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- PDB-6z1d: Crystal structure of the AAA domain of Rubisco Activase from Nost... -

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Basic information

Entry
Database: PDB / ID: 6z1d
TitleCrystal structure of the AAA domain of Rubisco Activase from Nostoc sp. (strain PCC 7120), Gadolinium complex
ComponentsRibulose bisphosphate carboxylase/oxygenase activase
KeywordsCHAPERONE / AAA+ domain
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
Ribulose bisphosphate carboxylase/oxygenase activase-like / : / Ribulose bisphosphate carboxylase/oxygenase activase, AAA, helical / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GADOLINIUM ATOM / Ribulose bisphosphate carboxylase/oxygenase activase
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.705 Å
AuthorsPopilka, L. / Bracher, A.
CitationJournal: Cell / Year: 2020
Title: Dual Functions of a Rubisco Activase in Metabolic Repair and Recruitment to Carboxysomes.
Authors: Mirkko Flecken / Huping Wang / Leonhard Popilka / F Ulrich Hartl / Andreas Bracher / Manajit Hayer-Hartl /
Abstract: Rubisco, the key enzyme of CO fixation in photosynthesis, is prone to inactivation by inhibitory sugar phosphates. Inhibited Rubisco undergoes conformational repair by the hexameric AAA+ chaperone ...Rubisco, the key enzyme of CO fixation in photosynthesis, is prone to inactivation by inhibitory sugar phosphates. Inhibited Rubisco undergoes conformational repair by the hexameric AAA+ chaperone Rubisco activase (Rca) in a process that is not well understood. Here, we performed a structural and mechanistic analysis of cyanobacterial Rca, a close homolog of plant Rca. In the Rca:Rubisco complex, Rca is positioned over the Rubisco catalytic site under repair and pulls the N-terminal tail of the large Rubisco subunit (RbcL) into the hexamer pore. Simultaneous displacement of the C terminus of the adjacent RbcL opens the catalytic site for inhibitor release. An alternative interaction of Rca with Rubisco is mediated by C-terminal domains that resemble the small Rubisco subunit. These domains, together with the N-terminal AAA+ hexamer, ensure that Rca is packaged with Rubisco into carboxysomes. The cyanobacterial Rca is a dual-purpose protein with functions in Rubisco repair and carboxysome organization.
History
DepositionMay 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Ribulose bisphosphate carboxylase/oxygenase activase
B: Ribulose bisphosphate carboxylase/oxygenase activase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6388
Polymers65,5472
Non-polymers1,0926
Water543
1
A: Ribulose bisphosphate carboxylase/oxygenase activase
B: Ribulose bisphosphate carboxylase/oxygenase activase
hetero molecules

A: Ribulose bisphosphate carboxylase/oxygenase activase
B: Ribulose bisphosphate carboxylase/oxygenase activase
hetero molecules

A: Ribulose bisphosphate carboxylase/oxygenase activase
B: Ribulose bisphosphate carboxylase/oxygenase activase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,91524
Polymers196,6406
Non-polymers3,27518
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area24520 Å2
ΔGint-221 kcal/mol
Surface area68460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.990, 111.990, 283.818
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Ribulose bisphosphate carboxylase/oxygenase activase / RuBisCO activase


Mass: 32773.316 Da / Num. of mol.: 2 / Fragment: AAA+ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Gene: rca, alr1533 / Plasmid: pHUE / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): pBAD33-EcGroSEL / References: UniProt: P58555
#2: Chemical
ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Gd
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.61 Å3/Da / Density % sol: 52.92 % / Mosaicity: 0 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7 / Details: 2.2 M Na-acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.68745 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 9, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.68745 Å / Relative weight: 1
ReflectionResolution: 2.705→48.99 Å / Num. all: 19125 / Num. obs: 19125 / % possible obs: 99.9 % / Redundancy: 19.7 % / Biso Wilson estimate: 61.79 Å2 / Rpim(I) all: 0.015 / Rrim(I) all: 0.069 / Rsym value: 0.064 / Net I/av σ(I): 11 / Net I/σ(I): 37.2 / Num. measured all: 375979
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.705-2.8519.30.6241.327380.1480.6580.62499.5
2.85-3.02190.3752.126270.090.3950.375100
3.02-3.2319.80.2163.624420.0510.2270.216100
3.23-3.4920.70.1365.623030.0310.1430.136100
3.49-3.8320.30.0858.821070.020.0890.085100
3.83-4.2818.90.05413.119160.0130.0580.054100
4.28-4.9420.10.03917.917070.0090.0420.039100
4.94-6.0520.30.0417.414630.010.0440.04100
6.05-8.5518.40.02922.211480.0080.0350.029100
8.55-48.9919.30.017356740.0050.0220.01799.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PHENIX1.8.2refinement
XDSVERSION September 26, 2012data reduction
SCALA3.3.16data scaling
SHELXDEVersion 2006/3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.705→28.633 Å / FOM work R set: 0.8015 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2585 978 5.12 %
Rwork0.2159 18124 -
obs0.2179 19102 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.73 Å2 / Biso mean: 71.22 Å2 / Biso min: 36.87 Å2
Refinement stepCycle: final / Resolution: 2.705→28.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 44 3 4199
Biso mean--61.34 40.87 -
Num. residues----533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084260
X-RAY DIFFRACTIONf_angle_d1.0985775
X-RAY DIFFRACTIONf_chiral_restr0.054654
X-RAY DIFFRACTIONf_plane_restr0.005752
X-RAY DIFFRACTIONf_dihedral_angle_d14.1621587
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.705-2.84720.35361510.3115251399
2.8472-3.02540.33841570.26872561100
3.0254-3.25870.2821310.2642556100
3.2587-3.5860.2841350.24112575100
3.586-4.10360.24791460.21172577100
4.1036-5.16520.20181210.17792622100
5.1652-28.6330.24991370.19782720100
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)
13.2392-1.0338-1.03214.09-0.71085.22540.00470.19110.1079-0.54350.12060.06120.1273-0.0225-0.02760.5078-0.1143-0.09280.49460.04720.4992-28.0181-44.4704-34.2397
22.8070.7099-0.54285.57411.8972.3514-0.00930.14850.0103-0.14640.00570.4258-0.123-0.28520.06430.44880.02790.04360.57780.00220.434-41.9615-68.3384-14.7184
35.00520.0181-0.37734.58550.52313.3105-0.22160.0121-0.0279-0.27030.0719-0.0264-0.0763-0.14590.14550.46990.0506-0.07580.4399-0.06540.29672.5446-34.4851-27.6098
48.61932.77924.44821.51872.18353.6314-0.1996-0.82880.32250.00680.11180.5095-0.2126-0.43440.10180.60070.1916-0.01260.8489-0.08720.7956-29.0806-27.0409-16.3893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 179)A2 - 179
2X-RAY DIFFRACTION2chain 'A' and (resid 180 through 275 )A180 - 275
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 179)B2 - 179
4X-RAY DIFFRACTION4chain 'B' and (resid 180 through 278)B180 - 278

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