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Yorodumi- EMDB-6727: Folding intermediate of RuBisCO in complex with the GroEL chapero... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6727 | |||||||||
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Title | Folding intermediate of RuBisCO in complex with the GroEL chaperonin. Class3. | |||||||||
Map data | Folding intermediate of RuBisCO in complex with the GroEL chaperonin. Class3. | |||||||||
Sample |
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Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.0 Å | |||||||||
Authors | Natesh R / Clare DK / Farr GW / Horwich AL / Saibil HR | |||||||||
Citation | Journal: Int J Biol Macromol / Year: 2018 Title: A two-domain folding intermediate of RuBisCO in complex with the GroEL chaperonin. Authors: Ramanathan Natesh / Daniel K Clare / George W Farr / Arthur L Horwich / Helen R Saibil / Abstract: The chaperonins (GroEL and GroES in Escherichia coli) are ubiquitous molecular chaperones that assist a subset of essential substrate proteins to undergo productive folding to the native state. Using ...The chaperonins (GroEL and GroES in Escherichia coli) are ubiquitous molecular chaperones that assist a subset of essential substrate proteins to undergo productive folding to the native state. Using single particle cryo EM and image processing we have examined complexes of E. coli GroEL with the stringently GroE-dependent substrate enzyme RuBisCO from Rhodospirillum rubrum. Here we present snapshots of non-native RuBisCO - GroEL complexes. We observe two distinct substrate densities in the binary complex reminiscent of the two-domain structure of the RuBisCO subunit, so that this may represent a captured form of an early folding intermediate. The occupancy of the complex is consistent with the negative cooperativity of GroEL with respect to substrate binding, in accordance with earlier mass spectroscopy studies. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6727.map.gz | 1.9 MB | EMDB map data format | |
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Header (meta data) | emd-6727-v30.xml emd-6727.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
Images | emd_6727.png | 90.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6727 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6727 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6727.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Folding intermediate of RuBisCO in complex with the GroEL chaperonin. Class3. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Non-native RuBisCO in complex with chaperonin GroEL
Entire | Name: Non-native RuBisCO in complex with chaperonin GroEL |
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Components |
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-Supramolecule #1: Non-native RuBisCO in complex with chaperonin GroEL
Supramolecule | Name: Non-native RuBisCO in complex with chaperonin GroEL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Apo GroEL.D473C.His6 with unbound RuBisCO folding intermediate as seen in 3D reconstruction for Class3. Only GroEL region was observed in EM map. |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 812 KDa |
-Macromolecule #1: GroEL
Macromolecule | Name: GroEL / type: protein_or_peptide / ID: 1 / Details: GroEL.D473C.His6 Tetradecamer / Enantiomer: LEVO / EC number: ec: 3.6.4.9 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: AAKDVKFGND AGVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREIE LEDKFENMGA QMVKEVASKA NDAAGDGTTT ATVLAQAIIT EGLKAVAAGM NPMDLKRGID KAVTVAVEEL KALSVPCSDS KAIAQVGTIS ANSDETVGKL IAEAMDKVGK ...String: AAKDVKFGND AGVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREIE LEDKFENMGA QMVKEVASKA NDAAGDGTTT ATVLAQAIIT EGLKAVAAGM NPMDLKRGID KAVTVAVEEL KALSVPCSDS KAIAQVGTIS ANSDETVGKL IAEAMDKVGK EGVITVEDGT GLQDELDVVE GMQFDRGYLS PYFINKPETG AVELESPFIL LADKKISNIR EMLPVLEAVA KAGKPLLIIA EDVEGEALAT AVVNTIRGIV KVAAVKAPGF GDRRKAMLQD IATLTGGTVI SEEIGMELEK ATLEDLGQAK RVVINKDTTT IIDGVGEEAA IQGRVAQIRQ QIEEATSDYD REKLQERVAK LAGGVAVIKV GAATEVEMKE KKARVEDALH ATRAAVEEGV VAGGGVALIR VASKLADLRG QNEDQNVGIK VALRAMEAPL RQIVLNCGEE PSVVANTVKG GCGNYGYNAA TEEYGNMIDM GILDPTKVTR SALQYAASVA GLMITTECMV TDLP |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.0863 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
Details: Folding Buffer (FB) consists of 50 mM HEPES pH7.5, 10 mM KOAc, 10 mM Mg(OAc)2, 10 mM DTT. RuBisCO denatured in 20mM HCl, 10 M Urea, 20 mM DTT | |||||||||||||||
Grid | Model: Protochips Inc., USA / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR Details: The C-flat holey grids were coated with thin home made carbon film. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER / Details: Blot approx. 1 sec before plunging. Visual.. | |||||||||||||||
Details | RuBisCO denatured in acid urea was complexed with GroEL.D473C.His6 in Folding Buffer. This entry Class3 contains Apo GroEL and hence its real molecular weight would be be 0.812 M Da. Hence the real concentration of 1 uM would be actually 0.0812 mg/mL. |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 40.0 µm / Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Temperature | Min: 100.0 K / Max: 100.0 K |
Image recording | Film or detector model: KODAK SO-163 FILM / Digitization - Sampling interval: 7.0 µm / Number grids imaged: 11 / Number real images: 468 / Average exposure time: 1.0 sec. / Average electron dose: 10.0 e/Å2 Details: Images were collected on Kodak SO-163 Film. Dose was 10-15 e-/A2/sec. |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 15477 Details: 15477 particles were used in image processing after pruning bad particles in the dataset. 3 classes were obtained. This reconstruction is class 3 with non-native RuBisCO un-bound to GroELD473C.His6. |
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CTF correction | Software - Name: ctffind3, label and spider / Details: CTF phase flipping was perfomed |
Startup model | Type of model: OTHER Details: An image of side view generated from a 30 A filtered empty GroEL EM map previously constructed within the lab. |
Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: IMAGIC / Details: ANCHOR SET |
Final 3D classification | Number classes: 3 / Avg.num./class: 5000 / Software - Name: IMAGIC Details: approximately 5000 in each class, with total 15477 particles in total. |
Final angle assignment | Type: PROJECTION MATCHING Projection matching processing - Number reference projections: 260 Projection matching processing - Merit function: CC Projection matching processing - Angular sampling: 2.0 degrees Software - Name: SPIDER |
Final reconstruction | Number classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER Details: In 3D reconstruction for Class 3: Resolution is 9 A for C7 symmetrised map after iteration cycle 7. Resolution is 11 A for asymmetric C1 reconstruction after iteration cycle 13. Number images used: 6003 |
Details | For the binary complex data sets, the positions of particles were noted in MRC programme XIMDISP. Perl script was used to extract particles in boxes of 512 x 512 pixels using the MRC program LABEL, and phase corrected using SPIDER. After CTF correction, the box size was cropped and sampling reduced so that all images were at 2.8 A per pixel in 196 x 196 pixel boxes. Images were band-pass filtered between 285 A and 6 A and normalized to zero mean and the same sigma in SPIDER. |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Residue range: 2-525 |
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Details | Rigid body fit |
Refinement | Protocol: RIGID BODY FIT |