6OWG

Structure of a synthetic beta-carboxysome shell, T=4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 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

  • DOI: https://doi.org/10.1104/pp.19.00885
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Microcompartments protein
A,
AA [auth 0],
AB [auth q],
AC [auth AQ],
AD [auth BG],
AE [auth B6],
AF [auth CW],
AG [auth DM],
AH [auth EC],
AI [auth E2],
B,
BB [auth r],
BD [auth BH],
BF [auth CX],
BH [auth ED],
C,
CA [auth 2],
CB [auth s],
CC [auth AS],
CD [auth BI],
CE [auth B8],
CF [auth CY],
CG [auth DO],
CH [auth EE],
CI [auth E4],
DA [auth 3],
DC [auth AT],
DE [auth B9],
DG [auth DP],
DI [auth E5],
E,
EA [auth 4],
EB [auth u],
EC [auth AU],
ED [auth BK],
EE [auth CA],
EF [auth C0],
EG [auth DQ],
EH [auth EG],
EI [auth E6],
F,
FB [auth v],
FD [auth BL],
FF [auth C1],
FH [auth EH],
G,
GA [auth 6],
GB [auth w],
GC [auth AW],
GD [auth BM],
GE [auth CC],
GF [auth C2],
GG [auth DS],
GH [auth EI],
HA [auth 7],
HC [auth AX],
HE [auth CD],
HG [auth DT],
I,
IA [auth 8],
IB [auth y],
IC [auth AY],
ID [auth BO],
IE [auth CE],
IF [auth C4],
IG [auth DU],
IH [auth EK],
J,
JB [auth z],
JD [auth BP],
JF [auth C5],
JH [auth EL],
K,
KA [auth a],
KB [auth AA],
KC [auth A0],
KD [auth BQ],
KE [auth CG],
KF [auth C6],
KG [auth DW],
KH [auth EM],
LA [auth b],
LC [auth A1],
LE [auth CH],
LG [auth DX],
M,
MA [auth c],
MB [auth AC],
MC [auth A2],
MD [auth BS],
ME [auth CI],
MF [auth C8],
MG [auth DY],
MH [auth EO],
N,
NB [auth AD],
ND [auth BT],
NF [auth C9],
NH [auth EP],
O,
OA [auth e],
OB [auth AE],
OC [auth A4],
OD [auth BU],
OE [auth CK],
OF [auth DA],
OG [auth D0],
OH [auth EQ],
PA [auth f],
PC [auth A5],
PE [auth CL],
PG [auth D1],
Q,
QA [auth g],
QB [auth AG],
QC [auth A6],
QD [auth BW],
QE [auth CM],
QF [auth DC],
QG [auth D2],
QH [auth ES],
R,
RB [auth AH],
RD [auth BX],
RF [auth DD],
RH [auth ET],
S,
SA [auth i],
SB [auth AI],
SC [auth A8],
SD [auth BY],
SE [auth CO],
SF [auth DE],
SG [auth D4],
SH [auth EU],
TA [auth j],
TC [auth A9],
TE [auth CP],
TG [auth D5],
U,
UA [auth k],
UB [auth AK],
UC [auth BA],
UD [auth B0],
UE [auth CQ],
UF [auth DG],
UG [auth D6],
UH [auth EW],
V,
VB [auth AL],
VD [auth B1],
VF [auth DH],
VH [auth EX],
W,
WA [auth m],
WB [auth AM],
WC [auth BC],
WD [auth B2],
WE [auth CS],
WF [auth DI],
WG [auth D8],
WH [auth EY],
XA [auth n],
XC [auth BD],
XE [auth CT],
XG [auth D9],
Y,
YA [auth o],
YB [auth AO],
YC [auth BE],
YD [auth B4],
YE [auth CU],
YF [auth DK],
YG [auth EA],
YH [auth E0],
Z,
ZB [auth AP],
ZD [auth B5],
ZF [auth DL],
ZH [auth E1]
113Halothece sp. PCC 7418Mutation(s): 0 
Gene Names: PCC7418_3532
UniProt
Find proteins for K9YHS7 (Halothece sp. (strain PCC 7418))
Explore K9YHS7 
Go to UniProtKB:  K9YHS7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9YHS7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ethanolamine utilization protein EutN/carboxysome structural protein Ccml105Halothece sp. PCC 7418Mutation(s): 0 
Gene Names: PCC7418_3533
UniProt
Find proteins for K9YFK1 (Halothece sp. (strain PCC 7418))
Explore K9YFK1 
Go to UniProtKB:  K9YFK1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9YFK1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0b2

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references
  • Version 1.2: 2019-12-18
    Changes: Other
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references