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- PDB-4wt5: The C-terminal domain of Rubisco Accumulation Factor 1 from Arabi... -

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Basic information

Entry
Database: PDB / ID: 4wt5
TitleThe C-terminal domain of Rubisco Accumulation Factor 1 from Arabidopsis thaliana, crystal form II
ComponentsRubisco Accumulation Factor 1, isoform 2
KeywordsCHAPERONE / assembly chaperone
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / chloroplast stroma / chloroplast / cytosol
Similarity search - Function
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 1.2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.568 Å
AuthorsHauser, T. / Bhat, J.Y. / Milicic, G. / Wendler, P. / Hartl, F.U. / Bracher, A. / Hayer-Hartl, M.
CitationJournal: Nat Struct Mol Biol / Year: 2015
Title: Structure and mechanism of the Rubisco-assembly chaperone Raf1.
Authors: Thomas Hauser / Javaid Y Bhat / Goran Miličić / Petra Wendler / F Ulrich Hartl / Andreas Bracher / Manajit Hayer-Hartl /
Abstract: Biogenesis of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits, requires assembly chaperones. Here we analyzed the role of Rubisco accumulation ...Biogenesis of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits, requires assembly chaperones. Here we analyzed the role of Rubisco accumulation factor1 (Raf1), a dimer of ∼40-kDa subunits. We find that Raf1 from Synechococcus elongatus acts downstream of chaperonin-assisted RbcL folding by stabilizing RbcL antiparallel dimers for assembly into RbcL8 complexes with four Raf1 dimers bound. Raf1 displacement by RbcS results in holoenzyme formation. Crystal structures show that Raf1 from Arabidopsis thaliana consists of a β-sheet dimerization domain and a flexibly linked α-helical domain. Chemical cross-linking and EM reconstruction indicate that the β-domains bind along the equator of each RbcL2 unit, and the α-helical domains embrace the top and bottom edges of RbcL2. Raf1 fulfills a role similar to that of the assembly chaperone RbcX, thus suggesting that functionally redundant factors ensure efficient Rubisco biogenesis.
History
DepositionOct 29, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rubisco Accumulation Factor 1, isoform 2
B: Rubisco Accumulation Factor 1, isoform 2


Theoretical massNumber of molelcules
Total (without water)37,6792
Polymers37,6792
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-21 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.680, 60.789, 143.267
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 288 - 437 / Label seq-ID: 8 - 157

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
Detailsbiological unit is a dimer, a.u. contains one dimer

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Components

#1: Protein Rubisco Accumulation Factor 1, isoform 2 / AtRaf1.2


Mass: 18839.576 Da / Num. of mol.: 2 / Fragment: Raf1 beta-domain, UNP residues 281-449
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RAF2, At3g04550, F7O18.2 / Plasmid: pHUE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SR19
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 200 mM KH2PO4 and 20% (w/v) PEG-5000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.568→71.633 Å / Num. all: 11314 / Num. obs: 11314 / % possible obs: 96.7 % / Redundancy: 4.3 % / Rpim(I) all: 0.051 / Rrim(I) all: 0.11 / Rsym value: 0.097 / Net I/av σ(I): 5.931 / Net I/σ(I): 11.9 / Num. measured all: 48923
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.57-2.714.20.9090.8572713720.4770.9092.181.8
2.71-2.874.40.6511.1696615750.3320.651399.7
2.87-3.074.60.4061.8675914660.2020.4064.899.2
3.07-3.324.40.2492.7609113870.1280.2497.399.2
3.32-3.634.30.1394.5551212820.0720.13912.299.3
3.63-4.064.50.1124.9518811650.0570.11216.399.7
4.06-4.694.20.0619.6429010170.0330.0612398.8
4.69-5.744.40.04912.739509070.0260.04924.599.8
5.74-8.1240.04513.628697160.0250.04523.699.3
8.12-47.7563.70.03216.215714270.0180.03230.898.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.9 Å46.35 Å
Translation2.9 Å46.35 Å

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
MOLREP10.2.35phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WT4

4wt4


Resolution: 2.568→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.2643 / WRfactor Rwork: 0.1927 / FOM work R set: 0.7932 / SU B: 12.968 / SU ML: 0.271 / SU R Cruickshank DPI: 0.6741 / SU Rfree: 0.3411 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.674 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2792 530 4.7 %RANDOM
Rwork0.2098 10713 --
obs0.2128 10713 96.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.78 Å2 / Biso mean: 59.375 Å2 / Biso min: 26.46 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å2-0 Å20 Å2
2---3.93 Å2-0 Å2
3---5.73 Å2
Refinement stepCycle: final / Resolution: 2.568→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2282 0 0 9 2291
Biso mean---45.77 -
Num. residues----300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192323
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9883153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97624.09188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.32915405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8511517
X-RAY DIFFRACTIONr_chiral_restr0.0780.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211711
Refine LS restraints NCS

Ens-ID: 1 / Number: 120 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.21 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.568→2.634 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 12 -
Rwork0.328 533 -
all-545 -
obs--64.42 %

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