[English] 日本語
Yorodumi
- EMDB-62541: B. bacteriovorus MaeB holo form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62541
TitleB. bacteriovorus MaeB holo form
Map data
Sample
  • Complex: Malic enzyme B from Bdellovibrio bacteriovorus strain SSB218315 holo form
    • Protein or peptide: NADP-dependent malic enzyme
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Keywordsoxidoreductase / cryo-EM / allostery / STRUCTURAL PROTEIN
Function / homology
Function and homology information


malic enzyme activity / malate metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / acyltransferase activity / NAD binding / metal ion binding
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, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding ...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, 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 speciesBdellovibrio bacteriovorus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 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

-
Structure visualization

Supplemental images

emd_62541.png

Downloads & links

-
Map

FileDownload / File: emd_62541.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: 0.12
Minimum - Maximum-0.5844707 - 0.8802654
Average (Standard dev.)-0.00009229396 (±0.015341877)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_62541_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_62541_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #3

Fileemd_62541_msk_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62541_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62541_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Malic enzyme B from Bdellovibrio bacteriovorus strain SSB218315 h...

EntireName: Malic enzyme B from Bdellovibrio bacteriovorus strain SSB218315 holo form
Components
  • Complex: Malic enzyme B from Bdellovibrio bacteriovorus strain SSB218315 holo form
    • Protein or peptide: NADP-dependent malic enzyme
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

-
Supramolecule #1: Malic enzyme B from Bdellovibrio bacteriovorus strain SSB218315 h...

SupramoleculeName: Malic enzyme B from Bdellovibrio bacteriovorus strain SSB218315 holo form
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bdellovibrio bacteriovorus (bacteria)

-
Macromolecule #1: NADP-dependent malic enzyme

MacromoleculeName: NADP-dependent malic enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bdellovibrio bacteriovorus (bacteria)
Molecular weightTheoretical: 84.36593 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: METKTETKTG TTNFDQEALL YHQQGKPGKI EVISSKPCAT EKDLSLAYSP GVAAPCKAIA KDPAKVYDYT AKGNLVAVIS NGTAVLGLG NIGPAAGKPV MEGKGILFKQ FAGIDVFDIE VAATDVDTFC NAVRVLEPTF GGINLEDIKA PECFEIEERL K KEMNIPVF ...String:
METKTETKTG TTNFDQEALL YHQQGKPGKI EVISSKPCAT EKDLSLAYSP GVAAPCKAIA KDPAKVYDYT AKGNLVAVIS NGTAVLGLG NIGPAAGKPV MEGKGILFKQ FAGIDVFDIE VAATDVDTFC NAVRVLEPTF GGINLEDIKA PECFEIEERL K KEMNIPVF HDDQHGTAIV SGAALLNACS ITNRKMEDMR IVVNGAGASA NSCAKIFIAL GARRENIIMC DSQGVIYKGR TA GMNKYKE YFASETEART LTEALRGADV FVGLSVAGAL TPEMLKDMAK DPIIFAMANP EPEITPDKAR AARPDAIIAT GRS DYPNQV NNVLGFPSIF RGALDTRSTQ INEEMKLAAV HALAKLARMD VPDKVSATYG GKSFKFGRDY LIPKPFDTRV LLWV APEVA KAAMKSGVAT RAIEDWDQYR ESLEAQQGPS KVFIRSAINR VHQNSEANGG ELPRIVFPEG TSTKVLKALA TLVEE RICQ PILLGYPERV KEKIKALDIP LLNDVQIVHP SSHPKYFSFV EKLYSLRQRK GINLGEAERL MADPNYFAAM MVNMGE ADG MVSGSSINYA DAVRPILQTI GTYKEGIPAG LNFVLLEDKF LVLADTTVNF NPSAEQCAQI ALQAAKIVEY FGIEPRV AM LSYSNFSGAE GTPRKMKKAA EIARTLRPDL MIEGDMQADT AVNPEIMERL FPFSGLKGGA NVLVFPNLES SNIAYKLI Q QIGKAEVIGP FLTGVRRSAN VLQRTTTVDG IVNSVVFTAL EAQFIKDALK ARGKK

UniProtKB: NADP-dependent malic enzyme

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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..

-
Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9099 / 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

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: INSILICO MODEL
In silico model: The AlphaFold3 predicted model was used as a startup model.
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 449060
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
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