2024-11-27 REL RCSB RCSB RCSB 2024-04-22 2024-11-27 2024-11-27 2024-11-27 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM133325 United States Streptomyces griseus Family 2B encapsulin shell Andreas MP Giessen TW Encapsulin, nanocompartment, VIRUS LIKE PARTICLE Andreas MP Giessen TW The biosynthesis of the odorant 2-methylisoborneol is compartmentalized inside a protein shell. Nat Commun UK 15 9715 9715 2024 39521781 doi:10.1038/s41467-024-54175-4 2041-1723 9bhu FULLOVERLAP Streptomyces griseus Family 2B encapsulin shell Streptomyces griseus Family 2B encapsulin shell 0 1 Streptomyces griseus subsp. griseus Nucleotide-binding protein Streptomyces griseus subsp. griseus 0.052014137
Residues 1-39, 147-152, and 216-245 are unresolved in the map.
1 Escherichia coli BL21(DE3) LEVO MTVDSTSEARLEVPRQSSLGTAAARNLASTTKSAPQMQEITSRWLLRMLPWVETKGGAYRVNRRLTFTVGDGRVEFVQDG STVRVIPQELGELALLRDFDDAEVLSAIADRCVQRDFRAGETLVERGTAADELHLIAHGRIGQASAGSYGDEVTLDVLAD GDRFGEHALLDEDARWSQTATAETSGTLLTLSRADFAAVVANSPALRSHLAAFTARSEQRQNHRGEAEIAMSAGHVGEHE LPGAFADYELKPREYELSVAQTILRVHTRVADLYNGPMNQTEEQLRLTIEALRERQEHELINNREFGLLHNADFKQRIQT HSGPPTPDDLDELLCRRRGTKFFLAHPRTIAAMGREFNARGLYPDHTDLGGQQVPAWRGVPILPCGKIPITPERTSSILA LRTGEEDQGVIGLRQTGLPDEYEPGLSVRFMNIDEKAIISYLVSTYYSAAILVPDAVGVLENVQIANWPR Q54255 CALCIUM ION 4.0078e-05 1 CA singleParticle particle 2.5 7.5 150.0 NaCl sodium chloride 20.0 C4H11NO3 tris
150 mM NaCl, 20 mM Tris pH 7.5
 Quantifoil R1.2/1.3 COPPER 200 CARBON HOLEY GLOW DISCHARGE
60 seconds at 5 mA under vacuum
 ETHANE 100 295 FEI VITROBOT MARK IV
Blot force: 20 Blot time: 4 seconds.
TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 1.0 1.8 45000.0 GATAN K2 SUMMIT (4k x 4k) COUNTING 3710 3838 1 5.0 43.22 1 159394 Ab-initio model I 2.71 FSC 0.143 CUT-OFF cryoSPARC 4.4.0+231114 Homogeneous Refinement
Homogeneous refinement with I symmetry imposed, per-particle defocus optimization, per-group CTF parameterization, spherical aberration fit enabled, tetrafoil fit enabled, Ewald sphere correction with negative curvature, and minimize over per-particle scale enabled.
135027 MAXIMUM LIKELIHOOD cryoSPARC 4.4.0+231114 MAXIMUM LIKELIHOOD cryoSPARC 4.4.0+231114 emd_44553.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 400.40002 400.40002 400.40002 90.0 90.0 90.0 X Y Z -0.45272407 0.77573323 0.0013752987 0.03463632 0.91 0.91 0.91 0.08 AUTHOR Streptomyces griseus Family 2B encapsulin shell Q54255 AlphaFold in silico model FLEXIBLE FIT
An AlphaFold-generated model was fit into the map using ChimeraX v1.5. The model was then refined iteratively by alternating rounds of manual refinement in Coot v8.9.1 and real-space refinements using PHENIX v1.20.1-4487.
cross-correlation coefficient REAL 127.900000000000006 emd_44553_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 400.40002 400.40002 400.40002 90.0 90.0 90.0 X Y Z -0.4448704 0.78909683 0.0012425969 0.028931629 0.91 0.91 0.91 AUTHOR Homogeneous reconstruction (C1 symmetry) of a 3D class from focused 3D classification containing two cyclic nucleotide binding domains at the 2-fold symmetry axis in the focused mask. emd_44553_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 400.40002 400.40002 400.40002 90.0 90.0 90.0 X Y Z -0.062811635 0.20657124 0.00021036425 0.016258107 0.91 0.91 0.91 AUTHOR Half Map B emd_44553_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 400.40002 400.40002 400.40002 90.0 90.0 90.0 X Y Z -0.06473098 0.20630455 0.00021073669 0.01627665 0.91 0.91 0.91 AUTHOR Half Map A