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- PDB-7xde: Cryo-EM structures of human mitochondrial NAD(P)+-dependent malic... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xde | |||||||||
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Title | Cryo-EM structures of human mitochondrial NAD(P)+-dependent malic enzyme in apo form | |||||||||
![]() | NAD-dependent malic enzyme, mitochondrial | |||||||||
![]() | HYDROLASE / Human mitochondrial NAD(P)+-dependent malic enzyme (ME2) | |||||||||
Function / homology | ![]() 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 / Citric acid cycle (TCA cycle) / malate metabolic process / pyruvate metabolic process / 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 / Citric acid cycle (TCA cycle) / malate metabolic process / pyruvate metabolic process / Mitochondrial protein degradation / NAD binding / electron transfer activity / mitochondrial matrix / intracellular membrane-bounded organelle / mitochondrion / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 Å | |||||||||
![]() | Wang, C.H. / Hsieh, J.T. / Ho, M.C. / Hung, H.C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Suppression of the human malic enzyme 2 modifies energy metabolism and inhibits cellular respiration Authors: Hsieh, J.Y. / Chen, K.C. / Wang, C.H. / Liu, G.Y. / Ye, J.A. / Chou, Y.T. / Lin, Y.C. / Lyu, C.J. / Chang, R.Y. / Liu, Y.L. / Li, Y.H. / Lee, M.R. / Ho, M.C. / Hung, H.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 384.8 KB | Display | ![]() |
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PDB format | ![]() | 320.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 74.9 KB | Display | |
Data in CIF | ![]() | 108 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 33145MC ![]() 7xdfC ![]() 7xdgC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 65521.434 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P23368, malate dehydrogenase (oxaloacetate-decarboxylating) #2: Chemical | ChemComp-NAD / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: human mitochondrial NAD(P)+-dependent malic enzyme in apo form Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90061 / Symmetry type: POINT |