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- PDB-6hbb: Crystal Structure of the small subunit-like domain 1 of CcmM from... -

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Basic information

Entry
Database: PDB / ID: 6hbb
TitleCrystal Structure of the small subunit-like domain 1 of CcmM from Synechococcus elongatus (strain PCC 7942)
ComponentsCarbon dioxide concentrating mechanism protein CcmM
KeywordsPROTEIN BINDING / alpha-beta structure / Rubisco / Carboxysome
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis
Similarity search - Function
Carboxysome assembly protein CcmM / : / : / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
Carboxysome assembly protein CcmM
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsWang, H. / Yan, X. / Aigner, H. / Bracher, A. / Nguyen, N.D. / Hee, W.Y. / Long, B.M. / Price, G.D. / Hartl, F.U. / Hayer-Hartl, M.
CitationJournal: Nature / Year: 2019
Title: Rubisco condensate formation by CcmM in β-carboxysome biogenesis.
Authors: H Wang / X Yan / H Aigner / A Bracher / N D Nguyen / W Y Hee / B M Long / G D Price / F U Hartl / M Hayer-Hartl /
Abstract: Cells use compartmentalization of enzymes as a strategy to regulate metabolic pathways and increase their efficiency. The α- and β-carboxysomes of cyanobacteria contain ribulose-1,5-bisphosphate ...Cells use compartmentalization of enzymes as a strategy to regulate metabolic pathways and increase their efficiency. The α- and β-carboxysomes of cyanobacteria contain ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)-a complex of eight large (RbcL) and eight small (RbcS) subunits-and carbonic anhydrase. As HCO can diffuse through the proteinaceous carboxysome shell but CO cannot, carbonic anhydrase generates high concentrations of CO for carbon fixation by Rubisco. The shell also prevents access to reducing agents, generating an oxidizing environment. The formation of β-carboxysomes involves the aggregation of Rubisco by the protein CcmM, which exists in two forms: full-length CcmM (M58 in Synechococcus elongatus PCC7942), which contains a carbonic anhydrase-like domain followed by three Rubisco small subunit-like (SSUL) modules connected by flexible linkers; and M35, which lacks the carbonic anhydrase-like domain. It has long been speculated that the SSUL modules interact with Rubisco by replacing RbcS. Here we have reconstituted the Rubisco-CcmM complex and solved its structure. Contrary to expectation, the SSUL modules do not replace RbcS, but bind close to the equatorial region of Rubisco between RbcL dimers, linking Rubisco molecules and inducing phase separation into a liquid-like matrix. Disulfide bond formation in SSUL increases the network flexibility and is required for carboxysome function in vivo. Notably, the formation of the liquid-like condensate of Rubisco is mediated by dynamic interactions with the SSUL domains, rather than by low-complexity sequences, which typically mediate liquid-liquid phase separation in eukaryotes. Indeed, within the pyrenoids of eukaryotic algae, the functional homologues of carboxysomes, Rubisco adopts a liquid-like state by interacting with the intrinsically disordered protein EPYC1. Understanding carboxysome biogenesis will be important for efforts to engineer CO-concentrating mechanisms in plants.
History
DepositionAug 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Feb 6, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Feb 20, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_id_ISSN
Revision 1.5Jan 17, 2024Group: 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: Carbon dioxide concentrating mechanism protein CcmM
B: Carbon dioxide concentrating mechanism protein CcmM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7749
Polymers21,1012
Non-polymers6727
Water2,918162
1
A: Carbon dioxide concentrating mechanism protein CcmM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7433
Polymers10,5511
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbon dioxide concentrating mechanism protein CcmM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0316
Polymers10,5511
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.302, 87.821, 36.467
Angle α, β, γ (deg.)90.000, 107.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbon dioxide concentrating mechanism protein CcmM


Mass: 10550.686 Da / Num. of mol.: 2 / Fragment: SSUL domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / Gene: ccmM, Synpcc7942_1423 / Plasmid: pHue / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03513
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 1.98 Å3/Da / Density % sol: 37.77 % / Mosaicity: 0.04 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.5
Details: 1.95 M ammonium sulfate and 0.1 M Na-acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.2→43.91 Å / Num. obs: 48992 / % possible obs: 96 % / Redundancy: 2.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.041 / Rrim(I) all: 0.072 / Net I/σ(I): 9.4 / Num. measured all: 140389
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.2-1.2220.44717280.7230.3610.57864.6
6.35-43.913.20.0453550.9950.0310.05598.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation43.91 Å2.9 Å

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Processing

Software
NameVersionClassification
XDSVERSION November 3, 2014data reduction
Aimless0.1.27data scaling
MOLREP11.0.05phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HBA

6hba


Resolution: 1.2→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.464 / SU ML: 0.03 / SU R Cruickshank DPI: 0.0451 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.046
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1952 2513 5.1 %RANDOM
Rwork0.1591 ---
obs0.1609 46447 95.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.01 Å2 / Biso mean: 15.226 Å2 / Biso min: 5.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.22 Å2
2--0.32 Å20 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1404 0 35 162 1601
Biso mean--27.93 28 -
Num. residues----177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191510
X-RAY DIFFRACTIONr_bond_other_d0.0010.021401
X-RAY DIFFRACTIONr_angle_refined_deg2.1321.9792055
X-RAY DIFFRACTIONr_angle_other_deg0.97533205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0755187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77222.72777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.69915263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2111521
X-RAY DIFFRACTIONr_chiral_restr0.1650.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021731
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
X-RAY DIFFRACTIONr_rigid_bond_restr5.58532911
X-RAY DIFFRACTIONr_sphericity_free30.139549
X-RAY DIFFRACTIONr_sphericity_bonded10.27553005
LS refinement shellResolution: 1.2→1.232 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 136 -
Rwork0.241 2413 -
all-2549 -
obs--67.86 %

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