ISDA: 9LY8

Deposition Date 2025-02-19

Release Date 2025-12-31

Last Version Date 2025-12-31

Entry Detail

PDB ID:

9LY8

Keywords:

STRUCTURAL PROTEIN

Title:

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

Biological Source:

Source Organism:

Halothiobacillus neapolitanus c2 (Taxon ID: 555778)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.77 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Major carboxysome shell protein CsoS1A
Gene (Uniprot):csoS1A
Chain IDs:A (auth: A2), B (auth: B2), C (auth: C2), D (auth: D2), E (auth: E2), F (auth: F2), G (auth: G2), H (auth: H2), K (auth: A1), L (auth: B1), M (auth: C1), N (auth: D1), O (auth: E1), P (auth: F1), Q (auth: G1), T (auth: A5), U (auth: B5), V (auth: C5), W (auth: D5), X (auth: E5), Y (auth: F5), Z (auth: G5), AA (auth: H5), DA (auth: A3), EA (auth: B3), FA (auth: C3), GA (auth: D3), HA (auth: E3), IA (auth: F3), JA (auth: G3), KA (auth: H3), NA (auth: A4), OA (auth: B4), PA (auth: C4), QA (auth: D4), RA (auth: E4), SA (auth: F4), TA (auth: G4), UA (auth: H4), XA (auth: A7), YA (auth: B7), ZA (auth: C7), AB (auth: D7), BB (auth: E7), CB (auth: F7), DB (auth: G7), EB (auth: H7), HB (auth: A6), IB (auth: B6), JB (auth: C6), KB (auth: D6), LB (auth: E6), MB (auth: F6), NB (auth: G6), QB (auth: A0), RB (auth: B0), SB (auth: C0), TB (auth: D0), UB (auth: E0), VB (auth: F0), WB (auth: G0), XB (auth: H0), AC (auth: A8), BC (auth: B8), CC (auth: C8), DC (auth: D8), EC (auth: E8), FC (auth: F8), GC (auth: G8), HC (auth: H8), JC (auth: A9), KC (auth: B9), LC (auth: C9), MC (auth: D9), NC (auth: E9), OC (auth: F9), PC (auth: G9), QC (auth: H9), TC (auth: Ab), UC (auth: Bb), VC (auth: Cb), WC (auth: Db), XC (auth: Eb), YC (auth: Fb), ZC (auth: Gb), AD (auth: Hb), DD (auth: Aa), ED (auth: Ba), FD (auth: Ca), GD (auth: Da), HD (auth: Ea), ID (auth: Fa), JD (auth: Ga), KD (auth: Ha), ND (auth: Ae), OD (auth: Be), PD (auth: Ce), QD (auth: De), RD (auth: Ee), SD (auth: Fe), TD (auth: Ge), UD (auth: He), XD (auth: Ac), YD (auth: Bc), ZD (auth: Cc), AE (auth: Dc), BE (auth: Ec), CE (auth: Fc), DE (auth: Gc), EE (auth: Hc), GE (auth: Ad), HE (auth: Bd), IE (auth: Cd), JE (auth: Dd), KE (auth: Ed), LE (auth: Fd), ME (auth: Gd), NE (auth: Hd), QE (auth: Ag), RE (auth: Bg), SE (auth: Cg), TE (auth: Dg), UE (auth: Eg), VE (auth: Fg), WE (auth: Gg), XE (auth: Hg), AF (auth: Af), BF (auth: Bf), CF (auth: Cf), DF (auth: Df), EF (auth: Ef), FF (auth: Ff), GF (auth: Gf), JF (auth: Aj), KF (auth: Bj), LF (auth: Cj), MF (auth: Dj), NF (auth: Ej), OF (auth: Fj), PF (auth: Gj), QF (auth: Hj), TF (auth: Ah), UF (auth: Bh), VF (auth: Ch), WF (auth: Dh), XF (auth: Eh), YF (auth: Fh), ZF (auth: Gh), AG (auth: Hh), DG (auth: Ai), EG (auth: Bi), FG (auth: Ci), GG (auth: Di), HG (auth: Ei), IG (auth: Fi), JG (auth: Gi), KG (auth: Hi), NG (auth: Al), OG (auth: Bl), PG (auth: Cl), QG (auth: Dl), RG (auth: El), SG (auth: Fl), TG (auth: Gl), UG (auth: Hl), XG (auth: Ak), YG (auth: Bk), ZG (auth: Ck), AH (auth: Dk), BH (auth: Ek), CH (auth: Fk), DH (auth: Gk), GH (auth: Ao), HH (auth: Bo), IH (auth: Co), JH (auth: Do), KH (auth: Eo), LH (auth: Fo), MH (auth: Go), NH (auth: Ho), QH (auth: Am), RH (auth: Bm), SH (auth: Cm), TH (auth: Dm), UH (auth: Em), VH (auth: Fm), WH (auth: Gm), XH (auth: Hm), ZH (auth: An), AI (auth: Bn), BI (auth: Cn), CI (auth: Dn), DI (auth: En), EI (auth: Fn), FI (auth: Gn), GI (auth: Hn), JI (auth: Aq), KI (auth: Bq), LI (auth: Cq), MI (auth: Dq), NI (auth: Eq), OI (auth: Fq), PI (auth: Gq), QI (auth: Hq), TI (auth: Ap), UI (auth: Bp), VI (auth: Cp), WI (auth: Dp), XI (auth: Ep), YI (auth: Fp), ZI (auth: Gp), AJ (auth: Hp), DJ (auth: At), EJ (auth: Bt), FJ (auth: Ct), GJ (auth: Dt), HJ (auth: Et), IJ (auth: Ft), JJ (auth: Gt), KJ (auth: Ht), NJ (auth: Ar), OJ (auth: Br), PJ (auth: Cr), QJ (auth: Dr), RJ (auth: Er), SJ (auth: Fr), TJ (auth: Gr), UJ (auth: Hr), WJ (auth: As), XJ (auth: Bs), YJ (auth: Cs), ZJ (auth: Ds), AK (auth: Es), BK (auth: Fs), CK (auth: Gs), DK (auth: Hs), GK (auth: Av), HK (auth: Bv), IK (auth: Cv), JK (auth: Dv), KK (auth: Ev), LK (auth: Fv), MK (auth: Gv), NK (auth: Hv), QK (auth: Au), RK (auth: Bu), SK (auth: Cu), TK (auth: Du), UK (auth: Eu), VK (auth: Fu), WK (auth: Gu), ZK (auth: Ay), AL (auth: By), BL (auth: Cy), CL (auth: Dy), DL (auth: Ey), EL (auth: Fy), FL (auth: Gy), GL (auth: Hy), JL (auth: Aw), KL (auth: Bw), LL (auth: Cw), ML (auth: Dw), NL (auth: Ew), OL (auth: Fw), PL (auth: Gw), QL (auth: Hw), TL (auth: Ax), UL (auth: Bx), VL (auth: Cx), WL (auth: Dx), XL (auth: Ex), YL (auth: Fx), ZL (auth: Gx), AM (auth: Hx), DM (auth: AA), EM (auth: BA), FM (auth: CA), GM (auth: DA), HM (auth: EA), IM (auth: FA), JM (auth: GA), KM (auth: HA), NM (auth: Az), OM (auth: Bz), PM (auth: Cz), QM (auth: Dz), RM (auth: Ez), SM (auth: Fz), TM (auth: Gz), WM (auth: AD), XM (auth: BD), YM (auth: CD), ZM (auth: DD), AN (auth: ED), BN (auth: FD), CN (auth: GD), DN (auth: HD), GN (auth: AB), HN (auth: BB), IN (auth: CB), JN (auth: DB), KN (auth: EB), LN (auth: FB), MN (auth: GB), NN (auth: HB), PN (auth: AC), QN (auth: BC), RN (auth: CC), SN (auth: DC), TN (auth: EC), UN (auth: FC), VN (auth: GC), WN (auth: