[English] 日本語
Yorodumi
- PDB-7xdg: Cryo-EM structures of human mitochondrial NAD(P)+-dependent malic... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xdg
TitleCryo-EM structures of human mitochondrial NAD(P)+-dependent malic enzyme in a ternary complex with NAD+ and allosteric inhibitor MDSA
ComponentsNAD-dependent malic enzyme, mitochondrial
KeywordsHYDROLASE / Human mitochondrial NAD(P)+-dependent malic enzyme (ME2) / inhibitor
Function / homology
Function and homology information


malate dehydrogenase (oxaloacetate-decarboxylating) / malate dehydrogenase (decarboxylating) (NAD+) activity / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NADP+) activity / malic enzyme activity / oxaloacetate decarboxylase activity / malate metabolic process / Pyruvate metabolism / pyruvate metabolic process / Mitochondrial protein degradation ...malate dehydrogenase (oxaloacetate-decarboxylating) / malate dehydrogenase (decarboxylating) (NAD+) activity / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NADP+) activity / malic enzyme activity / oxaloacetate decarboxylase activity / malate metabolic process / Pyruvate metabolism / pyruvate metabolic process / 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
Chem-D5S / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD-dependent malic enzyme, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsWang, C.H. / Hsieh, J.T. / Ho, M.C. / Hung, H.C.
Funding support Taiwan, 2items
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, 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
DepositionMar 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD-dependent malic enzyme, mitochondrial
B: NAD-dependent malic enzyme, mitochondrial
C: NAD-dependent malic enzyme, mitochondrial
D: NAD-dependent malic enzyme, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,54616
Polymers262,0864
Non-polymers6,46012
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
NAD-dependent malic enzyme, mitochondrial / mitochondrial NAD(P)+-dependent malic enzyme / NAD-ME / Malic enzyme 2


Mass: 65521.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ME2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P23368, malate dehydrogenase (oxaloacetate-decarboxylating)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-D5S / 5-[(3-carboxy-4-oxidanyl-phenyl)methyl]-2-oxidanyl-benzoic acid / 5,5'-Methylenedisalicylic acid


Mass: 288.252 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H12O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: human mitochondrial NAD(P)+-dependent malic enzyme in apo form
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3300 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44386 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more