2024-03-20 REL RCSB RCSB RCSB 2019-02-12 2019-05-22 2019-05-22 2024-03-20 National Institutes of Health/National Cancer Institute (NIH/NCI) R21 AG061697 01 United States human m-AAA protease AFG3L2, substrate-bound Lander GC Puchades C AAA+, ATPase, protease, mitochondria, protein quality control, neurodegeneration, inner membrane, AFG3L2, m/AAA protease, translocase Puchades C Ding B Song A Wiseman RL Lander GC Glynn SE Unique Structural Features of the Mitochondrial AAA+ Protease AFG3L2 Reveal the Molecular Basis for Activity in Health and Disease. Mol.Cell US 75 1073 2019 31327635 doi:10.1016/j.molcel.2019.06.016 1097-2765 2168 MOCEFL 6nyy FULLOVERLAP AFG3L2 AFG3L2 0 1 2
Soluble domains of the AFG3L2, comprising the AAA+ ATPase and protease domains.
Homo sapiens .360 AFG3-like protein 2 Homo sapiens 0.058331628999999996 6 Escherichia coli LEVO SNARRGPAGIGRTGRGMGGLFSVGETTAKVLKDEIDVKFKDVAGCEEAKLEIMEFVNFLKNPKQYQDLGAKIPKGAILTG PPGTGKTLLAKATAGEANVPFITVSGSEFLEMFVGVGPARVRDLFALARKNAPCILFIDQIDAVGRKRGRGNFGGQSEQE NTLNQLLVEMDGFNTTTNVVILAGTNRPDILDPALLRPGRFDRQIFIGPPDIKGRASIFKVHLRPLKLDSTLEKDKLARK LASLTPGFSGADVANVCNEAALIAARHLSDSINQKHFEQAIERVIGGLEKKTQVLQPEEKKTVAYHQAGHAVAGWYLEHA DPLLKVSIIPRGKGLGYAQYLPKEQYLYTKEQLLDRMCMTLGGRVSEEIFFGRITTGAQDDLRKVTQSAYAQIVQFGMNE KVGQISFDLPRQGDMVLEKPYSEATARLIDDEVRILINDAYKRTVALLTEKKADVEKVALLLLEKEVLDKNDMVELLGPR PFAEKSTYEEFVEGTGSLDEDTSLPEGLKDWNKEREKEKEEPPGEKVAN Q9Y4W6 3.4.24.- Substrate Homo sapiens 0.000799871 4 Escherichia coli LEVO AAAAAAAAAAA ZINC ION 6.5409e-05 6 ZN PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER 0.000506196 3 ANP MAGNESIUM ION 2.4305e-05 3 MG ADENOSINE-5'-DIPHOSPHATE 0.000427201 1 ADP singleParticle particle 2 8.0 25.0 HEPES 100.0 KCl Potassium Chloride 5.0 MgCl Magnesium Chloride 1.0 ATP Adenosine TriPhosphate 1.0 DTT Dithiothreitol
DTT and ATP were added fresh before sample preparation
 Quantifoil, UltrAuFoil, R1.2/1.3 GOLD 300 PLASMA CLEANING OTHER
Grids were plasma cleaned using a Solarus plasma cleaner (Gatan, Inc.).
 ETHANE 100 278 FEI VITROBOT MARK III
Sample was blotted for 3 seconds using Whatman No. 1 filter paper immediately prio to plunge-freezing..
FEI TECNAI ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 70.0 2.7 8.0 18.0 36000.0 43478.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 100.0 100.0 0.07 GATAN K2 SUMMIT (4k x 4k) COUNTING 3710 3838 1-30 5 5707 7.0 40.0
Data collected with Leginon
 1 4541491
Picked with FindEM
 EMD-7023
YME1 EMDB-7023 map, low pass filtered to 30A
 C1 BACK PROJECTION 3.0 FSC 0.143 CUT-OFF RELION 3.0
Multi-body refinement was used to generate 3 different reconstructions that were stitched together
1129437 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0
Multi-body reconstruction
 emd_0552.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 147.2 147.2 147.2 90.0 90.0 90.0 X Y Z -0.028558984 0.46374786 0.009907013 0.023940364 1.15 1.15 1.15 0.07 AUTHOR Composite map containing the stitched maps of the ATPase domains from subunits B-E, the ATPase domains from subunits A & F, and the protease domains 6AZ0 PDB experimental model RIGID BODY FIT
The sequence was threaded onto the PDB ID 6AZ0 and built into the EM density with Coot.
REAL 85.0 emd_0552_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 147.2 147.2 147.2 90.0 90.0 90.0 X Y Z -0.03160992 0.08507775 -0.00028328615 0.0050864015 1.15 1.15 1.15 AUTHOR ATPase domains from subunits B-E half map 1 emd_0552_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 147.2 147.2 147.2 90.0 90.0 90.0 X Y Z -0.042758726 0.066160984 0.00017608552 0.007353162 1.15 1.15 1.15 AUTHOR ATPase domains from subunits A & F half map 2 emd_0552_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 147.2 147.2 147.2 90.0 90.0 90.0 X Y Z -0.043331455 0.07083401 0.00030837787 0.007135252 1.15 1.15 1.15 AUTHOR ATPase domains from subunits A & F half map 2 emd_0552_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 147.2 147.2 147.2 90.0 90.0 90.0 X Y Z -0.03348142 0.08661199 -0.0002791577 0.005087135 1.15 1.15 1.15 AUTHOR ATPase domains from subunits B-E half map 2 emd_0552_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 147.2 147.2 147.2 90.0 90.0 90.0 X Y Z -0.03232731 0.078550875 0.0003941555 0.0061497614 1.15 1.15 1.15 AUTHOR Protease domains half map 2 emd_0552_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 147.2 147.2 147.2 90.0 90.0 90.0 X Y Z -0.032883633 0.07917735 0.00038731933 0.0061528813 1.15 1.15 1.15 AUTHOR Protease domains half map 1