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- PDB-8pvi: Structure of PaaZ determined by cryoEM at 100 keV -

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Basic information

Entry
Database: PDB / ID: 8pvi
TitleStructure of PaaZ determined by cryoEM at 100 keV
ComponentsBifunctional protein PaaZ
KeywordsHYDROLASE / substrate channeling / bi-functional enzyme / dehydrogenase
Function / homology
Function and homology information


3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase / oxepin-CoA hydrolase / hydrolase activity, acting on acid carbon-carbon bonds, in ketonic substances / ether hydrolase activity / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / phenylacetate catabolic process / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / enoyl-CoA hydratase activity / identical protein binding
Similarity search - Function
Phenylacetic acid degradation protein PaaN / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Bifunctional protein PaaZ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsMcMullan, G. / Naydenova, K. / Mihaylov, D. / Peet, M.J. / Wilson, H. / Yamashita, K. / Dickerson, J.L. / Chen, S. / Cannone, G. / Lee, Y. ...McMullan, G. / Naydenova, K. / Mihaylov, D. / Peet, M.J. / Wilson, H. / Yamashita, K. / Dickerson, J.L. / Chen, S. / Cannone, G. / Lee, Y. / Hutchings, K.A. / Gittins, O. / Sobhy, M. / Wells, T. / El-Gomati, M.M. / Dalby, J. / Meffert, M. / Schulze-Briese, C. / Henderson, R. / Russo, C.J.
Funding support United Kingdom, 6items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC UP 120117 United Kingdom
Medical Research Council (MRC, United Kingdom)MC U105184322 United Kingdom
Wellcome Trust220526/B/20/Z United Kingdom
Engineering and Physical Sciences Research CouncilR122522 United Kingdom
Innovate UK103806 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T003677/1 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structure determination by cryoEM at 100 keV.
Authors: Greg McMullan / Katerina Naydenova / Daniel Mihaylov / Keitaro Yamashita / Mathew J Peet / Hugh Wilson / Joshua L Dickerson / Shaoxia Chen / Giuseppe Cannone / Yang Lee / Katherine A ...Authors: Greg McMullan / Katerina Naydenova / Daniel Mihaylov / Keitaro Yamashita / Mathew J Peet / Hugh Wilson / Joshua L Dickerson / Shaoxia Chen / Giuseppe Cannone / Yang Lee / Katherine A Hutchings / Olivia Gittins / Mohamed A Sobhy / Torquil Wells / Mohamed M El-Gomati / Jason Dalby / Matthias Meffert / Clemens Schulze-Briese / Richard Henderson / Christopher J Russo /
Abstract: Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose- ...Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose-built instrument operating at 100 keV-including advances in electron optics, detection, and processing-that makes structure determination fast and simple at a fraction of current costs. The instrument attains its theoretical performance limits, allowing atomic resolution imaging of gold test specimens and biological molecular structure determination in hours. We demonstrate its capabilities by determining the structures of eleven different specimens, ranging in size from 140 kDa to 2 MDa, using a fraction of the data normally required. CryoEM with a microscope designed specifically for high-efficiency, on-the-spot imaging of biological molecules will expand structural biology to a wide range of previously intractable problems.
History
DepositionJul 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional protein PaaZ


Theoretical massNumber of molelcules
Total (without water)73,9691
Polymers73,9691
Non-polymers00
Water00
1
A: Bifunctional protein PaaZ
x 6


Theoretical massNumber of molelcules
Total (without water)443,8166
Polymers443,8166
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-0.5, -0.866025404), (0.866025404, -0.5), (1)313.261763, 83.9382365
3generate(-0.5, 0.866025404), (-0.866025404, -0.5), (1)83.9382365, 313.261763
4generate(1), (-1, -1.2246468E-16), (1.2246468E-16, -1)264.8, 264.8
5generate(-0.5, 0.866025404, 1.06057524E-16), (0.866025404, 0.5, -6.123234E-17), (-1.06057524E-16, 6.123234E-17, -1)83.9382365, -48.4617635, 264.8
6generate(-0.5, -0.866025404, 1.06057524E-16), (-0.866025404, 0.5, 6.123234E-17), (-1.06057524E-16, -6.123234E-17, -1)313.261763, 180.861763, 264.8

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Components

#1: Protein Bifunctional protein PaaZ


Mass: 73969.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: paaZ, maoC, ydbN, b1387, JW1382 / Production host: Escherichia coli (E. coli)
References: UniProt: P77455, oxepin-CoA hydrolase, 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Phenylacetic acid enzyme Z (PaaZ) from E. coli / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 1400/HR + YPS FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingElectron dose: 80 e/Å2 / Film or detector model: DECTRIS SINGLA (1k x 1k)
Image scansSampling size: 75 µm / Width: 1030 / Height: 1066

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Processing

EM softwareName: Servalcat / Version: 0.4.27 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23716 / Symmetry type: POINT
Atomic model buildingSpace: RECIPROCAL
Atomic model buildingPDB-ID: 6jql

6jql


Accession code: 6jql / Source name: PDB / Type: experimental model

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