-4-oxidanyl-phenyl)methyl]-2-oxidanyl-benzoic acid

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44386
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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