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- PDB-8yxu: Crystal structure of CsoS1A/B (modeled with CsoS1A) -

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Basic information

Entry
Database: PDB / ID: 8yxu
TitleCrystal structure of CsoS1A/B (modeled with CsoS1A)
ComponentsMajor carboxysome shell protein CsoS1A
KeywordsSTRUCTURAL PROTEIN / Carboxysome / shell
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation
Similarity search - Function
Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily
Similarity search - Domain/homology
Major carboxysome shell protein CsoS1A
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsWang, P. / Li, J.X. / Li, T.P. / Li, K. / Ng, P.C. / Wang, S.M. / Chriscoli, V. / Basle, A. / Marles-Wright, J. / Zhang, Y.Z. / Liu, L.N.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32090109 China
CitationJournal: Sci Adv / Year: 2024
Title: Molecular principles of the assembly and construction of a carboxysome shell.
Authors: Peng Wang / Jianxun Li / Tianpei Li / Kang Li / Pei Cing Ng / Saimeng Wang / Vincent Chriscoli / Arnaud Basle / Jon Marles-Wright / Yu-Zhong Zhang / Lu-Ning Liu /
Abstract: Intracellular compartmentalization enhances biological reactions, crucial for cellular function and survival. An example is the carboxysome, a bacterial microcompartment for CO fixation. The ...Intracellular compartmentalization enhances biological reactions, crucial for cellular function and survival. An example is the carboxysome, a bacterial microcompartment for CO fixation. The carboxysome uses a polyhedral protein shell made of hexamers, pentamers, and trimers to encapsulate Rubisco, increasing CO levels near Rubisco to enhance carboxylation. Despite their role in the global carbon cycle, the molecular mechanisms behind carboxysome shell assembly remain unclear. Here, we present a structural characterization of α-carboxysome shells generated from recombinant systems, which contain all shell proteins and the scaffolding protein CsoS2. Atomic-resolution cryo-electron microscopy of the shell assemblies, with a maximal size of 54 nm, unveil diverse assembly interfaces between shell proteins, detailed interactions of CsoS2 with shell proteins to drive shell assembly, and the formation of heterohexamers and heteropentamers by different shell protein paralogs, facilitating the assembly of larger empty shells. Our findings provide mechanistic insights into the construction principles of α-carboxysome shells and the role of CsoS2 in governing α-carboxysome assembly and functionality.
History
DepositionApr 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major carboxysome shell protein CsoS1A
B: Major carboxysome shell protein CsoS1A


Theoretical massNumber of molelcules
Total (without water)19,9472
Polymers19,9472
Non-polymers00
Water88349
1
A: Major carboxysome shell protein CsoS1A
B: Major carboxysome shell protein CsoS1A

A: Major carboxysome shell protein CsoS1A
B: Major carboxysome shell protein CsoS1A

A: Major carboxysome shell protein CsoS1A
B: Major carboxysome shell protein CsoS1A


Theoretical massNumber of molelcules
Total (without water)59,8416
Polymers59,8416
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area11310 Å2
ΔGint-91 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.310, 67.310, 64.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Major carboxysome shell protein CsoS1A


Mass: 9973.478 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (bacteria)
Gene: csoS1A, csoS1, Hneap_0915 / Production host: Escherichia coli (E. coli) / References: UniProt: P45689
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 42.01 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium citrate tribasic tetrahydrate and 20% (w/v) polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→58.29 Å / Num. obs: 9780 / % possible obs: 99.9 % / Redundancy: 18.1 % / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.033 / Rrim(I) all: 0.147 / Net I/σ(I): 12.8
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.482 / Num. unique obs: 801 / CC1/2: 0.99 / Rpim(I) all: 0.108 / Rrim(I) all: 0.495 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→33.655 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 935 10.05 %
Rwork0.2159 --
obs0.2197 9299 95.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→33.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 0 49 1343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071306
X-RAY DIFFRACTIONf_angle_d0.91770
X-RAY DIFFRACTIONf_dihedral_angle_d3.387784
X-RAY DIFFRACTIONf_chiral_restr0.052216
X-RAY DIFFRACTIONf_plane_restr0.005234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.21070.3621360.23681235X-RAY DIFFRACTION99
2.2107-2.34920.3921020.3188918X-RAY DIFFRACTION73
2.3492-2.53050.32831380.22551235X-RAY DIFFRACTION99
2.5305-2.78510.26341410.22061237X-RAY DIFFRACTION99
2.7851-3.18780.21261410.22531240X-RAY DIFFRACTION99
3.1878-4.01530.21561340.20481226X-RAY DIFFRACTION97
4.0153-33.6540.22131430.18691273X-RAY DIFFRACTION99

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