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- PDB-6kkm: Crystal structure of RbcL-Raf1 complex from Anabaena sp. PCC 7120 -

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Basic information

Entry
Database: PDB / ID: 6kkm
TitleCrystal structure of RbcL-Raf1 complex from Anabaena sp. PCC 7120
Components
  • All5250 protein
  • Ribulose bisphosphate carboxylase large chain
KeywordsCHAPERONE/PHOTOSYNTHESIS / RuBisCO / Chaperone / Raf1 / RbcL / CHAPERONE-PHOTOSYNTHESIS complex
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / photosynthesis / monooxygenase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Rubisco accumulation factor 1, cyanobacterial / Rubisco accumulation factor 1 / Rubisco accumulation factor 1, helix turn helix domain / Rubisco accumulation factor 1, C-terminal / Rubisco accumulation factor 1, alpha helical domain / Rubisco Assembly chaperone C-terminal domain / Rubisco accumulation factor 1 alpha helical domain / Rubisco accumulation factor 1 helix turn helix domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain ...Rubisco accumulation factor 1, cyanobacterial / Rubisco accumulation factor 1 / Rubisco accumulation factor 1, helix turn helix domain / Rubisco accumulation factor 1, C-terminal / Rubisco accumulation factor 1, alpha helical domain / Rubisco Assembly chaperone C-terminal domain / Rubisco accumulation factor 1 alpha helical domain / Rubisco accumulation factor 1 helix turn helix domain / 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 / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase large chain / RuBisCO accumulation factor 1
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsXia, L.Y. / Jiang, Y.L. / Kong, W.W. / Chen, Y. / Zhou, C.Z.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2018YFA0903100 China
Ministry of Science and Technology (China)2016YFA0400900 China
National Natural Science Foundation of China31630001 China
National Natural Science Foundation of China31621002 China
Chinese Academy of Sciences China
CitationJournal: Nat Plants / Year: 2020
Title: Molecular basis for the assembly of RuBisCO assisted by the chaperone Raf1.
Authors: Ling-Yun Xia / Yong-Liang Jiang / Wen-Wen Kong / Hui Sun / Wei-Fang Li / Yuxing Chen / Cong-Zhao Zhou /
Abstract: The folding and assembly of RuBisCO, the most abundant enzyme in nature, needs a series of chaperones, including the RuBisCO accumulation factor Raf1, which is highly conserved in cyanobacteria and ...The folding and assembly of RuBisCO, the most abundant enzyme in nature, needs a series of chaperones, including the RuBisCO accumulation factor Raf1, which is highly conserved in cyanobacteria and plants. Here, we report the crystal structures of Raf1 from cyanobacteria Anabaena sp. PCC 7120 and its complex with RuBisCO large subunit RbcL. Structural analyses and biochemical assays reveal that each Raf1 dimer captures an RbcL dimer, with the C-terminal tail inserting into the catalytic pocket, and further mediates the assembly of RbcL dimers to form the octameric core of RuBisCO. Furthermore, the cryo-electron microscopy structures of the RbcL-Raf1-RbcS assembly intermediates enable us to see a dynamic assembly process from RbcLRaf1 to the holoenzyme RbcLRbcS. In vitro assays also indicate that Raf1 can attenuate and reverse CcmM-mediated cyanobacterial RuBisCO condensation. Combined with previous findings, we propose a putative model for the assembly of cyanobacterial RuBisCO coordinated by the chaperone Raf1.
History
DepositionJul 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
E: All5250 protein
F: All5250 protein
G: All5250 protein
H: All5250 protein
A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain


Theoretical massNumber of molelcules
Total (without water)383,8738
Polymers383,8738
Non-polymers00
Water0
1
E: All5250 protein
F: All5250 protein
G: All5250 protein
H: All5250 protein
A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain

E: All5250 protein
F: All5250 protein
G: All5250 protein
H: All5250 protein
A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain


Theoretical massNumber of molelcules
Total (without water)767,74516
Polymers767,74516
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area105560 Å2
ΔGint-370 kcal/mol
Surface area223850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.117, 228.541, 162.336
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
All5250 protein


Mass: 41055.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: all5250
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8YLP6
#2: Protein
Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


Mass: 54913.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: cbbL, rbc, rbcA, rbcL, alr1524
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P00879, ribulose-bisphosphate carboxylase

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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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 8-10% 2-Methyl-2,4-pentanediol and 0.1 M MES 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 82605 / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.195 / Net I/σ(I): 16
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 1.095 / Num. unique obs: 8166

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RBL

1rbl


Resolution: 3→49 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.86 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.527
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2781 3725 5.1 %RANDOM
Rwork0.2287 ---
obs0.2312 69615 88.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 204.14 Å2 / Biso mean: 72.104 Å2 / Biso min: 18.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å2-0 Å2
2---1.04 Å2-0 Å2
3---2.22 Å2
Refinement stepCycle: final / Resolution: 3→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24810 0 0 0 24810
Num. residues----3121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01925420
X-RAY DIFFRACTIONr_bond_other_d00.0223471
X-RAY DIFFRACTIONr_angle_refined_deg1.41.94934523
X-RAY DIFFRACTIONr_angle_other_deg3.751354275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64153105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20923.6181255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.197154161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.66615208
X-RAY DIFFRACTIONr_chiral_restr0.0760.23738
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02128505
X-RAY DIFFRACTIONr_gen_planes_other0.0050.025443
LS refinement shellResolution: 3→3.075 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.331 173 -
Rwork0.3 3306 -
obs--57.31 %

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