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- EMDB-20659: Cryo-EM structure of E. coli LonA S679A -

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Basic information

Entry
Database: EMDB / ID: EMD-20659
TitleCryo-EM structure of E. coli LonA S679A
Map datasharpened map
Sample
  • Complex: ATP-dependent protease LaEndopeptidase La
    • Protein or peptide: Lon proteaseLon protease family
Function / homology
Function and homology information


endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / response to X-ray / cellular response to heat / peptidase activity / response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity ...endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / response to X-ray / cellular response to heat / peptidase activity / response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / DNA binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Lon protease, bacterial / Lon protease, bacterial/eukaryotic-type / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. ...Lon protease, bacterial / Lon protease, bacterial/eukaryotic-type / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Lon protease / Lon protease
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBotos I / Lountos GT / Weimin W / Wlodawer A
Funding support United States, Russian Federation, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)HHSN261200800001E United States
Russian Foundation for Basic Research19-04-00646 Russian Federation
CitationJournal: Curr Res Struct Biol / Year: 2020
Title: Cryo-EM structure of substrate-free E. coli Lon protease provides insights into the dynamics of Lon machinery
Authors: Botos I / Lountos GT / Weimin W / Cherry S / Ghirlando R / Kudzhaev AM / Rotanova TV / de Val N / Tropea J / Gustchina A / Wlodawer A
History
DepositionAug 28, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseFeb 26, 2020-
UpdateFeb 26, 2020-
Current statusFeb 26, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6u5z
  • Surface level: 0.0048
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20659.png

Downloads & links

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Map

FileDownload / File: emd_20659.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Voxel sizeX=Y=Z: 0.848 Å
Density
Contour LevelBy AUTHOR: 0.0048 / Movie #1: 0.006
Minimum - Maximum-0.06279861 - 0.09925077
Average (Standard dev.)0.00000164301 (±0.0023003616)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8480.8480.848
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z271.360271.360271.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0630.0990.000

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Supplemental data

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Sample components

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Entire : ATP-dependent protease La

EntireName: ATP-dependent protease LaEndopeptidase La
Components
  • Complex: ATP-dependent protease LaEndopeptidase La
    • Protein or peptide: Lon proteaseLon protease family

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Supramolecule #1: ATP-dependent protease La

SupramoleculeName: ATP-dependent protease La / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: S679A mutant
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightExperimental: 87 KDa

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Macromolecule #1: Lon protease

MacromoleculeName: Lon protease / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: endopeptidase La
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 87.546266 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNPERSERIE IPVLPLRDVV VYPHMVIPLF VGREKSIRCL EAAMDHDKKI MLVAQKEAST DEPGVNDLFT VGTVASILQM LKLPDGTVK VLVEGLQRAR ISALSDNGEH FSAKAEYLES PTIDEREQEV LVRTAISQFE GYIKLNKKIP PEVLTSLNSI D DPARLADT ...String:
MNPERSERIE IPVLPLRDVV VYPHMVIPLF VGREKSIRCL EAAMDHDKKI MLVAQKEAST DEPGVNDLFT VGTVASILQM LKLPDGTVK VLVEGLQRAR ISALSDNGEH FSAKAEYLES PTIDEREQEV LVRTAISQFE GYIKLNKKIP PEVLTSLNSI D DPARLADT IAAHMPLKLA DKQSVLEMSD VNERLEYLMA MMESEIDLLQ VEKRIRNRVK KQMEKSQREY YLNEQMKAIQ KE LGEMDDA PDENEALKRK IDAAKMPKEA KEKAEAELQK LKMMSPMSAE ATVVRGYIDW MVQVPWNARS KVKKDLRQAQ EIL DTDHYG LERVKDRILE YLAVQSRVNK IKGPILCLVG PPGVGKTSLG QSIAKATGRK YVRMALGGVR DEAEIRGHRR TYIG SMPGK LIQKMAKVGV KNPLFLLDEI DKMSSDMRGD PASALLEVLD PEQNVAFSDH YLEVDYDLSD VMFVATSNSM NIPAP LLDR MEVIRLSGYT EDEKLNIAKR HLLPKQIERN ALKKGELTVD DSAIIGIIRY YTREAGVRGL EREISKLCRK AVKQLL LDK SLKHIEINGD NLHDYLGVQR FDYGRADNEN RVGQVTGLAW TEVGGDLLTI ETACVPGKGK LTYTGSLGEV MQESIQA AL TVVRARAEKL GINPDFYEKR DIHVHVPEGA TPKDGPAAGI AMCTALVSCL TGNPVRADVA MTGEITLRGQ VLPIGGLK E KLLAAHRGGI KTVLIPFENK RDLEEIPDNV IADLDIHPVK RIEEVLTLAL QNEPSGMQVV TAK

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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

Concentration1.0 mg/mL
BufferpH: 7.2
GridModel: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 889189
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 274765

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6u5z:
Cryo-EM structure of E. coli LonA S679A

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