2024-05-22 REL PDBe PDBe PDBe 2019-11-14 2020-08-12 2020-08-12 2024-05-22 Spanish Ministry of Economy and Competitiveness BFU2017-89143-P Spain Spanish Ministry of Economy and Competitiveness RYC-2015-19059 Spain Spanish Ministry of Economy and Competitiveness BFU2016-78606-P Spain Spanish Ministry of Economy and Competitiveness RYC-2014-16490 Spain Spanish Ministry of Science, Innovation, and Universities RTI2018-095204-B-C21 Spain Vip3Aa protoxin structure Nunez-Ramirez R Huesa J Vip3Aa, toxin, protoxin, beta prism, insecticidal protein, Vip3 Nunez-Ramirez R Huesa J Bel Y Ferre J Casino P Arias-Palomo E Molecular architecture and activation of the insecticidal protein Vip3Aa from Bacillus thuringiensis. Nat Commun UK 11 3974 3974 2020 32769995 doi:10.1038/s41467-020-17758-5 2041-1723 6tfj FULLOVERLAP Vip3Aa protoxin Vip3Aa protoxin 0 1 Bacillus thuringiensis 0.35 Vegetative insecticidal protein Bacillus thuringiensis 0.08876280499999999 4 Escherichia coli LEVO MNKNNTKLSTRALPSFIDYFNGIYGFATGIKDIMNMIFKTDTGGDLTLDEILKNQQLLNDISGKLDGVNGSLNDLIAQGN LNTELSKEILKIANEQNQVLNDVNNKLDAINTMLRVYLPKLTSMLSDVMKQNYALSLQIEYLSKQLQEISDKLDIINVNV LINSTLTEITPAYQRIKYVNEKFEELTFATETSSKVKKDGSPADILDELTELTELAKSVTKNDVDGFEFYLNTFHDVMVG NNLFGRSALKTASELITKENVKTSGSEVGNVYNFLIVLTALQAKAFLTLTTCRKLLGLADIDYTSIMNEHLNKEKEEFRV NILPTLSNTFSNPNYAKVKGSDEDAKMIVEAKPGHALIGFEISNDSITVLKVYEAKLKQNYQVDKDSLSEVIYGDMDKLL CPDQSEQIYYTNNIVFPNEYVITKIDFTKKMKTLRYEVTANFYDSSTGEIDLNKKKVESSEAEYRTLSANDDGVYMPLGV ISETFLTPINGFGLQADENSRLITLTCKSYLRELLLATDLSNKETKLIVPPSGFISNIVENGSIEEDNLEPWKANNKNAY VDHTGGVNGTKALYVHKDGGISQFIGDKLKPKTEYVIQYTVKGKPSIHLKDENTGYIHYEDTNNNLEDYQTINKRFTTGT DLKGVYLILKSQNGDEAWGDNFIILEISPSEKLLSPELINTNNWTSTGSTNISGNTLTLYQGGRGILKQNLQLDSFSTYR VYFSVSGDANVRIRNSREVLFEKRYMSGAKDVSEMFTTKFEKDNFYIELSQGNNLYGGPIVHFYDVSIK Q58XI2 singleParticle particle 8.0 Quantifoil R2/2 COPPER 300 CARBON CONTINUOUS GLOW DISCHARGE ETHANE FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) COUNTING 56.6 1
Initial model was obtained using the SGD algorithm implemented in RELION
 C2 2.9 FSC 0.143 CUT-OFF RELION 3.0 478797 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 emd_10492.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 264 264 264 0 0 0 264 264 264 276.672 276.672 276.672 90.0 90.0 90.0 X Y Z -0.14471115 0.24508579 0.00032655618 0.005373959 1.048 1.048 1.048 0.02 AUTHOR Half map 2 OTHER
The atomic coordinates were manually modeled de novo in the cryo-EM map using Coot, and then subjected to iterative rounds of real space refinement using Phenix
REAL emd_10492_msk_1.map emd_10492_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 264 264 264 0 0 0 264 264 264 276.672 276.672 276.672 90.0 90.0 90.0 X Y Z -0.034539167 0.0751133 -0.000022808272 0.0025571075 1.048 1.048 1.048 AUTHOR Unsharpened EM map of the Vip3Aa protoxin emd_10492_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 264 264 264 0 0 0 264 264 264 276.672 276.672 276.672 90.0 90.0 90.0 X Y Z -0.068037875 0.11136835 0.000053413023 0.001471607 1.048 1.048 1.048 AUTHOR Focused classification map of the C-terminal domains of the protoxin emd_10492_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 264 264 264 0 0 0 264 264 264 276.672 276.672 276.672 90.0 90.0 90.0 X Y Z -0.0353152 0.08983937 -0.000018553697 0.0033394494 1.048 1.048 1.048 AUTHOR Half map 1 emd_10492_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 264 264 264 0 0 0 264 264 264 276.672 276.672 276.672 90.0 90.0 90.0 X Y Z -0.036192432 0.08773029 -0.000017806984 0.003354887 1.048 1.048 1.048 AUTHOR Focused classification map of the C-terminal domains of the protoxin