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- PDB-7o4z: Crystal structure of the carbonic anhydrase-like domain of CcmM f... -

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Basic information

Entry
Database: PDB / ID: 7o4z
TitleCrystal structure of the carbonic anhydrase-like domain of CcmM from Synechococcus elongatus (strain PCC 7942)
ComponentsCarboxysome assembly protein CcmM
KeywordsPHOTOSYNTHESIS / protein binding 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
NICKEL (II) ION / Carboxysome assembly protein CcmM
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsZang, K. / Wang, H. / Hartl, F.U. / Hayer-Hartl, M.
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Scaffolding protein CcmM directs multiprotein phase separation in β-carboxysome biogenesis.
Authors: Kun Zang / Huping Wang / F Ulrich Hartl / Manajit Hayer-Hartl /
Abstract: Carboxysomes in cyanobacteria enclose the enzymes Rubisco and carbonic anhydrase to optimize photosynthetic carbon fixation. Understanding carboxysome assembly has implications in agricultural ...Carboxysomes in cyanobacteria enclose the enzymes Rubisco and carbonic anhydrase to optimize photosynthetic carbon fixation. Understanding carboxysome assembly has implications in agricultural biotechnology. Here we analyzed the role of the scaffolding protein CcmM of the β-cyanobacterium Synechococcus elongatus PCC 7942 in sequestrating the hexadecameric Rubisco and the tetrameric carbonic anhydrase, CcaA. We find that the trimeric CcmM, consisting of γCAL oligomerization domains and linked small subunit-like (SSUL) modules, plays a central role in mediation of pre-carboxysome condensate formation through multivalent, cooperative interactions. The γCAL domains interact with the C-terminal tails of the CcaA subunits and additionally mediate a head-to-head association of CcmM trimers. Interestingly, SSUL modules, besides their known function in recruiting Rubisco, also participate in intermolecular interactions with the γCAL domains, providing further valency for network formation. Our findings reveal the mechanism by which CcmM functions as a central organizer of the pre-carboxysome multiprotein matrix, concentrating the core components Rubisco and CcaA before β-carboxysome shell formation.
History
DepositionApr 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxysome assembly protein CcmM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3443
Polymers19,2501
Non-polymers942
Water2,288127
1
A: Carboxysome assembly protein CcmM
hetero molecules

A: Carboxysome assembly protein CcmM
hetero molecules

A: Carboxysome assembly protein CcmM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0329
Polymers57,7503
Non-polymers2826
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area4770 Å2
ΔGint-63 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.741, 89.741, 130.790
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-202-

CL

21A-336-

HOH

31A-401-

HOH

41A-414-

HOH

51A-415-

HOH

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Components

#1: Protein Carboxysome assembly protein CcmM / CcmM58 / M58 / Carbon dioxide concentrating mechanism protein CcmM / Carboxysome shell associated protein CcmM


Mass: 19249.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942 / FACHB-805) (bacteria)
Strain: PCC 7942 / FACHB-805 / Gene: ccmM, Synpcc7942_1423 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q03513
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG-3350 and 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 11, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.667→66.812 Å / Num. obs: 23881 / % possible obs: 99.9 % / Redundancy: 9.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.028 / Net I/σ(I): 13.8
Reflection shellResolution: 1.667→1.696 Å / Redundancy: 10 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1198 / CC1/2: 0.823 / Rpim(I) all: 0.319 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSJan 31, 2020data reduction
Aimless0.7.4data scaling
MOLREP11.7.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KWC

3kwc


Resolution: 1.67→66.81 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.55 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1998 1173 4.9 %RANDOM
Rwork0.1637 ---
obs0.1656 22708 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.83 Å2 / Biso mean: 28.717 Å2 / Biso min: 14.55 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.67→66.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 2 127 1377
Biso mean--35.48 41.76 -
Num. residues----165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131274
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171215
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.6321733
X-RAY DIFFRACTIONr_angle_other_deg1.4331.5762779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5645164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.99320.84571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10915193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.871512
X-RAY DIFFRACTIONr_chiral_restr0.0770.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021478
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02298
LS refinement shellResolution: 1.67→1.71 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.334 79 -
Rwork0.255 1670 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 33.123 Å / Origin y: 15.2309 Å / Origin z: -0.8084 Å
111213212223313233
T0.0278 Å2-0.001 Å20.0133 Å2-0.0186 Å20.0223 Å2--0.051 Å2
L1.0451 °20.0146 °2-0.4818 °2-2.5014 °20.0267 °2--1.9329 °2
S0.0104 Å °-0.0892 Å °-0.0987 Å °0.1603 Å °0.0367 Å °0.2847 Å °-0.0372 Å °-0.0641 Å °-0.0471 Å °

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