2024-09-25 REL RCSB RCSB RCSB 2024-04-03 2024-09-18 2024-09-18 2024-09-25 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM133325-05 United States Cargo-loaded Myxococcus xanthus EncA encapsulin engineered pore mutant with T=3 icosahedral symmetry Andreas MP Kwon S Giessen TW encapsulin, nanocompartment, pore mutant, VIRUS LIKE PARTICLE Kwon S Andreas MP Giessen TW Pore Engineering as a General Strategy to Improve Protein-Based Enzyme Nanoreactor Performance. Acs Nano US 18 25740 25753 2024 39226211 doi:10.1021/acsnano.4c08186 1936-086X 9b9q FULLOVERLAP Cargo-loaded Myxococcus xanthus EncA encapsulin engineered pore mutant with T=3 icosahedral symmetry Cargo-loaded Myxococcus xanthus EncA encapsulin engineered pore mutant with T=3 icosahedral symmetry 0 1 2 Myxococcus xanthus DK 1622 5.7 Myxococcus xanthus EncA encapsulin engineered pore mutant with T=3 icosahedral symmetry 1 1 Myxococcus xanthus DK 1622 SNAP-tag-targeting peptide cargo protein 2 2 Myxococcus xanthus DK 1622 Type 1 encapsulin shell protein EncA Myxococcus xanthus DK 1622 0.030901013999999997 3 Escherichia coli BL21(DE3) LEVO MPDFLGHAENPLREEEWARLNETVIQVARRSLVGRRILDIYGPLGAGVQTVPYDEFQGVSPGAVDIVGEQETAMVFTDAR KFKTIPIIYKDFLLHWRDIEAARTHNMPLDVSAAAGAAALCAQQEDELIFYGDARLGYEGLMTANGRLTVPLGDWTSPGG GFQAIVEATRKLNEQGHFGPYAVVLSPRLYSQLHRGGEIETIRQLASDGVYQSNRLRGESGVVVSTGRENMDLAVSMDMV AAYLGASRMNHPFRVLEALLLRIKHPDAICTLEGAGATERR Q1D6H4 Encapsulin nanocompartment cargo protein EncC Myxococcus xanthus DK 1622 0.0014156849999999999 3 Escherichia coli BL21(DE3) LEVO PEKRLTVGSLRR Q1D3Y8 singleParticle particle 4.1 7.5 150.0 NaCl sodium chloride 20.0 C4H11NO3 tris(hydroxymethyl)aminomethane
150 mM NaCl, 20 mM Tris pH 7.5
 Quantifoil R1.2/1.3 COPPER 200 CARBON HOLEY GLOW DISCHARGE AIR
The grid was glow discharged at 5 mA for 60 seconds under vacuum.
 ETHANE 100 295 FEI VITROBOT MARK IV
Blot force: 20 Blot time: 4 seconds Wait time: 0 seconds.
FEI TECNAI ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 1.0 1.8 45000.0 GATAN K2 SUMMIT (4k x 4k) COUNTING 3710 3838 1 706 6.0 39.18 1 37600
Ab-initio model
 I 3.14 FSC 0.143 CUT-OFF cryoSPARC 3.10.0 Homogeneous refinement
Homogeneous refinement was performed against the intial ab-initio map using I symmetry, per-particle defocus optimization, per-group CTF paramterization, and Ewald sphere correction.
12967 MAXIMUM LIKELIHOOD cryoSPARC 3.10.0 MAXIMUM LIKELIHOOD cryoSPARC 3.10.0 emd_44388.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 509.60004 509.60004 509.60004 90.0 90.0 90.0 X Y Z -0.5330662 1.1924132 0.0017669466 0.069834806 1.1581819 1.1581819 1.1581819 0.14 AUTHOR 7S4Q PDB experimental model FLEXIBLE FIT
ChimeraX v1.2.5 was first used to place the starting model (PDB: 7S4Q) in the cryo-EM map by using the fit in map command. The model was then manually refined using Coot v 0.9.8.1, followed by iterative real-space refinements in Phenix v1.20.1-4487-000. BioMT operators were identified from the cryo-EM map using map_symmetry command in Phenix then applied to the model using the apply_ncs command to assemble the complete shell. Real-space refinement was repeated in Phenix with NCS constraints applied. The BioMT operators were then identified using find_ncs command in Phenix and applied to the header of a protomer of the NCS-refined model.
cross-correlation coefficient REAL 93.099999999999994 emd_44388_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 509.60004 509.60004 509.60004 90.0 90.0 90.0 X Y Z -0.43777165 0.61427087 0.002010678 0.06540626 1.1581819 1.1581819 1.1581819 AUTHOR emd_44388_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 509.60004 509.60004 509.60004 90.0 90.0 90.0 X Y Z -1.2545027 0.60375357 0.002008629 0.065548025 1.1581819 1.1581819 1.1581819 AUTHOR