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- PDB-3rg6: Crystal structure of a chaperone-bound assembly intermediate of f... -

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Basic information

Entry
Database: PDB / ID: 3rg6
TitleCrystal structure of a chaperone-bound assembly intermediate of form I Rubisco
Components
  • RbcX protein
  • Ribulose bisphosphate carboxylase large chain
KeywordsPHOTOSYNTHESIS / assembly chaperone / TIM barrel (RbcL) / carbon fixation (RbcL) complex assembly / protein folding / chaperone (RbcX) / RbcS (RbcL)
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / carbon fixation / reductive pentose-phosphate cycle / photosynthesis / protein folding chaperone / monooxygenase activity ...ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / carbon fixation / reductive pentose-phosphate cycle / photosynthesis / protein folding chaperone / monooxygenase activity / magnesium ion binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Chaperonin-like RbcX / RuBisCO chaperone RbcX / Chaperonin-like RbcX superfamily / RbcX protein / Chaperonin-like RbcX / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. ...Chaperonin-like RbcX / RuBisCO chaperone RbcX / Chaperonin-like RbcX superfamily / RbcX protein / Chaperonin-like RbcX / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase large subunit, type I / 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 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase large chain / RuBisCO chaperone RbcX
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
Anabaena sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsBracher, A. / Starling-Windhof, A. / Hartl, F.U. / Hayer-Hartl, M.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Crystal structure of a chaperone-bound assembly intermediate of form I Rubisco.
Authors: Bracher, A. / Starling-Windhof, A. / Hartl, F.U. / Hayer-Hartl, M.
#1: Journal: Nature / Year: 2010
Title: Coupled chaperone action in folding and assembly of hexadecameric Rubisco.
Authors: Cuimin Liu / Anna L Young / Amanda Starling-Windhof / Andreas Bracher / Sandra Saschenbrecker / Bharathi Vasudeva Rao / Karnam Vasudeva Rao / Otto Berninghausen / Thorsten Mielke / F Ulrich ...Authors: Cuimin Liu / Anna L Young / Amanda Starling-Windhof / Andreas Bracher / Sandra Saschenbrecker / Bharathi Vasudeva Rao / Karnam Vasudeva Rao / Otto Berninghausen / Thorsten Mielke / F Ulrich Hartl / Roland Beckmann / Manajit Hayer-Hartl /
Abstract: Form I Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), a complex of eight large (RbcL) and eight small (RbcS) subunits, catalyses the fixation of atmospheric CO(2) in photosynthesis. The ...Form I Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), a complex of eight large (RbcL) and eight small (RbcS) subunits, catalyses the fixation of atmospheric CO(2) in photosynthesis. The limited catalytic efficiency of Rubisco has sparked extensive efforts to re-engineer the enzyme with the goal of enhancing agricultural productivity. To facilitate such efforts we analysed the formation of cyanobacterial form I Rubisco by in vitro reconstitution and cryo-electron microscopy. We show that RbcL subunit folding by the GroEL/GroES chaperonin is tightly coupled with assembly mediated by the chaperone RbcX(2). RbcL monomers remain partially unstable and retain high affinity for GroEL until captured by RbcX(2). As revealed by the structure of a RbcL(8)-(RbcX(2))(8) assembly intermediate, RbcX(2) acts as a molecular staple in stabilizing the RbcL subunits as dimers and facilitates RbcL(8) core assembly. Finally, addition of RbcS results in RbcX(2) release and holoenzyme formation. Specific assembly chaperones may be required more generally in the formation of complex oligomeric structures when folding is closely coupled to assembly.
#2: Journal: Cell(Cambridge,Mass.) / Year: 2007
Title: Structure and function of RbcX, an assembly chaperone for hexadecameric Rubisco.
Authors: Saschenbrecker, S. / Bracher, A. / Rao, K.V. / Rao, B.V. / Hartl, F.U. / Hayer-Hartl, M.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Structure determination and refinement of ribulose 1,5-bisphosphate carboxylase/oxygenase from Synechococcus PCC6301.
Authors: Newman, J. / Branden, C.I. / Jones, T.A.
History
DepositionApr 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references
Revision 1.2Aug 17, 2011Group: Database references
Revision 1.3Jul 16, 2014Group: Other
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Nov 20, 2019Group: Database references / Category: pdbx_database_related / struct_ref_seq_dif
Item: _pdbx_database_related.content_type / _pdbx_database_related.db_id / _struct_ref_seq_dif.details
Revision 1.6Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase large chain
C: RbcX protein
D: RbcX protein
B: Ribulose bisphosphate carboxylase large chain
E: RbcX protein
F: RbcX protein


