8YVF | pdb_00008yvf

cryo-EM structure of carboxysomal midi-shell: assembly from CsoS4A/4B/1A/1B/1C/1D and CsoS2 C-terminal co-expression (T=9 Q=12)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
JB [auth z]SCOP2B SuperfamilyEutN/CcmL-like 8036790 3000362 SCOP2B (2022-06-29)
IB [auth y]SCOP2B SuperfamilyEutN/CcmL-like 8036790 3000362 SCOP2B (2022-06-29)
HB [auth x]SCOP2B SuperfamilyEutN/CcmL-like 8036790 3000362 SCOP2B (2022-06-29)
GB [auth w]SCOP2B SuperfamilyEutN/CcmL-like 8036790 3000362 SCOP2B (2022-06-29)
E [auth 4]SCOP2B SuperfamilyEutN/CcmL-like 8036790 3000362 SCOP2B (2022-06-29)
B [auth 1]SCOP2B SuperfamilyEutN/CcmL-like 8036790 3000362 SCOP2B (2022-06-29)
ZA [auth p]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
Z [auth P]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
YA [auth o]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
Y [auth O]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
XA [auth n]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
X [auth N]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
WA [auth m]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
W [auth M]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
VA [auth l]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
V [auth L]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
UA [auth k]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
U [auth K]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
TA [auth j]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
T [auth J]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
SB [auth A1]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
SA [auth i]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
S [auth I]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
RA [auth h]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
R [auth H]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
QA [auth g]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
Q [auth G]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
PA [auth f]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
P [auth F]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
OA [auth e]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
O [auth E]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
NA [auth d]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
N [auth D]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
MA [auth c]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
M [auth C]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
LA [auth b]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
L [auth B]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
KA [auth a]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
K [auth A]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
JA [auth Z]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
J [auth 9]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
IA [auth Y]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
I [auth 8]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
HA [auth X]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
H [auth 7]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
GA [auth W]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
G [auth 6]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
FB [auth v]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
FA [auth V]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
F [auth 5]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
EB [auth u]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
EA [auth U]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
DB [auth t]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
DA [auth T]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
D [auth 3]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
CB [auth s]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
CA [auth S]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
C [auth 2]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
BB [auth r]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
BA [auth R]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
AB [auth q]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
AA [auth Q]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)
A [auth 0]SCOP2B SuperfamilyCcmK-like 8040240 3001326 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
JB [auth z]e8yvfz1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
IB [auth y]e8yvfy1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
HB [auth x]e8yvfx1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
GB [auth w]e8yvfw1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
E [auth 4]e8yvf41 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
B [auth 1]e8yvf11 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
ZA [auth p]e8yvfp1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
Z [auth P]e8yvfP1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
YA [auth o]e8yvfo1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
Y [auth O]e8yvfO1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
XA [auth n]e8yvfn1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
X [auth N]e8yvfN1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
WA [auth m]e8yvfm1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
W [auth M]e8yvfM1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
VA [auth l]e8yvfl1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
V [auth L]e8yvfL1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
UA [auth k]e8yvfk1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
U [auth K]e8yvfK1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
TA [auth j]e8yvfj1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
T [auth J]e8yvfJ1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
SB [auth A1]e8yvfA11 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
SA [auth i]e8yvfi1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
S [auth I]e8yvfI1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
RA [auth h]e8yvfh1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
R [auth H]e8yvfH1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
QA [auth g]e8yvfg1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
Q [auth G]e8yvfG1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
PA [auth f]e8yvff1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
P [auth F]e8yvfF1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
OA [auth e]e8yvfe1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
O [auth E]e8yvfE1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
NA [auth d]e8yvfd1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
N [auth D]e8yvfD1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
MA [auth c]e8yvfc1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
M [auth C]e8yvfC1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
LA [auth b]e8yvfb1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
L [auth B]e8yvfB1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
KA [auth a]e8yvfa1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
K [auth A]e8yvfA1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
JA [auth Z]e8yvfZ1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
J [auth 9]e8yvf91 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
IA [auth Y]e8yvfY1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
I [auth 8]e8yvf81 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
HA [auth X]e8yvfX1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
H [auth 7]e8yvf71 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
GA [auth W]e8yvfW1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
G [auth 6]e8yvf61 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
FB [auth v]e8yvfv1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
FA [auth V]e8yvfV1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
F [auth 5]e8yvf51 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
EB [auth u]e8yvfu1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
EA [auth U]e8yvfU1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
DB [auth t]e8yvft1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
DA [auth T]e8yvfT1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
D [auth 3]e8yvf31 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
CB [auth s]e8yvfs1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
CA [auth S]e8yvfS1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
C [auth 2]e8yvf21 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
BB [auth r]e8yvfr1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
BA [auth R]e8yvfR1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
AB [auth q]e8yvfq1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
AA [auth Q]e8yvfQ1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)
A [auth 0]e8yvf01 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF:ECOD (v295)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF03319Ethanolamine utilisation protein EutN/carboxysome (EutN_CcmL)Ethanolamine utilisation protein EutN/carboxysomeThe crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel (PDB:2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a ...The crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel (PDB:2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a hole in the center. this suggests that EutN forms a pore, with an opening of 26 Angstrom in diameter on one face and 14 Angstrom on the other face [2]. EutN is involved in the cobalamin-dependent degradation of ethanolamine [1].
Domain
PF03319Ethanolamine utilisation protein EutN/carboxysome (EutN_CcmL)Ethanolamine utilisation protein EutN/carboxysomeThe crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel (PDB:2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a ...The crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel (PDB:2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a hole in the center. this suggests that EutN forms a pore, with an opening of 26 Angstrom in diameter on one face and 14 Angstrom on the other face [2]. EutN is involved in the cobalamin-dependent degradation of ethanolamine [1].
Domain
PF00936BMC domain (BMC)BMC domainBacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric struc ...Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure [1].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Carboxysome assembly protein CsoS2B
Carboxysome shell vertex protein CsoS4A-
Major carboxysome shell protein CsoS1A

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR020990Carboxysome assembly protein CsoS2/2BFamily
IPR004992Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmLFamily
IPR036677EutN/Ccml superfamilyHomologous Superfamily
IPR014076Carboxysome shell vertex protein CsoS4AFamily
IPR020808Bacterial microcompartments protein, conserved siteConserved Site
IPR000249Bacterial microcompartment domainDomain
IPR050575Bacterial microcompartment shellFamily
IPR044872CcmK/CsoS1, bacterial microcompartment domainDomain
IPR037233CcmK-like superfamilyHomologous Superfamily