REL RCSB RCSB RCSB 2015-01-23 2015-02-18 2015-02-18 2015-05-27 Negative stain reconstruction of the Pex1/Pex6 complex in presence of ADP Gardner BM Chowdhury S Lander GC Martin A Peroxisome, AAA+ ATPase, Pex1, Pex6 Gardner BM Chowdhury S Lander GC Martin A The Pex1/Pex6 complex is a heterohexameric AAA+ motor with alternating and highly coordinated subunits. J.MOL.BIOL. 427 1375 1388 2015 25659908 doi:10.1016/j.jmb.2015.01.019 Pex1/Pex6 complex in presence of 3 mM ADP Pex1/Pex6 complex in presence of 3 mM ADP
22 nM Pex1/Pex6 complex in presence of 3 mM ADP was used for negative stain electron microscopy. The sample was monodisperse.
Heterohexamer containing three copies of Pex1 and three copies of Pex6 2 0.707076 Peroxisomal ATPase PEX1 Saccharomyces cerevisiae Baker's yeast peroxisome, cytosol peroxisome membrane 0.117 0.117 3 Heterohexamer true Escherichia coli BL21(DE3) pCOLA-DUET P24004 GO:0000166 GO:0005515 GO:0005524 GO:0005737 GO:0005777 GO:0005778 GO:0006625 GO:0007031 GO:0016020 GO:0016562 GO:0016887 GO:0042623 GO:0046982 IPR003593 IPR003959 IPR003960 IPR029067 IPR027417 IPR015342 IPR025653 Peroxisomal ATPase PEX6 Saccharomyces cerevisiae Baker's yeast peroxisome, cytosol peroxisome membrane 0.115 0.115 3 Heterohexamer true Escherichia coli BL21(DE3) pET-DUET P33760 GO:0000166 GO:0001302 GO:0005515 GO:0005524 GO:0005737 GO:0005777 GO:0005778 GO:0005829 GO:0007031 GO:0016020 GO:0016562 GO:0016887 GO:0046982 IPR003593 IPR003959 IPR003960 IPR027417 singleParticle particle 0.016 7.6
60 mM HEPES, 50 mM NaCl, 50 mM KCl, 10 mM MgCl2, 0.5 mM EDTA, 1 mM TCEP, 3 mM ADP
 NEGATIVE
4 microliters of sample was applied to a freshly plasma-cleaned thin carbon surface that was pre-treated with 0.1% w/v poly-L-lysine hydrobromide. After removing excess protein, negative staining was performed with 2% w/v uranyl formate solution.
400 mesh Cu-Rh Maxtaform grid with a thin continuous carbon film on top
 NONE OTHER FEI TECNAI SPIRIT FLOOD BEAM BRIGHT FIELD LAB6 120 2.20 0.3 1.5 52000.0 52000.0 SIDE ENTRY, EUCENTRIC 294 297 295 Objective astigmatism was corrected using a quadrupole stigmator at 52,000 times magnification.
Data were collected at room temperature.
2014-03-28 TVIPS TEMCAM-F416 (4k x 4k) 694 20
Data collected with the Leginon automated image acquisition software.
 Room temperature side entry holder 0 0
Processing leading up to 3D reconstruction was performed using the Appion package. Particles were selected using the Difference of Gaussians (DoG)-based automated particle picker from micrographs. The stack was subjected to five iterations of iterative 2D alignment and classification using multivariate statistical analysis (MSA) and multi-reference alignment (MRA). The clean particle stack was subjected to twenty five iterations of 3D classification with five classes using the Relion suite. Particles belonging to well-resolved 3D class averages were used for further refinement by projection matching in Relion.
Phase flipping of whole micrograph
 OTHER 17.26 OTHER Relion
Processing leading up to 3D reconstruction was performed using the Appion package. Particles were selected using the Difference of Gaussians (DoG)-based automated particle picker from micrographs. The stack was subjected to five iterations of iterative 2D alignment and classification using multivariate statistical analysis (MSA) and multi-reference alignment (MRA). The clean particle stack was subjected to twenty five iterations of 3D classification with five classes using the Relion suite. Particles belonging to well-resolved 3D class averages were used for further refinement by projection matching in Relion.
23989
Theta 45 degrees, phi 45 degrees
 emd_6253.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 80 80 80 0 0 0 80 80 80 328.0 328.0 328.0 90.0 90.0 90.0 X Y Z -7.59317732 9.19866371 0.0040821 0.99199212 4.1 4.1 4.1 2.49 AUTHOR Negative stain reconstruction of the Pex1/Pex6 complex in presence of 3 mM ADP
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 emd_6253_fsc.xml