Theoretical massNumber of molelcules
Total (without water)175,8136
Polymers175,8136
Non-polymers00
Water00
1
A: Ribulose bisphosphate carboxylase large chain
C: RbcX protein
D: RbcX protein
B: Ribulose bisphosphate carboxylase large chain
E: RbcX protein
F: RbcX protein

A: Ribulose bisphosphate carboxylase large chain
C: RbcX protein
D: RbcX protein
B: Ribulose bisphosphate carboxylase large chain
E: RbcX protein
F: RbcX protein

A: Ribulose bisphosphate carboxylase large chain
C: RbcX protein
D: RbcX protein
B: Ribulose bisphosphate carboxylase large chain
E: RbcX protein
F: RbcX protein

A: Ribulose bisphosphate carboxylase large chain
C: RbcX protein
D: RbcX protein
B: Ribulose bisphosphate carboxylase large chain
E: RbcX protein
F: RbcX protein


Theoretical massNumber of molelcules
Total (without water)703,25224
Polymers703,25224
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area6020 Å2
ΔGint-49 kcal/mol
Surface area29370 Å2
Unit cell
Length a, b, c (Å)244.750, 244.750, 99.669
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22E
13D
23E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A18 - 61
2114B18 - 61
1214A72 - 329
2214B72 - 329
1314A334 - 401
2314B334 - 401
1414A405 - 469
2414B405 - 469
1124C2 - 115
2124E2 - 115
1134D1 - 105
2134E1 - 105

NCS ensembles :
ID
1
2
3
DetailsAUTHORS STATE THAT THIS COMPLEX COMPOSITION HAS BEEN VERIFIED BY ELECTRON MICROSCOPY AND SIZE EXCLUSION CHROMATOGRAPHY (SEE REFERENCE 1).

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Components

#1: Protein Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


Mass: 52516.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: ATCC 27144 / PCC 6301 / SAUG 1402/1 / Gene: cbbL, rbcA, rbcL, syc0130_c / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00880, ribulose-bisphosphate carboxylase
#2: Protein
RbcX protein


Mass: 17694.930 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. (bacteria) / Gene: rbcX / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q44212

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.24 Å3/Da / Density % sol: 71.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.7
Details: 15-17 % 2-methyl-2,4-pentanediol, 0.1 M KCl, 0.1 M Tris-HCl, pH 8.7, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97908 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 3.2→47.999 Å / Num. all: 41265 / Num. obs: 41265 / % possible obs: 84.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.2-3.372.30.3112.4796133930.31148.7
3.37-3.582.50.2363.11094243580.23665.5
3.58-3.832.60.2033.61372152160.20383
3.83-4.1330.1554.71640155450.15595.3
4.13-4.533.40.1215.71813653760.12199.1
4.53-5.063.60.1096.31781049010.10999.9
5.06-5.843.70.1245.71607543570.124100
5.84-7.163.60.1096.61338136770.10999.9
7.16-10.123.50.05510.81003828480.05599.6
10.12-47.9993.60.03714.9566715940.03798.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.72 Å47.65 Å
Translation3.72 Å47.65 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RBL

