9LY8 | pdb_00009ly8

Cryo-EM structure of carboxysomal midi-shell: T=9 shell under C1 symmetry


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Symmetry-adjusted cryo-EM analysis unveils the detailed linker protein CsoS2 interactions within the alpha-carboxysome shell.

Li, J.Li, T.Wang, S.Zhang, Y.Z.Liu, L.N.Wang, P.

(2025) Plant Physiol 198

  • DOI: https://doi.org/10.1093/plphys/kiaf165
  • Primary Citation of Related Structures:  
    9LY8, 9LY9

  • PubMed Abstract: 

    Excessive symmetry in cryo-EM data processing can distort key structural details of bacterial microcompartments, highlighting the importance of balanced symmetry for accurate structural insights.


  • Organizational Affiliation
    • Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major carboxysome shell protein CsoS1A
A [auth A2],
AA [auth H5],
AB [auth D7],
AC [auth A8],
AD [auth Hb],
AE [auth Dc],
AF [auth Af],
AG [auth Hh],
AH [auth Dk],
AI [auth Bn],
AJ [auth Hp],
AK [auth Es],
AL [auth By],
AM [auth Hx],
AN [auth ED],
AO [auth BF],
AP [auth HI],
AQ [auth EK],
AR [auth AL],
AS [auth GP],
AT [auth DQ],
AV [auth FV],
AW [auth HO],
B [auth B2],
BB [auth E7],
BC [auth B8],
BE [auth Ec],
BF [auth Bf],
BH [auth Ek],
BI [auth Cn],
BK [auth Fs],
BL [auth Cy],
BN [auth FD],
BO [auth CF],
BQ [auth FK],
BR [auth BL],
BS [auth HP],
BT [auth EQ],
BU [auth AT],
BV [auth GV],
C [auth C2],
CB [auth F7],
CC [auth C8],
CE [auth Fc],
CF [auth Cf],
CH [auth Fk],
CI [auth Dn],
CK [auth Gs],
CL [auth Dy],
CN [auth GD],
CO [auth DF],
CQ [auth GK],
CR [auth CL],
CT [auth FQ],
CU [auth BT],
CV [auth HV],
D [auth D2],
DA [auth A3],
DB [auth G7],
DC [auth D8],
DD [auth Aa],
DE [auth Gc],
DF [auth Df],
DG [auth Ai],
DH [auth Gk],
DI [auth En],
DJ [auth At],
DK [auth Hs],
DL [auth Ey],
DM [auth AA],
DN [auth HD],
DO [auth EF],
DP [auth AG],
DQ [auth HK],
DR [auth DL],
DT [auth GQ],
DU [auth CT],
E [auth E2],
EA [auth B3],
EB [auth H7],
EC [auth E8],
ED [auth Ba],
EE [auth Hc],
EF [auth Ef],
EG [auth Bi],
EI [auth Fn],
EJ [auth Bt],
EL [auth Fy],
EM [auth BA],
EO [auth FF],
EP [auth BG],
ER [auth EL],
ES [auth AO],
ET [auth HQ],
EU [auth DT],
EV [auth AW],
F [auth F2],
FA [auth C3],
FC [auth F8],
FD [auth Ca],
FF [auth Ff],
FG [auth Ci],
FI [auth Gn],
FJ [auth Ct],
FL [auth Gy],
FM [auth CA],
FO [auth GF],
FP [auth CG],
FR [auth FL],
FS [auth BO],
FU [auth ET],
FV [auth BW],
G [auth G2],
GA [auth D3],
GC [auth G8],
GD [auth Da],
GE [auth Ad],
GF [auth Gf],
GG [auth Di],
GH [auth Ao],
GI [auth Hn],
GJ [auth Dt],
GK [auth Av],
GL [auth Hy],
GM [auth DA],
GN [auth AB],
GO [auth HF],
GP [auth DG],
GQ [auth AJ],
GR [auth GL],
GS [auth CO],
GU [auth FT],
GV [auth CW],
H [auth H2],
HA [auth E3],
HB [auth A6],
HC [auth H8],
HD [auth Ea],
HE [auth Bd],
HG [auth Ei],
HH [auth Bo],
HJ [auth Et],
HK [auth Bv],
HM [auth EA],
HN [auth BB],
HP [auth EG],
HQ [auth BJ],
HR [auth HL],
