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- PDB-4upb: Electron cryo-microscopy of the complex formed between the hexame... -

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Basic information

Entry
Database: PDB / ID: 4upb
TitleElectron cryo-microscopy of the complex formed between the hexameric ATPase RavA and the decameric inducible decarboxylase LdcI
Components
  • ATPASE RAVA
  • LYSINE DECARBOXYLASE, INDUCIBLE
KeywordsLYASE/HYDROLASE / LYASE-HYDROLASE COMPLEX / LYSINE DECARBOXYLASE / AAA+ ATPASE / BACTERIAL ACID STRESS
Function / homology
Function and homology information


lysine decarboxylase / lysine catabolic process / lysine decarboxylase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / guanosine tetraphosphate binding / ATP hydrolysis activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
: / ATPase, RavA, C-terminal / ATPase RavA / ATPase RavA-like, AAA lid domain / MoxR domain / ATPase RavA, LARA domain / ATPase RavA, LARA domain superfamily / ATPase, RavA, C-terminal / AAA lid domain / MoxR domain in the MoxR-vWA-beta-propeller ternary systems ...: / ATPase, RavA, C-terminal / ATPase RavA / ATPase RavA-like, AAA lid domain / MoxR domain / ATPase RavA, LARA domain / ATPase RavA, LARA domain superfamily / ATPase, RavA, C-terminal / AAA lid domain / MoxR domain in the MoxR-vWA-beta-propeller ternary systems / ATPase, RavA, LARA domain / Orn/Lys/Arg decarboxylase, N-terminal / Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal domain / Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site. / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal domain / AAA domain (dynein-related subfamily) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Inducible lysine decarboxylase / ATPase RavA
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E
AuthorsMalet, H. / Liu, K. / El Bakkouri, M. / Chan, S.W.S. / Effantin, G. / Bacia, M. / Houry, W.A. / Gutsche, I.
CitationJournal: Elife / Year: 2014
Title: Assembly principles of a unique cage formed by hexameric and decameric E. coli proteins.
Authors: Hélène Malet / Kaiyin Liu / Majida El Bakkouri / Sze Wah Samuel Chan / Gregory Effantin / Maria Bacia / Walid A Houry / Irina Gutsche /
Abstract: A 3.3 MDa macromolecular cage between two Escherichia coli proteins with seemingly incompatible symmetries-the hexameric AAA+ ATPase RavA and the decameric inducible lysine decarboxylase LdcI-is ...A 3.3 MDa macromolecular cage between two Escherichia coli proteins with seemingly incompatible symmetries-the hexameric AAA+ ATPase RavA and the decameric inducible lysine decarboxylase LdcI-is reconstructed by cryo-electron microscopy to 11 Å resolution. Combined with a 7.5 Å resolution reconstruction of the minimal complex between LdcI and the LdcI-binding domain of RavA, and the previously solved crystal structures of the individual components, this work enables to build a reliable pseudoatomic model of this unusual architecture and to identify conformational rearrangements and specific elements essential for complex formation. The design of the cage created via lateral interactions between five RavA rings is unique for the diverse AAA+ ATPase superfamily.
History
DepositionJun 15, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Jul 13, 2016Group: Derived calculations
Revision 1.3Aug 30, 2017Group: Data collection / Category: em_image_scans / em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.4May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: LYSINE DECARBOXYLASE, INDUCIBLE
B: LYSINE DECARBOXYLASE, INDUCIBLE
C: ATPASE RAVA
D: ATPASE RAVA
E: ATPASE RAVA


Theoretical massNumber of molelcules
Total (without water)332,6435
Polymers332,6435
Non-polymers00
Water00
1
A: LYSINE DECARBOXYLASE, INDUCIBLE
B: LYSINE DECARBOXYLASE, INDUCIBLE
C: ATPASE RAVA
D: ATPASE RAVA
E: ATPASE RAVA
x 10


Theoretical massNumber of molelcules
Total (without water)3,326,42550
Polymers3,326,42550
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation9
MethodPISA

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Components

#1: Protein LYSINE DECARBOXYLASE, INDUCIBLE / LDC / Coordinate model: Cα atoms only


Mass: 81357.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Variant: MG1655 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CF1693 / References: UniProt: P0A9H3, lysine decarboxylase
#2: Protein ATPASE RAVA / REGULATORY ATPASE VARIANT A / Coordinate model: Cα atoms only


Mass: 56642.836 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Variant: MG1655 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD PLYSS / References: UniProt: P31473, EC: 3.6.3.1

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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: LDCI-RAVA COMPLEX / Type: COMPLEX
Buffer solutionName: 25MM MES PH 6.5, 200MM NACL, 3MM ADP, 0.8MM PLP, 1MM DTT
pH: 6.5
Details: 25MM MES PH 6.5, 200MM NACL, 3MM ADP, 0.8MM PLP, 1MM DTT
SpecimenConc.: 0.94 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: OTHER
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Apr 8, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 59000 X / Nominal defocus max: 3300 nm / Nominal defocus min: 1300 nm / Cs: 2 mm
Specimen holderTemperature: 91 K / Tilt angle max: 0 ° / Tilt angle min: -0.1 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameVersionCategoryDetails
1CTFFIND3CTF correction
2Flex-EMmodel fitting
3EMANparticle selectionBOXER
4FPM3D reconstruction
5IMOD3D reconstruction
6PEET3D reconstruction
7SPIDER3D reconstruction
CTF correctionDetails: PHASE FLIPPING
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 11 Å / Num. of particles: 21265 / Nominal pixel size: 2.37 Å / Actual pixel size: 2.37 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2679. (DEPOSITION ID: 12571).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: ENERGY,CROSS-CORRELATION / Details: METHOD--FLEX-EM REFINEMENT PROTOCOL--X-RAY
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13N75

3n75

13N751PDBexperimental model
23N75

3n75

13N751PDBexperimental model
RefinementHighest resolution: 11 Å
Refinement stepCycle: LAST / Highest resolution: 11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2775 0 0 0 2775

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