1rbl


Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.876 / WRfactor Rfree: 0.2306 / WRfactor Rwork: 0.2046 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8518 / SU B: 42.556 / SU ML: 0.32 / SU R Cruickshank DPI: 0.3933 / SU Rfree: 0.4375 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 2067 5 %RANDOM
Rwork0.216 ---
obs0.2175 41214 84.5 %-
all-43281 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 262.25 Å2 / Biso mean: 89.9627 Å2 / Biso min: 35.18 Å2
Baniso -1Baniso -2Baniso -3
1-3.33 Å20 Å20 Å2
2--3.33 Å20 Å2
3----6.66 Å2
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10078 0 0 0 10078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02110302
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.94914002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.17851311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15323.658462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.117151591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3291568
X-RAY DIFFRACTIONr_chiral_restr0.0740.21573
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027910
X-RAY DIFFRACTIONr_nbd_refined0.2090.25007
X-RAY DIFFRACTIONr_nbtor_refined0.3020.27049
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2326
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.25
X-RAY DIFFRACTIONr_mcbond_it0.1741.56686
X-RAY DIFFRACTIONr_mcangle_it0.331210411
X-RAY DIFFRACTIONr_scbond_it0.54634045
X-RAY DIFFRACTIONr_scangle_it0.9544.53591
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3333MEDIUM POSITIONAL0.230.5
1A3333MEDIUM THERMAL0.22
2C851MEDIUM POSITIONAL0.310.5
2C851MEDIUM THERMAL0.082
3D767MEDIUM POSITIONAL0.450.5
3D767MEDIUM THERMAL0.142
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 71 -
Rwork0.332 1439 -
all-1510 -
obs--42.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.866-0.29680.31521.0938-0.42372.2522-0.0164-0.08270.22490.0744-0.08440.2114-0.4846-0.64220.1008-0.3890.16580.0135-0.2752-0.0976-0.4432-31.63615.884512.9478
21.0614-0.3267-0.66722.05940.36942.3648-0.1050.05520.1233-0.08690.06610.2651-0.4312-0.6930.0388-0.32550.2425-0.0975-0.40280.0061-0.4283-22.077827.4682-12.9232
31.2369-0.6401-0.41245.85120.54895.8975-0.05720.29160.8923-0.80460.23180.0203-1.42380.2529-0.17450.86620.4944-0.18530.63810.29090.6761-50.154153.0446-31.7337
41.2269-1.05060.07747.1088-0.4014.99430.1730.37170.5485-0.1830.1110.0813-1.1126-0.4685-0.2840.39750.6281-0.20720.47010.08790.0591-50.235241.7221-25.9675
55.2186-0.08390.83821.1958-0.28045.75870.2753-0.7037-0.30350.33060.12031.10470.7854-1.432-0.39560.75220.32230.38170.7163-0.0550.785-62.898639.235531.7365
68.06181.17160.21913.92220.25654.68270.0451-0.3198-0.00750.19140.07671.018-0.0407-0.7894-0.12180.43740.58010.1440.0046-0.17730.1187-51.458140.780425.8693
778.9139-15.0324-16.421517.47763.101720.92880.56813.3852-3.0380.8414-0.63071.73180.4818-0.56640.06260.01220.0313-0.0580.0017-0.01250.0246-49.278637.951836.4137
817.2703-26.924817.317873.8894-33.65139.8265-2.53-1.47371.21462.28113.7128-2.0892-2.5468-0.9235-1.18280.00780.0013-0.00880.00390.00890.0048-46.675839.8841-36.3528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 63
2X-RAY DIFFRACTION1A71 - 401
3X-RAY DIFFRACTION1A405 - 458
4X-RAY DIFFRACTION2B18 - 61
5X-RAY DIFFRACTION2B71 - 331
6X-RAY DIFFRACTION2B334 - 401
7X-RAY DIFFRACTION2B405 - 458
8X-RAY DIFFRACTION3C1 - 115
9X-RAY DIFFRACTION4D1 - 107
10X-RAY DIFFRACTION5E2 - 115
11X-RAY DIFFRACTION6F1 - 106
12X-RAY DIFFRACTION7A459 - 469
13X-RAY DIFFRACTION8B459 - 469

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