REL RCSB RCSB RCSB 2014-09-30 2014-10-08 2014-12-03 2015-05-27 Electron cryo-microscopy of human papillomavirus 16 and H16.V5 Fab fragments Lee H Brendle SA Bywaters SM Guan J Ashley RE Yoder JD Makhov AM Conway JF Christensen ND Hafenstein S virus-Fab complex, neutralization antibody, maturation Lee H Brendle SA Bywaters SM Guan J Ashley RE Yoder JD Makhov AM Conway JF Christensen ND Hafenstein S A CryoEM study identifies the complete H16.V5 epitope and reveals global conformational changes initiated by binding of the neutralizing antibody fragment. J.VIROL. 89 1428 1438 2015 25392224 doi:10.1128/JVI.02898-14 Mature HPV16 quasivirus capsid complexed with H16.V5 Fabs Mature HPV16 quasivirus capsid complexed with H16.V5 Fabs Three hundred H16.V5 Fabs bind to one HPV16 capsid 2 42 Human papillomavirus 16
The virus sample was incubated with excessive Fab fragments for 72 hrs.
Human papillomavirus 16 Homo sapiens VERTEBRATES 27 L1/L2 600 7 VIRION OTHER false false H16.V5 Fab Mus musculus hybridoma 0.05 300 monomer false singleParticle particle 1.0 7.4
137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4
glow-discharged holey carbon Quantifoil grids
 ETHANE 90 102 GATAN CRYOPLUNGE 3 Blot for 0.7 seconds before plunging. JEOL 2100 SPOT SCAN BRIGHT FIELD LAB6 200 2 1.63 5.18 40000.0 GATAN LIQUID NITROGEN 95 2014-08-18 GATAN ULTRASCAN 4000 (4k x 4k) 102 15
The particles were selected using semi-automatic program e2boxer.py (EMAN2).
Each particle
 OTHER 15.8 OTHER Auto3dem
Semi-automatic particle selection was performed using e2boxer.py to obtain the particle coordinates, followed by particle boxing, linearization, normalization, and apodization of the images using Robem. Defocus and astigmatism values to perform contrast transfer function (CTF) correction were assessed using Robem for the extracted particles. The icosahedrally averaged reconstructions were initiated using a random model generated with setup_rmc and reached 14 A resolution estimated at a Fourier Shell Correlation (FSC) of 0.5. For the last step of refinement, the final maps were CTF-corrected using a B factor of 200 A2.
2075 emd_6118.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 311 311 311 -155 -155 -155 311 311 311 889.45996 889.45996 889.45996 90.0 90.0 90.0 X Y Z -5.65556288 5.93166399 0.0 0.99999994 2.86 2.86 2.86 1.0 AUTHOR Reconstruction of mature human papillomavirus 16 capsid complexed with Fab fragments after 72 hr incubation
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