[English] 日本語
Yorodumi
- EMDB-3486: Substrate specificity in plant nitrilase helical assemblies is de... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3486
TitleSubstrate specificity in plant nitrilase helical assemblies is determined by their twist.
Map dataArabidopsis thaliana NITRILASE 1 filament
Sample
  • Complex: Arabidopsis thaliana NITRILASE 1 filament
    • Protein or peptide: NITRILASE 1
Biological speciesArabidopsis thaliana (thale cress)
Methodhelical reconstruction / negative staining / Resolution: 20.0 Å
AuthorsWoodward JD / Trompetter I / Sewell BT / Piotrowski M
CitationJournal: Commun Biol / Year: 2018
Title: Substrate specificity of plant nitrilase complexes is affected by their helical twist.
Authors: Jeremy D Woodward / Inga Trompetter / B Trevor Sewell / Markus Piotrowski /
Abstract: Nitrilases are oligomeric, helix-forming enzymes from plants, fungi and bacteria that are involved in the metabolism of various natural and artificial nitriles. These biotechnologically important ...Nitrilases are oligomeric, helix-forming enzymes from plants, fungi and bacteria that are involved in the metabolism of various natural and artificial nitriles. These biotechnologically important enzymes are often specific for certain substrates, but directed attempts at modifying their substrate specificities by exchanging binding pocket residues have been largely unsuccessful. Thus, the basis for their selectivity is still unknown. Here we show, based on work with two highly similar nitrilases from the plant , that modifying nitrilase helical twist, either by exchanging an interface residue or by imposing a different twist, without altering any binding pocket residues, changes substrate preference. We reveal that helical twist and substrate size correlate and when binding pocket residues are exchanged between two nitrilases that show the same twist but different specificities, their specificities change. Based on these findings we propose that helical twist influences the overall size of the binding pocket.
History
DepositionNov 11, 2016-
Header (metadata) releaseDec 14, 2016-
Map releaseJan 17, 2018-
UpdateNov 14, 2018-
Current statusNov 14, 2018Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0333
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0333
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3486.png

Downloads & links

-
Map

FileDownload / File: emd_3486.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationArabidopsis thaliana NITRILASE 1 filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.22 Å/pix.
x 64 pix.
= 270.08 Å		4.22 Å/pix.
x 64 pix.
= 270.08 Å		4.22 Å/pix.
x 64 pix.
= 270.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.22 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0333 / Movie #1: 0.0333
Minimum - Maximum-0.06635013 - 0.12902926
Average (Standard dev.)0.0029505903 (±0.021580728)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-32-32-32
Dimensions646464
Spacing646464
CellA=B=C: 270.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.224.224.22
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z270.080270.080270.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-0.0660.1290.003

-
Supplemental data

-
Sample components

-
Entire : Arabidopsis thaliana NITRILASE 1 filament

EntireName: Arabidopsis thaliana NITRILASE 1 filament
Components
  • Complex: Arabidopsis thaliana NITRILASE 1 filament
    • Protein or peptide: NITRILASE 1

-
Supramolecule #1: Arabidopsis thaliana NITRILASE 1 filament

SupramoleculeName: Arabidopsis thaliana NITRILASE 1 filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: Columbia
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET21-b(+)
Molecular weightTheoretical: 27 kDa/nm

-
Macromolecule #1: NITRILASE 1

MacromoleculeName: NITRILASE 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: nitrilase
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: Columbia
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSSTKDMSTV QNATPFNGVA PSTTVRVTIV QSSTVYNDTP ATIDKAEKYI VEAASKGAEL VLFPEGFIGG YPRGFRFGLA VGVHNEEGRD EFRKYHASAI HVPGPEVARL ADVARKNHVY LVMGAIEKEG YTLYCTVLFF SPQGQFLGKH RKLMPTSLER CIWGQGDGST ...String:
MSSTKDMSTV QNATPFNGVA PSTTVRVTIV QSSTVYNDTP ATIDKAEKYI VEAASKGAEL VLFPEGFIGG YPRGFRFGLA VGVHNEEGRD EFRKYHASAI HVPGPEVARL ADVARKNHVY LVMGAIEKEG YTLYCTVLFF SPQGQFLGKH RKLMPTSLER CIWGQGDGST IPVYDTPIGK LGAAICWENR MPLYRTALYA KGIELYCAPT ADGSKEWQSS MLHIAIEGGC FVLSACQFCQ RKHFPDHPDY LFTDWYDDKE HDSIVSQGGS VIISPLGQVL AGPNFESEGL VTADIDLGDI ARAKLYFDSV GHYSRPDVLH LTVNEHPRKS VTFVTKVEKA EDDSNK

-
Experimental details

-
Structure determination

Methodnegative staining
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
50.0 mMC4H11NO3TRIS-Hcl
StainingType: NEGATIVE / Material: Uranyl Acetate
Details: The protein was allowed to adhere for 30 s, blotted, washed three-times with distilled water and stained with uranyl acetate, blotted again and allowed to dry at room temperature.
GridModel: Grid-tech / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 20.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa

-
Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 31 / Average exposure time: 1.0 sec. / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 0.5 µm / Calibrated defocus min: 0.3 µm / Calibrated magnification: 50200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.2 mm / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: PHILIPS ROTATION HOLDER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

Final reconstructionNumber classes used: 90
Applied symmetry - Helical parameters - Δz: 14.0 Å
Applied symmetry - Helical parameters - Δ&Phi: -67 °
Applied symmetry - Helical parameters - Axial symmetry: D2 (2x2 fold dihedral)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER (ver. 11) / Software - details: IHRSR / Number images used: 1078
Segment selectionNumber selected: 1091 / Software - Name: EMAN / Software - details: Boxer / Details: Picked using Eman Boxer in helix mode
Startup modelType of model: INSILICO MODEL
In silico model: Featureless cylinder approximating the diameter of the filament.
Final angle assignmentType: NOT APPLICABLE / Software - Name: SPIDER (ver. 11) / Software - details: IHRSR

+
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