HS [auth DO],
HT [auth AR],
HU [auth GT],
HV [auth DW],
IA [auth F3],
IB [auth B6],
ID [auth Fa],
IE [auth Cd],
IG [auth Fi],
IH [auth Co],
IJ [auth Ft],
IK [auth Cv],
IM [auth FA],
IN [auth CB],
IP [auth FG],
IQ [auth CJ],
IS [auth EO],
IT [auth BR],
IU [auth HT],
IV [auth EW],
JA [auth G3],
JB [auth C6],
JC [auth A9],
JD [auth Ga],
JE [auth Dd],
JF [auth Aj],
JG [auth Gi],
JH [auth Do],
JI [auth Aq],
JJ [auth Gt],
JK [auth Dv],
JL [auth Aw],
JM [auth GA],
JN [auth DB],
JO [auth AE],
JP [auth GG],
JQ [auth DJ],
JS [auth FO],
JT [auth CR],
JV [auth FW],
K [auth A1],
KA [auth H3],
KB [auth D6],
KC [auth B9],
KD [auth Ha],
KE [auth Ed],
KF [auth Bj],
KG [auth Hi],
KH [auth Eo],
KI [auth Bq],
KJ [auth Ht],
KK [auth Ev],
KL [auth Bw],
KM [auth HA],
KN [auth EB],
KO [auth BE],
KP [auth HG],
KQ [auth EJ],
KR [auth AM],
KS [auth GO],
KT [auth DR],
KV [auth GW],
L [auth B1],
LB [auth E6],
LC [auth C9],
LE [auth Fd],
LF [auth Cj],
LH [auth Fo],
LI [auth Cq],
LK [auth Fv],
LL [auth Cw],
LN [auth FB],
LO [auth CE],
LQ [auth FJ],
LR [auth BM],
LT [auth ER],
LU [auth AX],
LV [auth HW],
M [auth C1],
MB [auth F6],
MC [auth D9],
ME [auth Gd],
MF [auth Dj],
MH [auth Go],
MI [auth Dq],
MK [auth Gv],
ML [auth Dw],
MN [auth GB],
MO [auth DE],
MP [auth AH],
MQ [auth GJ],
MR [auth CM],
MT [auth FR],
MU [auth BX],
N [auth D1],
NA [auth A4],
NB [auth G6],
NC [auth E9],
ND [auth Ae],
NE [auth Hd],
NF [auth Ej],
NG [auth Al],
NH [auth Ho],
NI [auth Eq],
NJ [auth Ar],
NK [auth Hv],
NL [auth Ew],
NM [auth Az],
NN [auth HB],
NO [auth EE],
NP [auth BH],
NQ [auth HJ],
NR [auth DM],
NS [auth AS],
NT [auth GR],
NU [auth CX],
O [auth E1],
OA [auth B4],
OC [auth F9],
OD [auth Be],
OF [auth Fj],
OG [auth Bl],
OI [auth Fq],
OJ [auth Br],
OL [auth Fw],
OM [auth Bz],
OO [auth FE],
OP [auth CH],
OR [auth EM],
OS [auth BS],
OT [auth HR],
OU [auth DX],
OV [auth H1],
P [auth F1],
PA [auth C4],
PC [auth G9],
PD [auth Ce],
PF [auth Gj],
PG [auth Cl],
PI [auth Gq],
PJ [auth Cr],
PL [auth Gw],
PM [auth Cz],
PN [auth AC],
PO [auth GE],
PP [auth DH],
PR [auth FM],
PS [auth CS],
PU [auth EX],
PV [auth H6],
Q [auth G1],
QA [auth D4],
QB [auth A0],
QC [auth H9],
QD [auth De],
QE [auth Ag],
QF [auth Hj],
QG [auth Dl],
QH [auth Am],
QI [auth Hq],
QJ [auth Dr],
QK [auth Au],
QL [auth Hw],
QM [auth Dz],
QN [auth BC],
QO [auth HE],
QP [auth EH],
QQ [auth AN],
QR [auth GM],
QS [auth DS],
QU [auth FX],
RA [auth E4],
RB [auth B0],
RD [auth Ee],
RE [auth Bg],
RG [auth El],
RH [auth Bm],
RJ [auth Er],
RK [auth Bu],
RM [auth Ez],
RN [auth CC],
RP [auth FH],
RQ [auth BN],
RR [auth HM],
RS [auth ES],
RT [auth AU],
RU [auth GX],
SA [auth F4],
SB [auth C0],
SD [auth Fe],
SE [auth Cg],
SG [auth Fl],
SH [auth Cm],
SJ [auth Fr],
SK [auth Cu],
SM [auth Fz],
SN [auth DC],
SP [auth GH],
SQ [auth CN],
SS [auth FS],
ST [auth BU],
SU [auth HX],
SV [auth Hf],
T [auth A5],
TA [auth G4],
TB [auth D0],
TC [auth Ab],
