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- EMDB-37863: Cryo-EM structure of H. thermophilus GroEL-GroES bullet complex -

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Basic information

Entry
Database: EMDB / ID: EMD-37863
TitleCryo-EM structure of H. thermophilus GroEL-GroES bullet complex
Map data
Sample
  • Complex: H. thermophilus GroEL-GroES bullet complex
    • Complex: chaperonin GroEL
      • Protein or peptide: Chaperonin GroEL
    • Complex: co-chaperonin GroES
      • Protein or peptide: Co-chaperonin GroES
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: POTASSIUM ION
KeywordsChaperone / Chaperonin / ATPase / protein folding
Function / homology
Function and homology information


chaperonin ATPase / : / isomerase activity / protein folding chaperone / ATP-dependent protein folding chaperone / unfolded protein binding / protein-folding chaperone binding / protein refolding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily ...Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / 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 / GroES-like superfamily
Similarity search - Domain/homology
Co-chaperonin GroES / Chaperonin GroEL
Similarity search - Component
Biological speciesHydrogenobacter thermophilus TK-6 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsLiao Z / Gopalasingam CC / Kameya M / Gerle C / Shigematsu H / Ishii M / Arakawa T / Fushinobu S
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H00322 Japan
Japan Science and TechnologyJPMJSP2108 Japan
CitationJournal: Structure / Year: 2024
Title: Structural insights into thermophilic chaperonin complexes.
Authors: Zengwei Liao / Chai C Gopalasingam / Masafumi Kameya / Christoph Gerle / Hideki Shigematsu / Masaharu Ishii / Takatoshi Arakawa / Shinya Fushinobu /
Abstract: Group I chaperonins are dual heptamer protein complexes that play significant roles in protein homeostasis. The structure and function of the Escherichia coli chaperonin are well characterized. ...Group I chaperonins are dual heptamer protein complexes that play significant roles in protein homeostasis. The structure and function of the Escherichia coli chaperonin are well characterized. However, the dynamic properties of chaperonins, such as large ATPase-dependent conformational changes by binding of lid-like co-chaperonin GroES, have made structural analyses challenging, and our understanding of these changes during the turnover of chaperonin complex formation is limited. In this study, we used single-particle cryogenic electron microscopy to investigate the structures of GroES-bound chaperonin complexes from the thermophilic hydrogen-oxidizing bacteria Hydrogenophilus thermoluteolus and Hydrogenobacter thermophilus in the presence of ATP and AMP-PNP. We captured the structure of an intermediate state chaperonin complex, designated as an asymmetric football-shaped complex, and performed analyses to decipher the dynamic structural variations. Our structural analyses of inter- and intra-subunit communications revealed a unique mechanism of complex formation through the binding of a second GroES to a bullet-shaped complex.
History
DepositionOct 21, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37863.png

Downloads & links

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Map

FileDownload / File: emd_37863.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 512 pix.
= 385.024 Å		0.75 Å/pix.
x 512 pix.
= 385.024 Å		0.75 Å/pix.
x 512 pix.
= 385.024 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.752 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0549
Minimum - Maximum-0.18163256 - 0.58043927
Average (Standard dev.)0.0014323621 (±0.015908549)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 385.024 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37863_msk_1.map
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Additional map: #1

Fileemd_37863_additional_1.map
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Additional map: #2

Fileemd_37863_additional_2.map
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Half map: #1

Fileemd_37863_half_map_1.map
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Half map: #2

Fileemd_37863_half_map_2.map
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Sample components

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Entire : H. thermophilus GroEL-GroES bullet complex

EntireName: H. thermophilus GroEL-GroES bullet complex
Components
  • Complex: H. thermophilus GroEL-GroES bullet complex
    • Complex: chaperonin GroEL
      • Protein or peptide: Chaperonin GroEL
    • Complex: co-chaperonin GroES
      • Protein or peptide: Co-chaperonin GroES
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: POTASSIUM ION

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Supramolecule #1: H. thermophilus GroEL-GroES bullet complex

SupramoleculeName: H. thermophilus GroEL-GroES bullet complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Hydrogenobacter thermophilus TK-6 (bacteria)

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Supramolecule #2: chaperonin GroEL

SupramoleculeName: chaperonin GroEL / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

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Supramolecule #3: co-chaperonin GroES

SupramoleculeName: co-chaperonin GroES / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Macromolecule #1: Chaperonin GroEL

MacromoleculeName: Chaperonin GroEL / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: chaperonin ATPase
Source (natural)Organism: Hydrogenobacter thermophilus TK-6 (bacteria) / Strain: TK-6
Molecular weightTheoretical: 56.600918 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AAKKVIYGED ARARLKAGVD KLANAVKVTL GPRGREVIIE KKWGTPVVTK DGVTVAKEIE FKDPYENMGA QLVKEVASKT SDVAGDGTT TATVLAQAIF NEGLRAIASG ANPMDIKRGI DKAVETVVNE IKKLSIPVSG RKEIEQVATI SANNDATIGK I IADAMEAV ...String:
AAKKVIYGED ARARLKAGVD KLANAVKVTL GPRGREVIIE KKWGTPVVTK DGVTVAKEIE FKDPYENMGA QLVKEVASKT SDVAGDGTT TATVLAQAIF NEGLRAIASG ANPMDIKRGI DKAVETVVNE IKKLSIPVSG RKEIEQVATI SANNDATIGK I IADAMEAV GKDGVITVEE SKSAETTLET VQGMQFDRGY LSPYFVTNPD KMEAVLEDPF ILIYEKKISN VKDLLPVLEN VV RAGKPLL IIAEDVEAEA LATLVVNHIK GVIRACAVKA PGFGQRRKDY LQDIAILTGG TAITEELGIK LESVTLDMLG RAD KVIVDK DNTTIVGGKG SKEAIQARIE QIKRQILETT SDYDREKLQE RLAKLSGGVA IIRVGAATEA ELKEKKARVE DAVH ATKAA VEEGIVPGGG VALVRASEAL DNLKVDNADQ QLGIDIIKKA CRTPIRQIAA NSGFEGYVVL EKVLQLGKEK GKNWG FDAG VGDYKDMVEA GIIDPTKVVR VAIQNAASVA GTMLTAEALV AEIPE

UniProtKB: Chaperonin GroEL

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Macromolecule #2: Co-chaperonin GroES

MacromoleculeName: Co-chaperonin GroES / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Hydrogenobacter thermophilus TK-6 (bacteria) / Strain: TK-6
Molecular weightTheoretical: 10.440112 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
RLRPLYDKIV VKRMEEQEQK TPSGIIIPDT AKEKPQIGEV IAVGDGKLLS NGQIVSPKVK KGDKVVFNKY AGTEVELDGE KYLIMSEDE VLAVI

UniProtKB: Co-chaperonin GroES

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 14 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 14 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #5: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 7 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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

BufferpH: 7.4
Component:
ConcentrationName
20.0 mMHEPES
100.0 mMpotassium chloride
5.0 mMmagnesium chloride
2.0 mMadenylyl-imidodiphosphate
1.0 mMdithiothreitol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.007 kPa
Details: glow discharged at 7 Pa, 10 mA, 10 sec by a JEOL JEC-3000FC auto fine coater
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5650 / Average exposure time: 2.264 sec. / Average electron dose: 49.97 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 60000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 20238
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.3)

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Atomic model buiding 1

Initial modelPDB ID:

7pbj


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-8wux:
Cryo-EM structure of H. thermophilus GroEL-GroES bullet complex

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