REL PDBe PDBe PDBe 2012-03-13 2012-04-10 2012-04-10 2016-03-30 Cryo-EM structure of the UPF-EJC complex Melero R Buchwald G Castano R Raabe M Gil D Lazaro M Urlaub H Conti E Llorca O NMD, EJC, UPF1, UPF2, UPF3, RNA degradation, GraFix Melero R Buchwald G Castano R Raabe M Gil D Lazaro M Urlaub H Conti E Llorca O The cryo-EM structure of the UPF-EJC complex shows UPF1 poised toward the RNA 3' end. NAT.STRUCT.MOL.BIOL. 19 498 505 2012 22522823 doi:10.1038/nsmb.2287 Complex containing the NMD proteins UPF1, UPF2 and UPF3 bound to the exon junction complex (EJC) Complex containing the NMD proteins UPF1, UPF2 and UPF3 bound to the exon junction complex (EJC) Hetero-octameric 8 0.390 0.390 Up-frameshift protein 1 Homo sapiens Human 0.090
115-914
1 Monomer true Escherichia coli GO:0000184 IPR018999 Up-frameshift protein 2 Homo sapiens Human 0.148
full length
1 Monomer true Escherichia coli GO:0000184 IPR018999 Up-frameshift protein 3b Homo sapiens Human 0.056
full length
1 Monomer true Escherichia coli GO:0000184 IPR005120 MAGO Homo sapiens Human 0.016
full length
1 Monomer true Escherichia coli GO:0000184 IPR015362 Y14 Homo sapiens Human 0.010
residues 66-154
1 Monomer true Escherichia coli GO:0000184 IPR015362 Btz Homo sapiens Human 0.017
residues 136-286
1 Monomer true Escherichia coli GO:0000184 IPR018545 eIF4AIII Homo sapiens Human 0.045
full length
1 Monomer true Escherichia coli GO:0000184 IPR018545 (U)8 RNA Homo sapiens Human 0.003
Oligo(U) 8nt
UUUUUUUU OTHER SINGLE STRANDED true singleParticle particle 0.175 7.5
50 mM K-phosphate,150 mM NaCl, 3 mM MgCl2, 20% sucrose, 0.1% glutaraldehyde
Quantifoil grids (R2/2) with thin carbon film on top
 ETHANE 95 FEI VITROBOT MARK III Manual Application (3.5 microliters) Humidifier Off During Process Blot offset: -2 mm Blot Total: 2 Blot Time: 2 s Wait Time: 30 s Drain Time: 1 s JEOL 2200FS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.0 1.112 4.0 50000.0 69494.0 GATAN LIQUID NITROGEN 83 100 91.5 Objective lens astigmatism was corrected calculating the Fourier Transform of the CCD frames. Phase flipping FEI 0.0 10.0 2010-10-20 GATAN ULTRASCAN 4000 (4k x 4k) 15 15
0.22 nm per pixel, final sampling
16. Eucentric. 626 cryo-holder (Gatan Inc., Warrendale, PA, USA)
Each CCD Frame using BSOFT
 C1 OTHER 16.0 FSC 0.5 CUT-OFF EMAN, XMIPP, SPIDER, BSOFT
Initial reference obtained by random conical tilt of negative-stained images
85000 emd_2048.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 136 136 136 0 0 0 136 136 136 299.2 299.2 299.2 90.0 90.0 90.0 X Y Z -6.43814659 17.813716889999998 -0.02877257 0.96611029 2.2 2.2 2.2 2.4 AUTHOR Cryo-EM reconstruction of the nonsense-mediated mRNA decay (NMD) complex containing proteins UPF1, UPF2, UPF3 and the Exon Junction Complex (EJC).
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 1UW4 RIGID BODY FIT Chimera
Protocol: Rigid body
R-factor REAL 2XB2 RIGID BODY FIT Chimera
Protocol: Rigid body
R-factor REAL 2WJV RIGID BODY FIT Chimera
Protocol: Rigid body
R-factor REAL