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Atomic Model of Mm-cpn in the Closed State

by single particle reconstruction, at 4.3 A resolution

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#1: Deposited structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-5137, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3los
TitleAtomic Model of Mm-cpn in the Closed State
DescriptorChaperonin
KeywordsCHAPERONE, Group II chaperonin, Protein Folding, Mm-cpn, Single Particle Reconstruction, Methanococcus maripaludis, Chaperone, ATP-binding, Nucleotide-binding
AuthorsZhang, J., Baker, M.L., Schroeder, G., Douglas, N.R., Reissmann, S., Jakana, J., Dougherty, M., Fu, C.J., Levitt, M., Ludtke, S.J., Frydman, J., Chiu, W.
DateDeposition: 2010-02-04, Release: 2010-03-16
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-5137, Image by UCSF CHIMERA

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EMDB-5137

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Article
Citation - primary
ArticleNature, Vol. 463, Issue 7279, Page 379-83, Year 2010
TitleMechanism of folding chamber closure in a group II chaperonin.
AuthorsJunjie Zhang, Matthew L Baker, Gunnar F Schröder, Nicholai R Douglas, Stefanie Reissmann, Joanita Jakana, Matthew Dougherty, Caroline J Fu, Michael Levitt, Steven J Ludtke, Judith Frydman, Wah Chiu
Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.
KeywordsAdenosine Triphosphate (chemistry), Allosteric Regulation, Binding Sites, Cryoelectron Microscopy, Group II Chaperonins (chemistry, 3.6.1.-), Hydrolysis (drug effects), Methanococcus (chemistry), Models, Molecular, Protein Binding, Protein Conformation (drug effects), Protein Folding, Protein Subunits (chemistry), Structure-Activity Relationship
LinksDOI: 10.1038/nature08701, PubMed: 20090755, PMC: PMC2834796
Components
ID 1 : Chaperonin GroEL (Thermosome, HSP60 family)
Image
DescriptionChaperonin
Typepolypeptide(L)
Formula weight58290.793 Da
Number of molecules16
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: hsp60, MMP1515, ID:39152, Methanococcus maripaludis
Host: ID:562, Escherichia coli

LinksUniProt: Q877G8, Sequence view
Sample
Assembly
Aggregation statePARTICLE
Composition16-mer
Experimental Mass0.96
Theoretical Mass0.96
NameMm-cpn with 1mM ATP/AlFx
Num components1
Entity assembly
Assembly-ID1
NameMethanococcus maripaludis chaperonin
TypePROTEIN
Buffer
NameATPase buffer
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.5
Vitrification
Cryogen nameETHANE
Humidity100
InstrumentVitrobot
Method1 blot 3 seconds
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: JEM3200FSC
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose20 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 112000 X, Nominal: 80000 X
CsNominal: 4.1 mm
Astigmatismobjective lens astigmatism was corrected at 100,000 times magnification
Detector distance0.0
Nominal defocusMax: 3000 nm, Min: 1000 nm
Energy filterin column omega filter
Energy window0-10 eV
Specimen holder
Specimen holderModel: JEM3200FSC CRYOHOLDER, Type: side-entry
Tilt angleMin: 0.0 degrees, Max: 0.0 degrees
Temperature100 Kelvin
Detector
TypeGatan 4kX4k CCD Camera
Processing
Single particle entity
Symmetry typeDIHEDRAL
3D reconstruction
CTF correction methodEach micrograph
DetailsTHE SINGLE SUBUNIT MODEL OF MM-CPN WAS MANUALLY BUILT IN THE CRYO-EM DENSITY USING COOT. THE ENTIRE 16-SUBUNIT COMPLEX WAS GENERATED BASED ON THE D8 SYMMETRY.
MethodProjection-match
Resolution4.3 A
Resolution methodFSC at 0.5 cut-off
SoftwareEMAN
3D fitting
DetailsTHE SINGLE SUBUNIT MODEL OF MM-CPN WAS MANUALLY BUILT IN THE CRYO-EM DENSITY USING COOT. THE ENTIRE 16-SUBUNIT COMPLEX WAS GENERATED BASED ON THE D8 SYMMETRY.
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms63712
Protein atoms63712
Download
PDB format
Allpdb3los.ent.gz
pdb3los.ent (uncompressed file)
Header onlypdb3los.ent.gz
mmCIF format
mmCIF3los.cif.gz
XML format
All3los.xml.gz
No-atom3los-noatom.xml.gz
Ext-atom3los-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.7 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.7 MB