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- EMDB-15944: CryoEM structure of GroEL-GroES-ADP.AlF3-Rubisco, class II. -

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Basic information

Entry
Database: EMDB / ID: EMD-15944
TitleCryoEM structure of GroEL-GroES-ADP.AlF3-Rubisco, class II.
Map data
Sample
  • Complex: GroEL-GroES-ADP.AlF3-Rubisco
    • Protein or peptide: Chaperonin GroEL
    • Protein or peptide: Co-chaperonin GroES
    • Protein or peptide: Ribulose bisphosphate carboxylase
  • Ligand: ALUMINUM FLUORIDE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: POTASSIUM ION
KeywordsGroEL / GroES / Chaperone
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / GroEL-GroES complex / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chaperonin ATPase / virion assembly / : / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone ...ribulose-bisphosphate carboxylase / GroEL-GroES complex / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chaperonin ATPase / virion assembly / : / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / monooxygenase activity / 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 / metal ion binding / identical protein binding / membrane / 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 (E. coli) / Escherichia coli (strain K12) (bacteria) / Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsGardner S / Saibil HR
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M009513/1 United Kingdom
CitationJournal: To Be Published
Title: CryoEM snapshots of non-native Rubisco bound to GroEL, GroEL-ADP.BeF3, and GroEL-GroES.
Authors: Gardner S / Lukyanova N / Darrow MC / Thalassinos K / Saibil HR
History
DepositionOct 11, 2022-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15944.png

Downloads & links

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Map

FileDownload / File: emd_15944.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 448 pix.
= 380.522 Å		0.85 Å/pix.
x 448 pix.
= 380.522 Å		0.85 Å/pix.
x 448 pix.
= 380.522 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84938 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.7378143 - 1.3690245
Average (Standard dev.)0.0025617073 (±0.035144843)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 380.52225 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15944_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15944_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15944_half_map_2.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 : GroEL-GroES-ADP.AlF3-Rubisco

EntireName: GroEL-GroES-ADP.AlF3-Rubisco
Components
  • Complex: GroEL-GroES-ADP.AlF3-Rubisco
    • Protein or peptide: Chaperonin GroEL
    • Protein or peptide: Co-chaperonin GroES
    • Protein or peptide: Ribulose bisphosphate carboxylase
  • Ligand: ALUMINUM FLUORIDE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: POTASSIUM ION

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Supramolecule #1: GroEL-GroES-ADP.AlF3-Rubisco

SupramoleculeName: GroEL-GroES-ADP.AlF3-Rubisco / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 802 KDa

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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: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 57.260504 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AAKDVKFGND ARVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREIE LEDKFENMGA QMVKEVASKA NDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVEE LKALSVPCSD SKAIAQVGTI SANSDETVGK L IAEAMDKV ...String:
AAKDVKFGND ARVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREIE LEDKFENMGA QMVKEVASKA NDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVEE LKALSVPCSD SKAIAQVGTI SANSDETVGK L IAEAMDKV GKEGVITVED GTGLQDELDV VEGMQFDRGY LSPYFINKPE TGAVELESPF ILLADKKISN IREMLPVLEA VA KAGKPLL IIAEDVEGEA LATLVVNTMR GIVKVAAVKA PGFGDRRKAM LQDIATLTGG TVISEEIGME LEKATLEDLG QAK RVVINK DTTTIIDGVG EEAAIQGRVA QIRQQIEEAT SDYDREKLQE RVAKLAGGVA VIKVGAATEV EMKEKKARVE DALH ATRAA VEEGVVAGGG VALIRVASKL ADLRGQNEDQ NVGIKVALRA MEAPLRQIVL NCGEEPSVVA NTVKGGDGNY GYNAA TEEY GNMIDMGILD PTKVTRSALQ YAASVAGLMI TTECMVTDLP KNDAADLGAA GGMGGMGGMG GMM

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: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 10.400938 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MNIRPLHDRV IVKRKEVETK SAGGIVLTGS AAAKSTRGEV LAVGNGRILE NGEVKPLDVK VGDIVIFNDG YGVKSEKIDN EEVLIMSES DILAIVEA

UniProtKB: Co-chaperonin GroES

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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 (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria)
Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
Molecular weightTheoretical: 50.538918 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (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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Macromolecule #4: ALUMINUM FLUORIDE

MacromoleculeName: ALUMINUM FLUORIDE / type: ligand / ID: 4 / Number of copies: 7 / Formula: AF3
Molecular weightTheoretical: 83.977 Da
Chemical component information

ChemComp-AF3:
ALUMINUM FLUORIDE

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 14 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 14 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #7: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 7 / 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

Concentration2.7 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 293 K / Instrument: SPOTITON
Details: The grid was prepared using a chameleon (SPT Labtech)..

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Average electron dose: 40.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7712622
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1ss8

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 8237
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final 3D classificationNumber classes: 8 / Avg.num./class: 25000 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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