HC), ZN (auth: AF), AO (auth: BF), BO (auth: CF), CO (auth: DF), DO (auth: EF), EO (auth: FF), FO (auth: GF), GO (auth: HF), JO (auth: AE), KO (auth: BE), LO (auth: CE), MO (auth: DE), NO (auth: EE), OO (auth: FE), PO (auth: GE), QO (auth: HE), TO (auth: AI), UO (auth: BI), VO (auth: CI), WO (auth: DI), XO (auth: EI), YO (auth: FI), ZO (auth: GI), AP (auth: HI), DP (auth: AG), EP (auth: BG), FP (auth: CG), GP (auth: DG), HP (auth: EG), IP (auth: FG), JP (auth: GG), KP (auth: HG), MP (auth: AH), NP (auth: BH), OP (auth: CH), PP (auth: DH), QP (auth: EH), RP (auth: FH), SP (auth: GH), TP (auth: HH), WP (auth: AK), XP (auth: BK), YP (auth: CK), ZP (auth: DK), AQ (auth: EK), BQ (auth: FK), CQ (auth: GK), DQ (auth: HK), GQ (auth: AJ), HQ (auth: BJ), IQ (auth: CJ), JQ (auth: DJ), KQ (auth: EJ), LQ (auth: FJ), MQ (auth: GJ), NQ (auth: HJ), QQ (auth: AN), RQ (auth: BN), SQ (auth: CN), TQ (auth: DN), UQ (auth: EN), VQ (auth: FN), WQ (auth: GN), XQ (auth: HN), AR (auth: AL), BR (auth: BL), CR (auth: CL), DR (auth: DL), ER (auth: EL), FR (auth: FL), GR (auth: GL), HR (auth: HL), KR (auth: AM), LR (auth: BM), MR (auth: CM), NR (auth: DM), OR (auth: EM), PR (auth: FM), QR (auth: GM), RR (auth: HM), UR (auth: AP), VR (auth: BP), WR (auth: CP), XR (auth: DP), YR (auth: EP), ZR (auth: FP), AS (auth: GP), BS (auth: HP), ES (auth: AO), FS (auth: BO), GS (auth: CO), HS (auth: DO), IS (auth: EO), JS (auth: FO), KS (auth: GO), NS (auth: AS), OS (auth: BS), PS (auth: CS), QS (auth: DS), RS (auth: ES), SS (auth: FS), TS (auth: GS), US (auth: HS), XS (auth: AQ), YS (auth: BQ), ZS (auth: CQ), AT (auth: DQ), BT (auth: EQ), CT (auth: FQ), DT (auth: GQ), ET (auth: HQ), HT (auth: AR), IT (auth: BR), JT (auth: CR), KT (auth: DR), LT (auth: ER), MT (auth: FR), NT (auth: GR), OT (auth: HR), RT (auth: AU), ST (auth: BU), TT (auth: CU), UT (auth: DU), VT (auth: EU), WT (auth: FU), XT (auth: GU), YT (auth: HU), BU (auth: AT), CU (auth: BT), DU (auth: CT), EU (auth: DT), FU (auth: ET), GU (auth: FT), HU (auth: GT), IU (auth: HT), LU (auth: AX), MU (auth: BX), NU (auth: CX), OU (auth: DX), PU (auth: EX), QU (auth: FX), RU (auth: GX), SU (auth: HX), VU (auth: AV), WU (auth: BV), XU (auth: CV), YU (auth: DV), ZU (auth: EV), AV (auth: FV), BV (auth: GV), CV (auth: HV), EV (auth: AW), FV (auth: BW), GV (auth: CW), HV (auth: DW), IV (auth: EW), JV (auth: FW), KV (auth: GW), LV (auth: HW), OV (auth: H1), PV (auth: H6), SV (auth: Hf), TV (auth: Hk), WV (auth: Hu), XV (auth: Hz), AW (auth: HO)
Chain Length:98
Number of Molecules:480
Biological Source:Halothiobacillus neapolitanus c2

