[English] 日本語
Yorodumi
- EMDB-79675: Cryo-EM structure of glutamate mutase from Carboxydothermus hydro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-79675
TitleCryo-EM structure of glutamate mutase from Carboxydothermus hydrogenoformans in the pre-activation state
Map data
Sample
  • Complex: glutamate mutase
    • Protein or peptide: Glutamate mutase epsilon subunit
    • Protein or peptide: Glutamate mutase sigma subunit
  • Ligand: 5'-DEOXYADENOSINE
  • Ligand: COBALAMIN
Keywordsisomerase / glutamate mutase / adenosylcobalamin / intact Co-C bond / pre-activation state / cryo-EM
Function / homology
Function and homology information


methylaspartate mutase / methylaspartate mutase activity / cobalamin binding / metal ion binding
Similarity search - Function
Glutamate mutase epsilon subunit / Glutamate mutase E subunit, C-terminal domain superfamily / Methylaspartate mutase E chain (MutE) / Glutamate mutase sigma subunit / Methylmalonyl-CoA mutase, C-terminal / Cobalamin (vitamin B12)-dependent enzyme, catalytic / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain
Similarity search - Domain/homology
Glutamate mutase epsilon subunit / Glutamate mutase sigma subunit
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhang XY / Tjia-Fleck SK / Tian SL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM155016 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of glutamate mutase from Carboxydothermus hydrogenoformans in the pre-activation state
Authors: Zhang XY / Tjia-Fleck SK / Tian SL
History
DepositionOct 20, 2026-
Header (metadata) releaseOct 28, 2026-
Map releaseOct 28, 2026-
UpdateOct 28, 2026-
Current statusOct 28, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_79675.png

Downloads & links

-
Map

FileDownload / File: emd_79675.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 200 pix.
= 211.6 Å		1.06 Å/pix.
x 200 pix.
= 211.6 Å		1.06 Å/pix.
x 200 pix.
= 211.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.72
Minimum - Maximum-25.490164 - 37.446064
Average (Standard dev.)-0.005918594 (±0.9874726)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 211.59999 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #3

Fileemd_79675_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #2

Fileemd_79675_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_79675_additional_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_79675_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_79675_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : glutamate mutase

EntireName: glutamate mutase
Components
  • Complex: glutamate mutase
    • Protein or peptide: Glutamate mutase epsilon subunit
    • Protein or peptide: Glutamate mutase sigma subunit
  • Ligand: 5'-DEOXYADENOSINE
  • Ligand: COBALAMIN

-
Supramolecule #1: glutamate mutase

SupramoleculeName: glutamate mutase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Carboxydothermus hydrogenoformans Z-2901 (bacteria)

-
Macromolecule #1: Glutamate mutase epsilon subunit

MacromoleculeName: Glutamate mutase epsilon subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: methylaspartate mutase
Source (natural)Organism: Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Molecular weightTheoretical: 53.632426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKGKIDLEKF LQSRKEVLAT WPTGAEVSLE DGINYHKALP PEKNFAVKLK KVKEEGITAI QPRAGVALLN EHIALLKYLE KEGEADFLP TTIDSYTRQN RYQEAQRGIE ESLAEGRSML NGFPAVNYGV YPCRKIIEEV NVPVQVRHGT PDARLLAEIT L AGGFSSFE ...String:
MKGKIDLEKF LQSRKEVLAT WPTGAEVSLE DGINYHKALP PEKNFAVKLK KVKEEGITAI QPRAGVALLN EHIALLKYLE KEGEADFLP TTIDSYTRQN RYQEAQRGIE ESLAEGRSML NGFPAVNYGV YPCRKIIEEV NVPVQVRHGT PDARLLAEIT L AGGFSSFE GGGITYNIPY AKEVPLRKSI EDWQYVDRLI GYYAEHGVLI NRESFGPLTG TLVPPSVTIA INILELLLAV EQ GVKSFTL GLGQCGNLNQ DVAALHGMVE LAEEYLKRFG FQDVDLTTVF HQWMGGFPQD EARAFAVIAW GAVAAALAKA NKV IVKTPH EALGVPTKEA NAQGLKTTRQ IVNMLKDQRF MVNEEYLLEK EMVKKEARAI VERTLELGEG DLVAGIERAF AAGV IDVPF APSRFNLGKI LPARDDTGAV RILEFGNLPF DSEIREFHRE RLKRRGEKEG REPSFQMVID DIYAIGKGML VGKPR TK

UniProtKB: Glutamate mutase epsilon subunit

-
Macromolecule #2: Glutamate mutase sigma subunit

MacromoleculeName: Glutamate mutase sigma subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: methylaspartate mutase
Source (natural)Organism: Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Molecular weightTheoretical: 14.886253 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKEVNLVLGV IGADVHAIGN KILEYALTNA GFKVHNLGVM VSQEEFVKAA LETDAKAVLV SSLYGHGEID CRGLKEKFIE AGLDDVLLY VGGNLVVGKQ DFSEVERKFK AMGFDRVFPP GTMPEEAIKA LKEDLGLM

UniProtKB: Glutamate mutase sigma subunit

-
Macromolecule #3: 5'-DEOXYADENOSINE

MacromoleculeName: 5'-DEOXYADENOSINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: 5AD
Molecular weightTheoretical: 251.242 Da
Chemical component information

ChemComp-5AD:
5'-DEOXYADENOSINE

-
Macromolecule #4: COBALAMIN

MacromoleculeName: COBALAMIN / type: ligand / ID: 4 / Number of copies: 1 / Formula: B12
Molecular weightTheoretical: 1.330356 KDa
Chemical component information

ChemComp-B12:
COBALAMIN

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX
Details: Two local refinements were performed in cryoSPARC using gold-standard half-set separation. Corresponding half-maps from the two local refinements were combined separately in Phenix to ...Details: Two local refinements were performed in cryoSPARC using gold-standard half-set separation. Corresponding half-maps from the two local refinements were combined separately in Phenix to generate the final combined half-map pair.
Number images used: 509882
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
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