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- EMDB-22186: Cryo-EM structure of octadecameric TF55 (beta-only) complex from ... -

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Basic information

Entry
Database: EMDB / ID: EMD-22186
TitleCryo-EM structure of octadecameric TF55 (beta-only) complex from S. solfataricus bound to ADP
Map dataTF55 (beta-only) complex from S. solfataricus bound to ADP
Sample
  • Complex: ADP-bound Octadecameric TF55 beta-subunit chaperonin
    • Protein or peptide: Thermosome subunit beta
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsChaperonin / Complex / CHAPERONE
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
Thermosome, archaeal / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
Thermosome subunit beta
Similarity search - Component
Biological speciesSaccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.19 Å
AuthorsZeng YC / Sobti M
Funding support Australia, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1159347 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1146403 Australia
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2021
Title: Structural analysis of the Sulfolobus solfataricus TF55β chaperonin by cryo-electron microscopy.
Authors: Yi Cheng Zeng / Meghna Sobti / Alastair G Stewart /
Abstract: Chaperonins are biomolecular complexes that assist in protein folding. Thermophilic factor 55 (TF55) is a group II chaperonin found in the archaeal genus Sulfolobus that has α, β and γ subunits. ...Chaperonins are biomolecular complexes that assist in protein folding. Thermophilic factor 55 (TF55) is a group II chaperonin found in the archaeal genus Sulfolobus that has α, β and γ subunits. Using cryo-electron microscopy, structures of the β-only complex of S. solfataricus TF55 (TF55β) were determined to 3.6-4.2 Å resolution. The structures of the TF55β complexes formed in the presence of ADP or ATP highlighted an open state in which nucleotide exchange can occur before progressing in the refolding cycle.
History
DepositionJun 18, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xhi
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6xhi
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22186.png

Downloads & links

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Map

FileDownload / File: emd_22186.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTF55 (beta-only) complex from S. solfataricus bound to ADP
Voxel sizeX=Y=Z: 0.98 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-1.5502678 - 2.4455507
Average (Standard dev.)-0.001637636 (±0.07484734)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 431.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.980.980.98
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z431.200431.200431.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-1.5502.446-0.002

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Supplemental data

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Sample components

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Entire : ADP-bound Octadecameric TF55 beta-subunit chaperonin

EntireName: ADP-bound Octadecameric TF55 beta-subunit chaperonin
Components
  • Complex: ADP-bound Octadecameric TF55 beta-subunit chaperonin
    • Protein or peptide: Thermosome subunit beta
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: ADP-bound Octadecameric TF55 beta-subunit chaperonin

SupramoleculeName: ADP-bound Octadecameric TF55 beta-subunit chaperonin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2
Molecular weightTheoretical: 1.08 MDa

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Macromolecule #1: Thermosome subunit beta

MacromoleculeName: Thermosome subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2
Molecular weightTheoretical: 60.035891 KDa
SequenceString: MATATVATTP EGIPVIILKE GSSRTYGKEA LRANIAAVKA IEEALKSTYG PRGMDKMLVD SLGDITITND GATILDKMDL QHPTGKLLV QIAKGQDEET ADGTKTAVIL AGELAKKAED LLYKEIHPTI IVSGYKKAEE IALKTIQEIA QPVTINDTDV L RKVALTSL ...String:
MATATVATTP EGIPVIILKE GSSRTYGKEA LRANIAAVKA IEEALKSTYG PRGMDKMLVD SLGDITITND GATILDKMDL QHPTGKLLV QIAKGQDEET ADGTKTAVIL AGELAKKAED LLYKEIHPTI IVSGYKKAEE IALKTIQEIA QPVTINDTDV L RKVALTSL GSKAVAGARE YLADLVVKAV AQVAELRGDK WYVDLDNVQI VKKHGGSVND TQLVYGIVVD KEVVHPGMPK RI ENAKIAL LDASLEVEKP ELDAEIRIND PTQMHKFLEE EENILKEKVD KIAATGANVV ICQKGIDEVA QHYLAKKGIL AVR RAKKSD LEKLARATGG RVISNIDELT SQDLGYAALV EERKVGEDKM VFVEGAKNPK SVSILIRGGL ERVVDETERA LRDA LGTVA DVIRDGRAVA GGGAVEIEIA KRLRKYAPQV GGKEQLAIEA YANAIEGLIM ILAENAGLDP IDKLMQLRSL HENET NKWY GLNLFTGNPE DMWKLGVIEP ALVKMNAVKA ATEAVTLVLR IDDIVAAGKK SGSEPSGKKE KDKEEKSSED

UniProtKB: Thermosome subunit beta

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration12 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris.HCl
2.0 mMMagnesium chlorideMgCl2
1.0 mMEDTAEthylenediaminetetraacetic acid
100.0 mMSodium chlorideNaClSodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: 3.5 uL drop with 5 s blotting.

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 1 / Number real images: 2321 / Average exposure time: 61.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 395079
Startup modelType of model: OTHER
Details: Stochastic Gradient Descent (ab initio reconstruction in cryoSPARC)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.12.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2.12.0)
Final reconstructionApplied symmetry - Point group: D9 (2x9 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12.0) / Number images used: 43528
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4xcd


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6xhi:
Cryo-EM structure of octadecameric TF55 (beta-only) complex from S. solfataricus bound to ADP

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