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- EMDB-32164: CryoEM structure of football-shaped GroEL:ES2 with RuBisCO -

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Basic information

Entry
Database: EMDB / ID: EMD-32164
TitleCryoEM structure of football-shaped GroEL:ES2 with RuBisCO
Map data
Sample
  • Complex: Football-shaped GroEL:ES complex encapsulating native-like folded substrate RuBisCO
    • Complex: Football-shaped GroEL:ES
      • Protein or peptide: Co-chaperonin GroES
      • Protein or peptide: Chaperonin GroEL
    • Complex: RuBisCO
      • Protein or peptide: Ribulose bisphosphate carboxylase
Keywordschaperone / GroEL/ES system / substrate folding / folding assistance
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / GroEL-GroES complex / reductive pentose-phosphate cycle / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / monooxygenase activity ...ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / GroEL-GroES complex / reductive pentose-phosphate cycle / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / monooxygenase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / protein-folding chaperone binding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / metal ion binding / cytosol
Similarity search - Function
Ribulose bisphosphate carboxylase large subunit, type II / Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal ...Ribulose bisphosphate carboxylase large subunit, type II / Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / 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
Chaperonin GroEL / Co-chaperonin GroES / Ribulose bisphosphate carboxylase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Rhodospirillum rubrum ATCC 11170 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.6 Å
AuthorsKim H / Roh SH
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: iScience / Year: 2022
Title: Cryo-EM structures of GroEL:ES with RuBisCO visualize molecular contacts of encapsulated substrates in a double-cage chaperonin.
Authors: Hyunmin Kim / Junsun Park / Seyeon Lim / Sung-Hoon Jun / Mingyu Jung / Soung-Hun Roh /
Abstract: The GroEL/GroES chaperonin system assists the folding of many proteins, through conformational transitions driven by ATP hydrolysis. Although structural information about bullet-shaped GroEL:ES ...The GroEL/GroES chaperonin system assists the folding of many proteins, through conformational transitions driven by ATP hydrolysis. Although structural information about bullet-shaped GroEL:ES complexes has been extensively reported, the substrate interactions of another functional complex, the football-shaped GroEL:ES, remain elusive. Here, we report single-particle cryo-EM structures of reconstituted wild-type GroEL:ES complexes with a chemically denatured substrate, ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO). Our structures demonstrate that native-like folded RuBisCO density is captured at the lower part of the GroEL chamber and that GroEL's bulky hydrophobic residues Phe281, Tyr360, and Phe44 contribute to direct contact with RuBisCO density. In addition, our analysis found that GroEL:ES can be occupied by two substrates simultaneously, one in each chamber. Together, these observations provide insights to the football-shaped GroEL:ES complex as a functional state to assist the substrate folding with visualization.
History
DepositionNov 12, 2021-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7vwx
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32164.png

Downloads & links

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Map

FileDownload / File: emd_32164.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.97 Å/pix.
x 200 pix.
= 394. Å		1.97 Å/pix.
x 200 pix.
= 394. Å		1.97 Å/pix.
x 200 pix.
= 394. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.663 / Movie #1: 0.9
Minimum - Maximum-1.6234943 - 3.768817
Average (Standard dev.)0.015195711 (±0.20375815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 394.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.971.971.97
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z394.000394.000394.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-1.6233.7690.015

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Supplemental data

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Additional map: #1

Fileemd_32164_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Football-shaped GroEL:ES complex encapsulating native-like folded...

EntireName: Football-shaped GroEL:ES complex encapsulating native-like folded substrate RuBisCO
Components
  • Complex: Football-shaped GroEL:ES complex encapsulating native-like folded substrate RuBisCO
    • Complex: Football-shaped GroEL:ES
      • Protein or peptide: Co-chaperonin GroES
      • Protein or peptide: Chaperonin GroEL
    • Complex: RuBisCO
      • Protein or peptide: Ribulose bisphosphate carboxylase

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Supramolecule #1: Football-shaped GroEL:ES complex encapsulating native-like folded...

