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- PDB-6kkn: Crystal structure of RuBisCO accumulation factor Raf1 from Anabae... -

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Basic information

Entry
Database: PDB / ID: 6kkn
TitleCrystal structure of RuBisCO accumulation factor Raf1 from Anabaena sp. PCC 7120
ComponentsAll5250 protein
KeywordsCHAPERONE / RuBisCO / Raf1
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / carbon fixation / photosynthesis / 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
Similarity search - Domain/homology
RuBisCO accumulation factor 1
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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
A: All5250 protein


Theoretical massNumber of molelcules
Total (without water)42,8561
Polymers42,8561
Non-polymers00
Water00
1
A: All5250 protein

A: All5250 protein


Theoretical massNumber of molelcules
Total (without water)85,7122
Polymers85,7122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7540 Å2
ΔGint-38 kcal/mol
Surface area35000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.740, 94.740, 117.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein All5250 protein


Mass: 42856.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Gene: all5250
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8YLP6

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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: 3.57 Å3/Da / Density % sol: 65.51 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4M Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 14798 / % possible obs: 99.9 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 18.3
Reflection shellResolution: 2.85→3.02 Å / Rmerge(I) obs: 0.76 / Num. unique obs: 2325

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WT3, 4WT4

4wt3

4wt4


Resolution: 2.85→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.5884 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.588 / ESU R Free: 0.33
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 748 5.1 %RANDOM
Rwork0.2257 ---
obs0.2274 14017 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 191.34 Å2 / Biso mean: 86.232 Å2 / Biso min: 46.93 Å2
Baniso -1Baniso -2Baniso -3
1-3.39 Å21.7 Å2-0 Å2
2--3.39 Å20 Å2
3----11 Å2
Refinement stepCycle: final / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2677 0 0 0 2677
Num. residues----332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192743
X-RAY DIFFRACTIONr_bond_other_d00.022548
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.9543728
X-RAY DIFFRACTIONr_angle_other_deg3.48335900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1535331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3523.83141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65115457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6661524
X-RAY DIFFRACTIONr_chiral_restr0.0390.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213065
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02583
LS refinement shellResolution: 2.85→2.921 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.385 78 -
Rwork0.406 964 -
obs--99.05 %

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