TD [auth Ge],
TE [auth Dg],
TF [auth Ah],
TG [auth Gl],
TH [auth Dm],
TI [auth Ap],
TJ [auth Gr],
TK [auth Du],
TL [auth Ax],
TM [auth Gz],
TN [auth EC],
TO [auth AI],
TP [auth HH],
TQ [auth DN],
TS [auth GS],
TT [auth CU],
TV [auth Hk],
U [auth B5],
UA [auth H4],
UB [auth E0],
UC [auth Bb],
UD [auth He],
UE [auth Eg],
UF [auth Bh],
UG [auth Hl],
UH [auth Em],
UI [auth Bp],
UJ [auth Hr],
UK [auth Eu],
UL [auth Bx],
UN [auth FC],
UO [auth BI],
UQ [auth EN],
UR [auth AP],
US [auth HS],
UT [auth DU],
V [auth C5],
VB [auth F0],
VC [auth Cb],
VE [auth Fg],
VF [auth Ch],
VH [auth Fm],
VI [auth Cp],
VK [auth Fu],
VL [auth Cx],
VN [auth GC],
VO [auth CI],
VQ [auth FN],
VR [auth BP],
VT [auth EU],
VU [auth AV],
W [auth D5],
WB [auth G0],
WC [auth Db],
WE [auth Gg],
WF [auth Dh],
WH [auth Gm],
WI [auth Dp],
WJ [auth As],
WK [auth Gu],
WL [auth Dx],
WM [auth AD],
WN [auth HC],
WO [auth DI],
WP [auth AK],
WQ [auth GN],
WR [auth CP],
WT [auth FU],
WU [auth BV],
WV [auth Hu],
X [auth E5],
XA [auth A7],
XB [auth H0],
XC [auth Eb],
XD [auth Ac],
XE [auth Hg],
XF [auth Eh],
XG [auth Ak],
XH [auth Hm],
XI [auth Ep],
XJ [auth Bs],
XL [auth Ex],
XM [auth BD],
XO [auth EI],
XP [auth BK],
XQ [auth HN],
XR [auth DP],
XS [auth AQ],
XT [auth GU],
XU [auth CV],
XV [auth Hz],
Y [auth F5],
YA [auth B7],
YC [auth Fb],
YD [auth Bc],
YF [auth Fh],
YG [auth Bk],
YI [auth Fp],
YJ [auth Cs],
YL [auth Fx],
YM [auth CD],
YO [auth FI],
YP [auth CK],
YR [auth EP],
YS [auth BQ],
YT [auth HU],
YU [auth DV],
Z [auth G5],
ZA [auth C7],
ZC [auth Gb],
ZD [auth Cc],
ZF [auth Gh],
ZG [auth Ck],
ZH [auth An],
ZI [auth Gp],
ZJ [auth Ds],
ZK [auth Ay],
ZL [auth Gx],
ZM [auth DD],
ZN [auth AF],
ZO [auth GI],
ZP [auth DK],
ZR [auth FP],
ZS [auth CQ],
ZU [auth EV]
98Halothiobacillus neapolitanus c2Mutation(s): 0 
Gene Names: csoS1AcsoS1Hneap_0915
UniProt
Find proteins for P45689 (Halothiobacillus neapolitanus (strain ATCC 23641 / c2))
Explore P45689 
Go to UniProtKB:  P45689
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45689
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxysome assembly protein CsoS2B869Halothiobacillus neapolitanus c2Mutation(s): 0 
Gene Names: csoS2Hneap_0920
UniProt
Find proteins for O85041 (Halothiobacillus neapolitanus (strain ATCC 23641 / c2))
Explore O85041 
Go to UniProtKB:  O85041
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO85041
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxysome shell vertex protein CsoS4A83Halothiobacillus neapolitanus c2Mutation(s): 0 
Gene Names: csoS4AorfAHneap_0918
UniProt
Find proteins for O85043 (Halothiobacillus neapolitanus (strain ATCC 23641 / c2))
Explore O85043 
Go to UniProtKB:  O85043
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO85043
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32070109

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-31
    Type: Initial release