[English] 日本語
Yorodumi- PDB-4upf: Assembly principles of the unique cage formed by the ATPase RavA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4upf | ||||||
---|---|---|---|---|---|---|---|
Title | Assembly principles of the unique cage formed by the ATPase RavA hexamer and the lysine decarboxylase LdcI decamer | ||||||
Components |
| ||||||
Keywords | LYASE/HYDROLASE / LYASE-HYDROLASE COMPLEX / LYSINE DECARBOXYLASE / AAA+ ATPASE / ACID STRESS RESPONSE | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI STR. K-12 SUBSTR. MG1655 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, D | ||||||
Authors | Malet, H. / Liu, K. / El Bakkouri, M. / Chan, S.W.S. / Effantin, G. / Bacia, M. / Houry, W.A. / Gutsche, I. | ||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4upf.cif.gz | 41.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4upf.ent.gz | 21.5 KB | Display | PDB format |
PDBx/mmJSON format | 4upf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4upf_validation.pdf.gz | 755.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4upf_full_validation.pdf.gz | 754.5 KB | Display | |
Data in XML | 4upf_validation.xml.gz | 16 KB | Display | |
Data in CIF | 4upf_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/4upf ftp://data.pdbj.org/pub/pdb/validation_reports/up/4upf | HTTPS FTP |
-Related structure data
Related structure data | 2681MC 2679C 4upbC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 81357.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI STR. K-12 SUBSTR. MG1655 (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): CF1693 SOURCE 7 / References: UniProt: P0A9H3, lysine decarboxylase |
---|---|
#2: Protein | Mass: 12619.461 Da / Num. of mol.: 1 / Fragment: LARA DOMAIN RESIDUES 329-440 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI STR. K-12 SUBSTR. MG1655 (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD PLYSS / References: UniProt: P31473, EC: 3.6.3.1 |
Sequence details | THE LARA DOMAIN (FROM GLN329 TO GLU440) WAS PCR AMPLIFIED FROM THE P11-RAVA PLASMID. THE PCR ...THE LARA DOMAIN (FROM GLN329 TO GLU440) WAS PCR AMPLIFIED FROM THE P11-RAVA PLASMID. THE PCR PRODUCT WAS DIGESTED WITH NDEI AND BAMHI (NEB) AND LIGATED INTO AN EMPTY P11 VECTOR TO PRODUCE P11-LARA. THE RESULTING CONSTRUCT HAS AN N-TERMINAL HIS6-TAG FOLLOWED BY A TOBACCO ETCH VIRUS (TEV) CUT SITE THAT LEAVES THE THREE RESIDUES GHM AT THE TERMINUS OF THE CONSTRUCT AFTER TEV CLEAVAGE. |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: COMPLEX BETWEEN A DECAMER OF INDUCIBLE LYSINE DECARBOXYLASE LDCI AND TEN LARA DOMAINS OF THE ATPASE RAVA Type: COMPLEX |
---|---|
Buffer solution | Name: 50MM MES PH 6.5, 100MM NACL, 0.2MM PLP, 1MM DTT, 0.01% GLUTARALDEHYDE pH: 6.5 Details: 50MM MES PH 6.5, 100MM NACL, 0.2MM PLP, 1MM DTT, 0.01% GLUTARALDEHYDE |
Specimen | Conc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: OTHER |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 91, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TECNAI F30 / Date: Sep 14, 2012 / Details: AUTOMATIC DATA ACQUISITION WITH FEI EPU SOFTWARE |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 51660 X / Calibrated magnification: 51660 X / Nominal defocus max: 2700 nm / Nominal defocus min: 1500 nm / Cs: 2 mm |
Specimen holder | Temperature: 91 K / Tilt angle max: 0 ° / Tilt angle min: -0.1 ° |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Image scans | Num. digital images: 911 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: PHASE FLIPPING | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D5 (2x5 fold dihedral) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Method: CROSS-COMMON LINE, PROJECTION MATCHING / Resolution: 7.5 Å / Num. of particles: 23540 / Nominal pixel size: 1.464 Å / Actual pixel size: 1.464 Å Details: CROSS-COMMON LINE, PROJECTION MATCHING SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2681. (DEPOSITION ID: 12595). Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: METHOD--FLEXIBLE FOR 3N75, RIGID FOR 3NBX REFINEMENT PROTOCOL--X-RAY | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 7.5 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 7.5 Å
|