- PDB-7lvk: Cfr-modified 50S subunit from Escherichia coli -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 7lvk
Title
Cfr-modified 50S subunit from Escherichia coli
Components
(50S ribosomal protein ...) x 28
23S rRNA
5S rRNA
Keywords
RIBOSOME / Cfr-modified 50S subunit
Function / homology
Function and homology information
positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / regulation of cell growth / large ribosomal subunit / ribosome binding / transferase activity ...positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / regulation of cell growth / large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function
Ribosomal protein L25, short-form / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast ...Ribosomal protein L25, short-form / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / : / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L32p / Ribosomal protein L24 / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L2 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L2, conserved site / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L5, N-terminal / Ribosomal protein L5 Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL34 / 50S ribosomal protein L17 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL34 / 50S ribosomal protein L17 / 50S ribosomal protein L23 / Large ribosomal subunit protein bL25 / 50S ribosomal protein L35 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L29 / 50S ribosomal protein L14 / 50S ribosomal protein L24 / 50S ribosomal protein L5 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L30 / 50S ribosomal protein L33 / 50S ribosomal protein L21 / 50S ribosomal protein L13 / 50S ribosomal protein L32 / 50S ribosomal protein L9 / 50S ribosomal protein L19 / 50S ribosomal protein L16 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / 50S ribosomal protein L28 Similarity search - Component
Biological species
Escherichia coli (E. coli)
Method
ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: 50S ribosomal subunit was purified from E. coli MRE600 using modified version of previously published protocol (Mehta et al. 2012)
Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K Details: Blot Force 5 Blot Time 10sec Hum 95% Temperature 10C Waiting time 1 min
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Electron microscopy imaging
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
Microscopy
Model: FEI TITAN KRIOS
Electron gun
Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 130 K / Temperature (min): 86 K / Residual tilt: 10 mradians
Image recording
Average exposure time: 8 sec. / Electron dose: 80 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2055
Image scans
Sampling size: 5 µm / Width: 7676 / Height: 7420 / Movie frames/image: 80 / Used frames/image: 0-80
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Processing
EM software
ID
Name
Version
Category
2
SerialEM
imageacquisition
4
CTFFIND
CTFcorrection
10
cryoSPARC
initialEulerassignment
11
cisTEM
1.0.0
finalEulerassignment
13
cisTEM
1.0.0
3Dreconstruction
CTF correction
Details: Relion / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selection
Num. of particles selected: 162713
Symmetry
Point symmetry: C1 (asymmetric)
3D reconstruction
Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141549 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model building
Protocol: FLEXIBLE FIT / Space: REAL
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