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- EMDB-23000: ClpP from Neisseria meningitidis - Compressed conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-23000
TitleClpP from Neisseria meningitidis - Compressed conformation
Map dataNmClpP compressed conformation
Sample
  • Complex: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
Function / homology
Function and homology information


ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsRipstein ZA / Vahidi S / Rubinstein JL / Kay LE
Funding support Canada, 3 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-503573 Canada
Canadian Institutes of Health Research (CIHR)PJT-162186 Canada
Canadian Institutes of Health Research (CIHR)PJT-148564 Canada
CitationJournal: To Be Published
Title: A pH-Dependent Conformational Switch Controls N. meningitidis ClpP Protease Function
Authors: Ripstein ZR / Vahidi S / Rubinstein JL / Kay LE
History
DepositionNov 18, 2020-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateNov 24, 2021-
Current statusNov 24, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.23
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.23
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kr2
  • Surface level: 1.23
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23000.png

Downloads & links

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Map

FileDownload / File: emd_23000.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNmClpP compressed conformation
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 1.23 / Movie #1: 1.23
Minimum - Maximum-4.4218483 - 8.090347
Average (Standard dev.)0.015883278 (±0.23058555)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z271.360271.360271.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ260260260
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-4.4228.0900.016

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Supplemental data

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Sample components

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Entire : ATP-dependent Clp protease proteolytic subunit

EntireName: ATP-dependent Clp protease proteolytic subunit
Components
  • Complex: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit

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Supramolecule #1: ATP-dependent Clp protease proteolytic subunit

SupramoleculeName: ATP-dependent Clp protease proteolytic subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Neisseria meningitidis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: Bl21(DE3) / Recombinant plasmid: pet28a
Molecular weightTheoretical: 860 KDa

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Macromolecule #1: ATP-dependent Clp protease proteolytic subunit

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Neisseria meningitidis (bacteria)
Molecular weightTheoretical: 22.700902 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSFDNYLVPT VIEQSGRGER AFDIYSRLLK ERIVFLVGPV TDESANLVVA QLLFLESENP DKDIFFYINS PGGSVTAGMS IYDTMNFIK PDVSTLCLGQ AASMGAFLLS AGEKGKRFAL PNSRIMIHQP LISGGLGGQA SDIEIHAREL LKIKEKLNRL M AKHCDRDL ...String:
MSFDNYLVPT VIEQSGRGER AFDIYSRLLK ERIVFLVGPV TDESANLVVA QLLFLESENP DKDIFFYINS PGGSVTAGMS IYDTMNFIK PDVSTLCLGQ AASMGAFLLS AGEKGKRFAL PNSRIMIHQP LISGGLGGQA SDIEIHAREL LKIKEKLNRL M AKHCDRDL ADLERDTDRD NFMSAEEAKE YGLIDQILEN RASLQL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7
Component:
ConcentrationName
50.0 mMImidazole
100.0 mMPotassium Chloride
2.0 mMATPAdenosine triphosphate
2.0 mMMagnesium Chloride
GridModel: Homemade / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 30.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III / Details: Blotted for 15 seconds at an offset of -5 mm.
DetailsMono-disperse complexes

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 70.0 K / Max: 77.0 K
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3594 / Average exposure time: 60.0 sec. / Average electron dose: 43.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 2.10)
Startup modelType of model: OTHER / Details: ab initio model in cryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.10)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 2.10)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.10)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D7 (2x7 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.10) / Number images used: 742377

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Atomic model buiding 1

Initial modelPDB ID:

5dzk

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7kr2:
ClpP from Neisseria meningitidis - Compressed conformation

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