6OWF | pdb_00006owf

Structure of a synthetic beta-carboxysome shell, T=3

PDB DOI: https://doi.org/10.2210/pdb6OWF/pdb
EM Map EMD-20208: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Halothece sp. PCC 7418
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-05-09 Released: 2019-09-25
Deposition Author(s): Sutter, M., Laughlin, T.G., Davies, K.M., Kerfeld, C.A.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of a Syntheticbeta-Carboxysome Shell.

Sutter, M., Laughlin, T.G., Sloan, N.B., Serwas, D., Davies, K.M., Kerfeld, C.A.

(2019) Plant Physiol 181: 1050-1058

PubMed: 31501298 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1104/pp.19.00885
Primary Citation Related Structures:
6OWF, 6OWG

PubMed Abstract:
Carboxysomes are capsid-like, CO ₂-fixing organelles that are present in all cyanobacteria and some chemoautotrophs and that substantially contribute to global primary production. They are composed of a selectively permeable protein shell that encapsulates Rubisco, the principal CO ₂-fixing enzyme, and carbonic anhydrase. As the centerpiece of the carbon-concentrating mechanism, by packaging enzymes that collectively enhance catalysis, the carboxysome shell enables the generation of a locally elevated concentration of substrate CO ₂ and the prevention of CO ₂ escape. A functional carboxysome consisting of an intact shell and cargo is essential for cyanobacterial growth under ambient CO ₂ concentrations. Using cryo-electron microscopy, we have determined the structure of a recombinantly produced simplified β-carboxysome shell. The structure reveals the sidedness and the specific interactions between the carboxysome shell proteins. The model provides insight into the structural basis of selective permeability of the carboxysome shell and can be used to design modifications to investigate the mechanisms of cargo encapsulation and other physiochemical properties such as permeability. Notably, the permeability properties are of great interest for modeling and evaluating this carbon-concentrating mechanism in metabolic engineering. Moreover, we find striking similarity between the carboxysome shell and the structurally characterized, evolutionarily distant metabolosome shell, implying universal architectural principles for bacterial microcompartment shells.

Organizational Affiliation

Environmental Genomics and Systems Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720.

Macromolecule Content

Total Structure Weight: 2,150.22 kDa
Atom Count: 133,500
Modeled Residue Count: 17,700
Deposited Residue Count: 19,860
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Microcompartments protein	A AB [auth q] AC [auth AQ] AE [auth B6] AF [auth CW] A, AB [auth q], AC [auth AQ], AE [auth B6], AF [auth CW], B, BA [auth 1], BC [auth AR], BD [auth BH], BF [auth CX], CA [auth 2], CB [auth s], CD [auth BI], CE [auth B8], D, DB [auth t], DC [auth AT], DE [auth B9], DF [auth CZ], E, EA [auth 4], EC [auth AU], ED [auth BK], EF [auth C0], FA [auth 5], FB [auth v], FD [auth BL], FE [auth CB], G, GB [auth w], GC [auth AW], GE [auth CC], GF [auth C2], H, HA [auth 7], HC [auth AX], HD [auth BN], HF [auth C3], IA [auth 8], IB [auth y], ID [auth BO], IE [auth CE], J, JB [auth z], JC [auth AZ], JE [auth CF], JF [auth C5], K, KA [auth a], KC [auth A0], KD [auth BQ], KF [auth C6], LA [auth b], LB [auth AB], LD [auth BR], LE [auth CH], M, MB [auth AC], MC [auth A2], ME [auth CI], MF [auth C8], N, NA [auth d], NC [auth A3], ND [auth BT], NF [auth C9], OA [auth e], OB [auth AE], OD [auth BU], OE [auth CK], P, PB [auth AF], PC [auth A5], PE [auth CL], PF [auth DB], Q, QA [auth g], QC [auth A6], QD [auth BW], QF [auth DC], RA [auth h], RB [auth AH], RD [auth BX], RE [auth CN], S, SB [auth AI], SC [auth A8], SE [auth CO], SF [auth DE], T, TA [auth j], TC [auth A9], TD [auth BZ], TF [auth DF], UA [auth k], UB [auth AK], UD [auth B0], UE [auth CQ], V, VB [auth AL], VC [auth BB], VE [auth CR], VF [auth DH], W, WA [auth m], WC [auth BC], WD [auth B2], WF [auth DI], XA [auth n], XB [auth AN], XD [auth B3], XE [auth CT], Y, YB [auth AO], YC [auth BE], YE [auth CU], Z, ZA [auth p], ZC [auth BF], ZD [auth B5]	113	Halothece sp. PCC 7418	Mutation(s): 0 Gene Names: PCC7418_3532

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ethanolamine utilization protein EutN/carboxysome structural protein Ccml	AA [auth 0] AD [auth BG] BB [auth r] BE [auth B7] C AA [auth 0], AD [auth BG], BB [auth r], BE [auth B7], C, CC [auth AS], CF [auth CY], DA [auth 3], DD [auth BJ], EB [auth u], EE [auth CA], F, FC [auth AV], FF [auth C1], GA [auth 6], GD [auth BM], HB [auth x], HE [auth CD], I, IC [auth AY], IF [auth C4], JA [auth 9], JD [auth BP], KB [auth AA], KE [auth CG], L, LC [auth A1], LF [auth C7], MA [auth c], MD [auth BS], NB [auth AD], NE [auth CJ], O, OC [auth A4], OF [auth DA], PA [auth f], PD [auth BV], QB [auth AG], QE [auth CM], R, RC [auth A7], RF [auth DD], SA [auth i], SD [auth BY], TB [auth AJ], TE [auth CP], U, UC [auth BA], UF [auth DG], VA [auth l], VD [auth B1], WB [auth AM], WE [auth CS], X, XC [auth BD], XF [auth DJ], YA [auth o], YD [auth B4], ZB [auth AP], ZE [auth CV]	105	Halothece sp. PCC 7418	Mutation(s): 0 Gene Names: PCC7418_3533