[English] 日本語
Yorodumi
- EMDB-12740: Structure of the borneol dehydrogenase 1 of salvia rosmarinus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12740
TitleStructure of the borneol dehydrogenase 1 of salvia rosmarinus
Map data
Sample
  • Complex: Homotetrameric complex of borneol dehydrogenase
    • Protein or peptide: borneol dehydrogenase
  • Ligand: water
KeywordsTERPENOID / ALCOHOL / OXIDOREDUCTASE / BORNEOL / ROSSMANN-LIKE FOLD
Biological speciesSalvia rosmarinus (rosemary)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.88 Å
AuthorsDimos N / Helmer CPO
Funding support Germany, Austria, 6 items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research031B050B Germany
Austrian Science FundP31001-B29 Austria
German Research Foundation (DFG)INST 335/588-1 Germany
German Research Foundation (DFG)INST 335/589-1 Germany
German Research Foundation (DFG)INST 335/590-1 Germany
German Research Foundation (DFG)HA 2549/15-2 Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: CryoEM analysis of small plant biocatalysts at sub-2 Å resolution.
Authors: Nicole Dimos / Carl P O Helmer / Andrea M Chánique / Markus C Wahl / Robert Kourist / Tarek Hilal / Bernhard Loll /
Abstract: Enzyme catalysis has emerged as a key technology for developing efficient, sustainable processes in the chemical, biotechnological and pharmaceutical industries. Plants provide large and diverse ...Enzyme catalysis has emerged as a key technology for developing efficient, sustainable processes in the chemical, biotechnological and pharmaceutical industries. Plants provide large and diverse pools of biosynthetic enzymes that facilitate complex reactions, such as the formation of intricate terpene carbon skeletons, with exquisite specificity. High-resolution structural analysis of these enzymes is crucial in order to understand their mechanisms and modulate their properties by targeted engineering. Although cryo-electron microscopy (cryoEM) has revolutionized structural biology, its applicability to high-resolution structural analysis of comparatively small enzymes has so far been largely unexplored. Here, it is shown that cryoEM can reveal the structures of plant borneol dehydrogenases of ∼120 kDa at or below 2 Å resolution, paving the way for the rapid development of new biocatalysts that can provide access to bioactive terpenes and terpenoids.
History
DepositionApr 12, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7o6q
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12740.png

Downloads & links

-
Map

FileDownload / File: emd_12740.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 384 pix.
= 252.288 Å		0.66 Å/pix.
x 384 pix.
= 252.288 Å		0.66 Å/pix.
x 384 pix.
= 252.288 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.657 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.0 - 2.549999
Average (Standard dev.)0.004700717 (±0.041884605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 252.288 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6570.6570.657
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z252.288252.288252.288
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0002.5500.005

-
Supplemental data

-
Sample components

-
Entire : Homotetrameric complex of borneol dehydrogenase

EntireName: Homotetrameric complex of borneol dehydrogenase
Components
  • Complex: Homotetrameric complex of borneol dehydrogenase
    • Protein or peptide: borneol dehydrogenase
  • Ligand: water

-
Supramolecule #1: Homotetrameric complex of borneol dehydrogenase

SupramoleculeName: Homotetrameric complex of borneol dehydrogenase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Salvia rosmarinus (rosemary)

-
Macromolecule #1: borneol dehydrogenase

MacromoleculeName: borneol dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Salvia rosmarinus (rosemary)
Molecular weightTheoretical: 30.284529 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MSCNTAVSRR LEGKVAIVTG GASGIGASTV RLFHDHGAKV VIADIQDDLG QTLADRLGRN ISYTHCDVT DEDQVRALVD AAVAKHGGVD IMFSNAGIVE GPNSIFDVDK DELERLMGIN LVGAFLAAKH AARVMVPAKK G CIIFTASA ...String:
MGSSHHHHHH SSGLVPRGSH MSCNTAVSRR LEGKVAIVTG GASGIGASTV RLFHDHGAKV VIADIQDDLG QTLADRLGRN ISYTHCDVT DEDQVRALVD AAVAKHGGVD IMFSNAGIVE GPNSIFDVDK DELERLMGIN LVGAFLAAKH AARVMVPAKK G CIIFTASA CTEIAGIAGH SYTASKYGIV GLMKSLAVEL GSHGIRANCV SPFGVLTGIV PDDEASKLMF EGIMSKVGNL KG KILTAED VAVTVLYLAS EEASYVSGVN LLVDGGYTVV NPTFINVITA GQS

-
Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 399 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1666 / Average exposure time: 30.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1635690
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6zz0


Details: The structure was solved by placing the tetrameric crystal structure with the PDB ID 6ZZ0 in the density.
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 1.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.19) / Number images used: 210505
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 2.19)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.19)
Final 3D classificationSoftware - 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