2024-05-15 REL PDBe PDBe PDBe 2018-08-10 2018-09-12 2018-12-12 2024-05-15 Structure of the repeat unit in the network formed by CcmM and Rubisco from Synechococcus elongatus Wang H Yan X CcmM, M58, M35, SSUL domain, Rubisco, Carboxysome, PROTEIN BINDING Wang H Yan X Aigner H Bracher A Nguyen ND Hee WY Long BM Price GD Hartl FU Hayer-Hartl M Rubisco condensate formation by CcmM in beta-carboxysome biogenesis. Nature UK 566 131 135 2019 30675061 doi:10.1038/s41586-019-0880-5 1476-4687 0006 NATUAS 6hbc FULLOVERLAP Repeat unit in the CcmM-Rubisco network consisting of a SSUL domain from CcmM and each two RbcL and two RbcS chains from Rubisco Repeat unit in the CcmM-Rubisco network consisting of a SSUL domain from CcmM and each two RbcL and two RbcS chains from Rubisco 0 1 2 3
CcmM contains a succession of three highly similar SSUL domains (residues 225-313, 340-428 and 455-539, respectively), which bind to cleft on the surface of Rubisco. Rubisco is a hexadecamer of eight RbcL and eight RbcS subunits. The complex has D4 symmetry. The SSUL-RbcL2-RbcS2 repeat units can have one of two orientations (up or down). Thus Rubisco complexes saturated with SSUL domains can have four different configurations (uuuu, uuud, uudd, udud). In reality, some SSUL binding sites are probably left unoccupied. The network is formed by flexible linkers connecting the SSUL domains in CcmM, which then interlink Rubisco hexadecamers.
Synechococcus elongatus PCC 7942 Carboxysome Carbon dioxide concentrating mechanism protein CcmM Synechococcus elongatus (strain PCC 7942) 0.010550685999999998 1 Escherichia coli BL21(DE3) LEVO SEFLSSEVITQVRSLLNQGYRIGTEHADKRRFRTSSWQPCAPIQSTNERQVLSELENCLSEHEGEYVRLLGIDTNTRSRV FEALIQRPDGSV Q03513 Ribulose bisphosphate carboxylase large chain Synechococcus elongatus (strain PCC 7942) 0.052516605 2 Escherichia coli BL21(DE3) LEVO MPKTQSAAGYKAGVKDYKLTYYTPDYTPKDTDLLAAFRFSPQPGVPADEAGAAIAAESSTGTWTTVWTDLLTDMDRYKGK CYHIEPVQGEENSYFAFIAYPLDLFEEGSVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLN KYGRPMLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVT APTCEEMMKRAEFAKELGMPIIMHDFLTAGFTANTTLAKWCRDNGVLLHIHRAMHAVIDRQRNHGIHFRVLAKCLRLSGG DHLHSGTVVGKLEGDKASTLGFVDLMREDHIEADRSRGVFFTQDWASMPGVLPVASGGIHVWHMPALVEIFGDDSVLQFG GGTLGHPWGNAPGATANRVALEACVQARNEGRDLYREGGDILREAGKWSPELAAALDLWKEIKFEFETMDKL Q31NB3 4.1.1.39 Ribulose 1,5-bisphosphate carboxylase small subunit Synechococcus elongatus (strain PCC 7942) 0.013349195999999999 2 Escherichia coli BL21(DE3) LEVO MSMKTLPKERRFETFSYLPPLSDRQIAAQIEYMIEQGFHPLIEFNEHSNPEEFYWTMWKLPLFDCKSPQQVLDEVRECRS EYGDCYIRVAGFDNIKQCQTVSFIVHRPGRY Q31NB2 4.1.1.39 singleParticle particle 5 8.0 50.0 KCl Potassium chloride 50.0 (HOCH2)3CNH2 Tris 10.0 Mg(CH3COO)2 Magnesium acetate 5.0 C4H10O2S2 DTT
Solutions were made fresh
 Quantifoil R2/1 COPPER 300 CARBON HOLEY PLASMA CLEANING AIR 101.325 ETHANE 90 298 FEI VITROBOT MARK IV
blot for 3 seconds before plunging.
This sample contained 10 nm gold beads and was not monodisperse
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 QUANTUM (4k x 4k) 0.15 1.05 1 C1 2.78 FSC 0.143 CUT-OFF 78916 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_0180.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 210.432 210.432 210.432 90.0 90.0 90.0 X Y Z -0.28270108 0.49959758 0.00016535513 0.013774122 0.822 0.822 0.822 0.0725 AUTHOR Map after post-processing AB INITIO MODEL
The cryoEM density for the repeat unit was masked by Refmac to the coordinates and converted into structure factors by Refmac. The model was adjusted with coot. This model was submitted to restrained refinement with Refmac against the structure factors.
Average Fourier shell correlation RECIPROCAL