SupramoleculeName: Football-shaped GroEL:ES complex encapsulating native-like folded substrate RuBisCO
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 1 MDa

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Supramolecule #2: Football-shaped GroEL:ES

SupramoleculeName: Football-shaped GroEL:ES / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Supramolecule #3: RuBisCO

SupramoleculeName: RuBisCO / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Rhodospirillum rubrum ATCC 11170 (bacteria)

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Macromolecule #1: Co-chaperonin GroES

MacromoleculeName: Co-chaperonin GroES / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 10.400938 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MNIRPLHDRV IVKRKEVETK SAGGIVLTGS AAAKSTRGEV LAVGNGRILE NGEVKPLDVK VGDIVIFNDG YGVKSEKIDN EEVLIMSES DILAIVEA

UniProtKB: Co-chaperonin GroES

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Macromolecule #2: Chaperonin GroEL

MacromoleculeName: Chaperonin GroEL / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO / EC number: chaperonin ATPase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 57.391711 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MAAKDVKFGN DARVKMLRGV NVLADAVKVT LGPKGRNVVL DKSFGAPTIT KDGVSVAREI ELEDKFENMG AQMVKEVASK ANDAAGDGT TTATVLAQAI ITEGLKAVAA GMNPMDLKRG IDKAVTAAVE ELKALSVPCS DSKAIAQVGT ISANSDETVG K LIAEAMDK ...String:
MAAKDVKFGN DARVKMLRGV NVLADAVKVT LGPKGRNVVL DKSFGAPTIT KDGVSVAREI ELEDKFENMG AQMVKEVASK ANDAAGDGT TTATVLAQAI ITEGLKAVAA GMNPMDLKRG IDKAVTAAVE ELKALSVPCS DSKAIAQVGT ISANSDETVG K LIAEAMDK VGKEGVITVE DGTGLQDELD VVEGMQFDRG YLSPYFINKP ETGAVELESP FILLADKKIS NIREMLPVLE AV AKAGKPL LIIAEDVEGE ALATLVVNTM RGIVKVAAVK APGFGDRRKA MLQDIATLTG GTVISEEIGM ELEKATLEDL GQA KRVVIN KDTTTIIDGV GEEAAIQGRV AQIRQQIEEA TSDYDREKLQ ERVAKLAGGV AVIKVGAATE VEMKEKKARV EDAL HATRA AVEEGVVAGG GVALIRVASK LADLRGQNED QNVGIKVALR AMEAPLRQIV LNCGEEPSVV ANTVKGGDGN YGYNA ATEE YGNMIDMGIL DPTKVTRSAL QYAASVAGLM ITTECMVTDL PKNDAADLGA AGGMGGMGGM GGMM

UniProtKB: Chaperonin GroEL

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Macromolecule #3: Ribulose bisphosphate carboxylase

MacromoleculeName: Ribulose bisphosphate carboxylase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase
Source (natural)Organism: Rhodospirillum rubrum ATCC 11170 (bacteria)
Molecular weightTheoretical: 50.538918 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MDQSSRYVNL ALKEEDLIAG GEHVLCAYIM KPKAGYGYVA TAAHFAAESS TGTNVEVCTT DDFTRGVDAL VYEVDEAREL TKIAYPVAL FDRNITDGKA MIASFLTLTM GNNQGMGDVE YAKMHDFYVP EAYRALFDGP SVNISALWKV LGRPEVDGGL V VGTIIKPK ...String:
MDQSSRYVNL ALKEEDLIAG GEHVLCAYIM KPKAGYGYVA TAAHFAAESS TGTNVEVCTT DDFTRGVDAL VYEVDEAREL TKIAYPVAL FDRNITDGKA MIASFLTLTM GNNQGMGDVE YAKMHDFYVP EAYRALFDGP SVNISALWKV LGRPEVDGGL V VGTIIKPK LGLRPKPFAE ACHAFWLGGD FIKNDEPQGN QPFAPLRDTI ALVADAMRRA QDETGEAKLF SANITADDPF EI IARGEYV LETFGENASH VALLVDGYVA GAAAITTARR RFPDNFLHYH RAGHGAVTSP QSKRGYTAFV HCKMARLQGA SGI HTGTMG FGKMEGESSD RAIAYMLTQD EAQGPFYRQS WGGMKACTPI ISGGMNALRM PGFFENLGNA NVILTAGGGA FGHI DGPVA GARSLRQAWQ AWRDGVPVLD YAREHKELAR AFESFPGDAD QIYPGWRKAL GVEDTRSALP A

UniProtKB: Ribulose bisphosphate carboxylase

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 3200FSC
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 35230
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4pko

source_name: PDB, initial_model_type: experimental model

9rub

chain_id: A, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7vwx:
CryoEM structure of football-shaped GroEL:ES2 with RuBisCO

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