VHH complexes with poliovirus: cryo-electron microscopy studies at near-atomic resolution

REL RCSB RCSB RCSB 2015-08-24 2015-09-23 2016-01-27 2016-03-30 VHH complexes with poliovirus: cryo-electron microscopy studies at near-atomic resolution Strauss M Schotte L Thys B Filman DJ Hogle JM poliovirus, nanobodies, VHH, neutralizing antibodies Strauss M Schotte L Thys B Filman DJ Hogle JM Five of five VHHs neutralizing poliovirus bind the receptor-binding site. J.VIROL. 90 3496 3505 2016 26764003 doi:10.1128/JVI.03017-15 3jbf FULLOVERLAP Nanobody PVSP19B in complex with poliovirus P1/Mahoney Nanobody PVSP19B in complex with poliovirus P1/Mahoney

60 nanobody VHH monomers bind to each poliovirion 2 9.0 9.0 1 Human poliovirus 1

The viral capsid is decorated with 60 copies of a single-domain antibody (PVSP19B).

Human poliovirus 1 Homo sapiens VERTEBRATES 7 7 350 3 VIRION SEROTYPE false false poliovirus 1 PVSP19B Camelus dromedarius camel blood lymocytes 0.015 0.015

60 copies of this single-domain antibody are attached to the viral capsid.

60 monomer true Escherichia coli WK6 pHEN6(c) singleParticle particle 1 7.4

145 mM NaCl, 50 mM Na2HPO4.12H2O

C-flat 1.2/1.3

ETHANE 154 HOMEMADE PLUNGER 4 second blot FEI POLARA 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.26 -1.4 -4.0 23000.0 25380.700000000000728 OTHER 80 110 80 0

Gatan K2 operated in Super-resolution mode

2013-11-27 GATAN K2 (4k x 4k) 2.5 300 25 8. Polara holder

The particles were processed using Frealign.

per particle

4.8 OTHER Frealign 18009 emd_6434.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 -256 -256 -256 512 512 512 504.32 504.32 504.32 90.0 90.0 90.0 X Y Z -0.00690961 0.02299565 -0.0009187 0.00356139 0.985 0.985 0.985 0.0075 AUTHOR Reconstruction of VHH-poliovirus complex (PVSP19B - Mahoney Type 1)

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1I3U FLEXIBLE FIT COOT, SPDBV, REFMAC5

Using stereochemically and icosahedrally restrained maximum likelihood refinement in REFMAC5, a representative subset of the full atomic model with all neighbors present was built and refined to fit the corresponding subset of the experimental map. Portions of the model whose density resembled a structural homolog were identified and restrained to agree with the homolog. Detailed atomic models were constructed in areas of difference wherever the resolution of the map permitted. The Fourier-amplitude-weighted average cosine of the phase discrepancy was tracked.

ML agreement with Fourier amplitudes and phases RECIPROCAL