UniProt ID:P45689 Pfam ID:PF00936

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Carboxysome shell vertex protein CsoS4A
Gene (Uniprot):csoS4A
Chain IDs:J (auth: P2), S (auth: P1), CA (auth: P5), MA (auth: P3), WA (auth: P4), GB (auth: P7), PB (auth: P6), ZB (auth: P0), IC (auth: P8), SC (auth: P9), CD (auth: Pb), MD (auth: Pa), WD (auth: Pe), FE (auth: Pc), PE (auth: Pd), ZE (auth: Pg), IF (auth: Pf), SF (auth: Pj), CG (auth: Ph), MG (auth: Pi), WG (auth: Pl), FH (auth: Pk), PH (auth: Po), YH (auth: Pm), II (auth: Pn), SI (auth: Pq), CJ (auth: Pp), MJ (auth: Pt), VJ (auth: Pr), FK (auth: Ps), PK (auth: Pv), YK (auth: Pu), IL (auth: Py), SL (auth: Pw), CM (auth: Px), MM (auth: PA), VM (auth: Pz), FN (auth: PD), ON (auth: PB), YN (auth: PC), IO (auth: PF), SO (auth: PE), CP (auth: PI), LP (auth: PG), VP (auth: PH), FQ (auth: PK), PQ (auth: PJ), ZQ (auth: PN), JR (auth: PL), TR (auth: PM), DS (auth: PP), MS (auth: PO), WS (auth: PS), GT (auth: PQ), QT (auth: PR), AU (auth: PU), KU (auth: PT), UU (auth: PX), DV (auth: PV), NV (auth: PW)
Chain Length:83
Number of Molecules:60
Biological Source:Halothiobacillus neapolitanus c2

UniProt ID:O85043 Pfam ID:PF03319

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Carboxysome assembly protein CsoS2B
Gene (Uniprot):csoS2
Chain IDs:I (auth: X2), R (auth: X1), BA (auth: X5), LA (auth: X3), VA (auth: X4), FB (auth: X7), OB (auth: X6), YB (auth: X0), RC (auth: X9), BD (auth: Xb), LD (auth: Xa), VD (auth: Xe), OE (auth: Xd), YE (auth: Xg), HF (auth: Xf), RF (auth: Xj), BG (auth: Xh), LG (auth: Xi), VG (auth: Xl), EH (auth: Xk), OH (auth: Xo), HI (auth: Xn), RI (auth: Xq), BJ (auth: Xp), LJ (auth: Xt), EK (auth: Xs), OK (auth: Xv), XK (auth: Xu), HL (auth: Xy), RL (auth: Xw), BM (auth: Xx), LM (auth: XA), UM (auth: Xz), EN (auth: XD), XN (auth: XC), HO (auth: XF), RO (auth: XE), BP (auth: XI), UP (auth: XH), EQ (auth: XK), OQ (auth: XJ), YQ (auth: XN), IR (auth: XL), SR (auth: XM), CS (auth: XP), LS (auth: XO), VS (auth: XS), FT (auth: XQ), PT (auth: XR), ZT (auth: XU), JU (auth: XT), TU (auth: XX), MV (auth: XW), QV (auth: X8), RV (auth: Xc), UV (auth: Xm), VV (auth: Xr), YV (auth: XB), ZV (auth: XG), BW (auth: XV)
Chain Length:869
Number of Molecules:60
Biological Source:Halothiobacillus neapolitanus c2

UniProt ID:O85041 Pfam ID:PF12288

Ligand Molecules

Primary Citation

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.Show

Plant Physiol. 198 ? ? (2025)

PMID: 40341945 DOI: 10.1093/plphys/kiaf165

Abstact

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.

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Chemical

Disease

Primary Citation of related structures

Abstact

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