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- PDB-4wt3: The N-terminal domain of Rubisco Accumulation Factor 1 from Arabi... -

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Basic information

Entry
Database: PDB / ID: 4wt3
TitleThe N-terminal domain of Rubisco Accumulation Factor 1 from Arabidopsis thaliana
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 / SIRAS / Resolution: 1.954 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

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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


Theoretical massNumber of molelcules
Total (without water)24,0051
Polymers24,0051
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.769, 29.769, 457.085
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Detailsbiological unit is the same as asym.

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Components

#1: Protein Rubisco Accumulation Factor 1, isoform 2


Mass: 24004.912 Da / Num. of mol.: 1 / Fragment: Raf1 alpha-domain, UNP residues 62-274
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 / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES-NaOH pH 6.0 and 26% (w/v) PEG-6000

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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 wavelength
IDWavelength (Å)Relative weight
10.97861
20.978561
ReflectionRedundancy: 14.4 % / Number: 76719 / Rsym value: 0.158 / D res high: 2.898 Å / D res low: 37.905 Å / Num. obs: 5346 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
9.1645.4910.0480.0489.5
6.489.1610.0690.06912.7
5.296.4810.1160.11613.7
4.585.2910.1380.13814.2
4.14.5810.1490.14914.5
3.744.110.1930.19315.5
3.463.7410.2880.28815.3
3.243.4610.390.3915
3.053.2410.5540.55416.3
2.93.0510.7060.70612.9
ReflectionResolution: 1.95→38.09 Å / Num. all: 16733 / Num. obs: 16733 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 42.22 Å2 / Rpim(I) all: 0.019 / Rrim(I) all: 0.071 / Rsym value: 0.068 / Net I/av σ(I): 8.75 / Net I/σ(I): 20.2 / Num. measured all: 222430
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.95-2.0612.61.0670.72889822890.3081.0672.199.8
2.06-2.1814.10.6241.23137722300.1710.6243.799.9
2.18-2.3413.60.38322878221170.1070.3835.9100
2.34-2.5214.30.2632.92796019530.0710.2638.7100
2.52-2.7613.70.1574.82557618610.0430.15713.8100
2.76-3.0913.70.1047.12259216530.0290.10421.1100
3.09-3.5713.50.066112036115130.0180.06633.7100
3.57-4.3712.60.03817.41673513280.0110.03856.6100
4.37-6.1811.90.03418.61284010780.010.03457100
6.18-45.70810.30.02222.973097110.0070.0226799.7

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Phasing

PhasingMethod: SIRAS
Phasing dmFOM : 0.61 / FOM acentric: 0.57 / FOM centric: 0.68 / Reflection: 6049 / Reflection acentric: 3783 / Reflection centric: 2266
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.9-37.8170.960.980.9533691245
4.9-7.90.880.90.87859430429
3.9-4.90.850.870.831053632421
3.4-3.90.740.740.74978642336
2.9-3.40.450.430.4917291207522
2.8-2.90.20.190.241094781313

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
SHELXphasing
RESOLVE2.13phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 1.954→29.706 Å / FOM work R set: 0.8175 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.33 / Phase error: 23.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 850 5.15 %
Rwork0.2113 15664 -
obs0.2129 16514 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.85 Å2 / Biso mean: 64.04 Å2 / Biso min: 28.34 Å2
Refinement stepCycle: final / Resolution: 1.954→29.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1548 0 0 60 1608
Biso mean---51.42 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111600
X-RAY DIFFRACTIONf_angle_d1.212171
X-RAY DIFFRACTIONf_chiral_restr0.067242
X-RAY DIFFRACTIONf_plane_restr0.005287
X-RAY DIFFRACTIONf_dihedral_angle_d14.563602
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.954-2.07640.35481380.321624742612
2.0764-2.23670.29581580.271225122670
2.2367-2.46170.27261400.234125512691
2.4617-2.81760.27661500.215825412691
2.8176-3.5490.25141340.233726582792
3.549-29.70950.20951300.182129283058
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)
15.14440.8252-0.10583.1693-4.08255.4311-0.480.106-0.4578-1.18750.61850.3369-0.048-1.5767-0.54321.81580.062-0.00150.67920.11060.5141-13.83621.5658-53.928
24.01961.7979-3.21483.6317-2.83067.6702-0.44460.411-0.3894-0.84060.0346-0.4096-0.3993-0.7422-0.25271.57060.1263-0.06390.4287-0.01660.3448-11.3718-0.6351-43.3422
35.0822-0.1683-1.07961.99140.34318.9251-0.01540.25990.4334-1.0713-0.01370.2506-0.3617-0.68510.03860.82470.0371-0.14680.3893-0.00320.4469-15.6868-3.6439-29.5629
44.0559-1.41931.35714.05291.11353.50590.1668-0.0437-0.0444-0.5622-0.2061-0.30870.46290.42530.02780.4888-0.075-0.01320.29330.02380.4233-9.173-9.5136-16.7972
50.4387-0.15350.18154.51251.94855.15150.0461-0.0506-0.0043-0.1749-0.0063-0.5156-0.05230.3568-0.12260.3565-0.1227-0.0250.23920.05140.4388-10.7893-0.8391-8.1786
64.9471-1.0635-0.32056.0957-2.56567.845-0.1409-0.1841-0.12730.4114-0.05260.36110.6109-0.68060.23640.3444-0.1441-0.01660.3368-0.00860.4113-19.4293-6.3249-3.6146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 72 through 97 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 98 through 155 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 187 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 217 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 218 through 250 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 251 through 269 )A0

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