[English] 日本語
Yorodumi
- EMDB-33146: Cryo-EM structures of human mitochondrial NAD(P)+-dependent malic... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33146
TitleCryo-EM structures of human mitochondrial NAD(P)+-dependent malic enzyme in a ternary complex with NAD+ and allosteric inhibitor EA
Map dataME2-EA Full Map
Sample
  • Complex: human mitochondrial NAD(P)+-dependent malic enzyme in a ternary complex with NAD+ and allosteric inhibitor EA
    • Protein or peptide: NAD-dependent malic enzyme, mitochondrial
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: 4-[(3-carboxy-2-oxidanyl-naphthalen-1-yl)methyl]-3-oxidanyl-naphthalene-2-carboxylic 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: 2.72 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-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33146.png

Downloads & links

-
Map

FileDownload / File: emd_33146.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationME2-EA 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: 0.7
Minimum - Maximum-1.9114475 - 3.6021388
Average (Standard dev.)0.0020906862 (±0.09504375)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: ME2-EA Half Map 1

Fileemd_33146_half_map_1.map
AnnotationME2-EA Half Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: ME2-EA Half Map 2

Fileemd_33146_half_map_2.map
AnnotationME2-EA Half Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : human mitochondrial NAD(P)+-dependent malic enzyme in a ternary c...

EntireName: human mitochondrial NAD(P)+-dependent malic enzyme in a ternary complex with NAD+ and allosteric inhibitor EA
Components
  • Complex: human mitochondrial NAD(P)+-dependent malic enzyme in a ternary complex with NAD+ and allosteric inhibitor EA
    • Protein or peptide: NAD-dependent malic enzyme, mitochondrial
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: 4-[(3-carboxy-2-oxidanyl-naphthalen-1-yl)methyl]-3-oxidanyl-naphthalene-2-carboxylic acid

-
Supramolecule #1: human mitochondrial NAD(P)+-dependent malic enzyme in a ternary c...

SupramoleculeName: human mitochondrial NAD(P)+-dependent malic enzyme in a ternary complex with NAD+ and allosteric inhibitor EA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
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

-
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

-
Macromolecule #3: 4-[(3-carboxy-2-oxidanyl-naphthalen-1-yl)methyl]-3-oxidanyl-napht...

MacromoleculeName: 4-[(3-carboxy-2-oxidanyl-naphthalen-1-yl)methyl]-3-oxidanyl-naphthalene-2-carboxylic acid
type: ligand / ID: 3 / Number of copies: 4 / Formula: JBR
Molecular weightTheoretical: 388.37 Da
Chemical component information

ChemComp-JBR:
4-[(3-carboxy-2-oxidanyl-naphthalen-1-yl)methyl]-3-oxidanyl-naphthalene-2-carboxylic acid

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75943
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

+
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