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FITTED COORDINATES FOR GROEL-ATP7-GROES CRYO-EM COMPLEX (EMD-1180)

by single particle reconstruction, at 7.7 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1180, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2c7c
TitleFITTED COORDINATES FOR GROEL-ATP7-GROES CRYO-EM COMPLEX (EMD-1180)
Descriptor60 KDA CHAPERONIN
10 KDA CHAPERONIN MOLECULE: GROES
PROTEIN CPN10
GROES PROTEIN
KeywordsCHAPERONE, ATP-BINDING, ATOMIC STRUCTURE FITTING, CELL CYCLE, CELL DIVISION, CHAPERONIN, NUCLEOTIDE-BINDING, PHOSPHORYLATION
AuthorsRanson, N.A., Clare, D.K., Farr, G.W., Houldershaw, D., Horwich, A.L., Saibil, H.R.
DateDeposition: 2005-11-22, Release: 2006-01-25
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1180, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-1180

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Article
Citation - primary
ArticleNat. Struct. Mol. Biol., Vol. 13, Issue 2, Page 147-52, Year 2006
TitleAllosteric signaling of ATP hydrolysis in GroEL-GroES complexes.
AuthorsNeil A Ranson, Daniel K Clare, George W Farr, David Houldershaw, Arthur L Horwich, Helen R Saibil
Astbury Centre for Structural Molecular Biology and Institute of Molecular & Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
KeywordsAdenosine Diphosphate (chemistry), Adenosine Triphosphate (metabolism), Allosteric Regulation, Chaperonin 10 (chemistry), Chaperonin 60 (chemistry), Cryoelectron Microscopy, Hydrolysis, Models, Molecular, Multiprotein Complexes (chemistry), Protein Binding, Protein Structure, Quaternary
LinksDOI: 10.1038/nsmb1046, PubMed: 16429154, PMC: PMC2871290
Components
ID 1 : GROEL, PROTEIN CPN60, GROEL PROTEIN
Image
Description60 KDA CHAPERONIN
Typepolypeptide(L)
Formula weight57261.059 Da
Number of molecules14
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI

LinksUniProt: P0A6F5, Sequence view
ID 2 : 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
Image
Description10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
Typepolypeptide(L)
Formula weight10401.031 Da
Number of molecules7
ID2
SourceMethod: Isolated from a genetically manipulated source
Gene: ID:562, ESCHERICHIA COLI
Host: ID:562, ESCHERICHIA COLI
LinksUniProt: P0A6F9, Sequence view
Sample
Assembly
Aggregation statePARTICLE
NameGROEL-ATP7-GROES
Buffer
Name12.5MM HEPES, 5MM KCL, 5MM MGCL2
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.5
Sample concentration1.0 mg/ml
Sample support
DetailsHOLEY CARBON
Vitrification
DetailsLIQUID ETHANE
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI F20
Electron gun
Accelerating voltage200 kV
Illumination modeLOW DOSE
Lens
ModeBRIGHT FIELD
MagnificationNominal: 50000 X
CsNominal: 2.0 mm
Nominal defocusMax: 3200 nm, Min: 1100 nm
Specimen holder
Temperature100 Kelvin
Detector
TypeKODAK SO-163 FILM
Image scans
Number digital images189
Processing
2D projection selection
Number of particles16281
Software nameSPIDER, IMAGIC
Single particle entity
Symmetry typeCYCLIC
3D reconstruction
CTF correction methodFULL CORRECTION ON 2D CLASS AVERAGES
DetailsRECIPROCAL SPACE FITTING OF SEVEN INDEPENDENT RIGID BODIES WITH URO. FITTED ENTITIES WERE GROEL EQUATORIAL (RESIDUES 3-136 AND 410-524), INTERMEDIATE (RESIDUES 137-192 AND 374-409) AND APICAL (RESIDUES 192-373) DOMAINS, PLUS A GROES SUBUNIT. THE MAP INTO WHICH THESE COORDINATES WERE FITTED IS AVAILABLE AT THE EMD (EMD-1180)
MethodPROJECTION MATCHING-BASED ANGULAR REFINEMENT OF MSA GENERATED CLASSES. ITERATIVE ALGEBRAIC RECONSTRUCTION IN SPIDER.
Nominal pixel size1.4 A/pix
Resolution7.7 A
3D fitting
MethodRECIPROCAL SPACE FITTING IN URO
Refine
Refine idELECTRON MICROSCOPY
Ls d res high7.70 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high7.70
Total atoms57946
Protein atoms57946
Download
PDB format
Allpdb2c7c.ent.gz
pdb2c7c.ent (uncompressed file)
Header onlypdb2c7c.ent.gz
mmCIF format
mmCIF2c7c.cif.gz
XML format
All2c7c.xml.gz
No-atom2c7c-noatom.xml.gz
Ext-atom2c7c-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.1 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 5.9 MB