2020-11-25 REL PDBe PDBe PDBe 2019-02-19 2020-03-25 2020-03-25 2020-11-25 Medical Research Council (United Kingdom) MR/N024842/1 United Kingdom Other government UCLH/NIHR Biomedical Research Centre United Kingdom Wellcome Trust Wellcome Trust 4-year PhD Interdisciplinary Programme in Structural, Computational and Chemical Biology United Kingdom A dimer component of alpha-1 antitrypsin heat-induced polymers generated from wild-type M plasma protein and decorated with Fab 4B12 Elliston ELK Redzej A Orlova EV Lomas DA Irving JA Faull SV Elliston ELK Gooptu B Jagger AM Aldobiyan I Redzej A Badaoui M Heyer-Chauhan N Rashid ST Reynolds GM Adams DH Miranda E Orlova EV Irving JA Lomas DA The structural basis for Z alpha 1 -antitrypsin polymerization in the liver. Sci Adv US 6 2020 33087346 doi:10.1126/sciadv.abc1370 2375-2548 EMD-4620 associated EM volume Polymers induced by heating monomeric wild-type alpha-1 antitrypsin and labelled with 4B12 Fab fragments Polymers induced by heating monomeric wild-type alpha-1 antitrypsin and labelled with 4B12 Fab fragments 0 1 2 3
Polymers of alpha-1 antitrypsin were prepared from purified plasma protein by heating at 55 degrees C for 48 hours and purified by chromatography. These were labelled with the Fab fragment of a non-conformationally selective monoclonal antibody (4B12).
Homo sapiens Plasma Complex between two 4B12 Fab fragments and a dimer component of polymers induced by heating of the wild-type M alpha-1 antitrypsin variant 1 1 2 3 Homo sapiens Plasma 0.2 Alpha-1 antitrypsin Homo sapiens Plasma
Wild-type M variant of alpha-1 antitrypsin
LEVO EDPQGDAAQKTDTSHHDQDHPTFNKITPNLAEFAFS LYRQLAHQSNSTNIFFSPVSIATAFAMLSLGTKADTHDEILEGLNFNLTEIPEAQIHEGF QELLRTLNQPDSQLQLTTGNGLFLSEGLKLVDKFLEDVKKLYHSEAFTVNFGDTEEAKKQ INDYVEKGTQGKIVDLVKELDRDTVFALVNYIFFKGKWERPFEVKDTEEEDFHVDQVTTV KVPMMKRLGMFNIQHCKKLSSWVLLMKYLGNATAIFFLPDEGKLQHLENELTHDIITKFL ENEDRRSASLHLPKLSITGTYDLKSVLGQLGITKVFSNGADLSGVTEEAPLKLSKAVHKA VLTIDEKGTEAAGAMFLEAIPMSIPPEVKFNKPFVFLMIEQNTKSPLFMGKVVNPTQK 4B12 Fab heavy chain Mus musculus BALB/c Spleen
Heavy chain of the Fab fragment of a non-conformationally-selective antibody (4B12) that binds to alpha-1-antitrypsin
LEVO QVKLEESGPELVKPGASVKISCKASGYSFIGYYMHWVKQSHVKSLEWIGRINPYNGATRYNQNFQDRATLTVDKSSSTAYMDFHSLTSEDSAVYYCVRWPGDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCTS 4B12 Fab light chain Mus musculus BALB/c Spleen
Light chain of the Fab fragment of a non-conformationally-selective antibody (4B12) that binds to alpha-1-antitrypsin
LEVO DIVMTQTPSSLSASLGGKVTITCKASQDINNYIAWYQLKPGKGPRQLIHYTSKLQPGIPSRFSGSGSGSDYSFSISNLEPEDIGTYYCLRYEDLWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFN singleParticle particle 0.04 7.4 50.0 2-Amino-2-(hydroxymethyl)propane-1,3-diol Tris 50.0 NaCl Sodium chloride 5.0 EDTA NEGATIVE Uranyl acetate
3 microlitres of prepared sample was applied to glow-discharged carbon film on 400 mesh copper (CF400-Cu) grids. Sample was bound to the grid for 1 minute before blotting excess solution with filter paper, rinsing with water twice. 4 microlitres of 2% w/v uranyl acetate was applied for 1 minute before blotting; this was repeated once.
 COPPER 400 CARBON GLOW DISCHARGE AIR
The sample comprises a mixed population of unbranched polymers of varying lengths, labelled with the Fab fragment of the 4B12 antibody.
 FEI TECNAI F20 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.0 0.233 1.15 41470.0 OTHER DIRECT ELECTRON DE-20 (5k x 3k) 5120 3840 6.4 1-18 1 169 1.8 28.0 1 40853
Highly filtered 2D references generated from manually picked dimeric components were used in autopicking.
 CTFFIND 3 CTF parameters Bsoft 1.8.9-20140223 Phase flipping (bctf -action 1)
All processing in RELION was performed on CTF-corrected images.
To avoid the introduction of bias in the relative orientation between the subunits of the dimer, a monomer (not dimer) reference was used; the reference was generated by averaging the two subunits of a Fab-bound dimer previously reconstructed from a different dataset.
 1 C1 BACK PROJECTION 26.4 FSC 0.33 CUT-OFF RELION 2.1 Refine3D RELION 2.1 PostProcess 6750 MAXIMUM LIKELIHOOD RELION 2.1 Class3D MAXIMUM LIKELIHOOD RELION 2.1 Refine3D 5 4897 RELION 2.1 Class3D
Successive rounds of 3D classification yielded a single dimer class that exhibited well-resolved Fab protuberances.
 emd_4620.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 150 150 150 0 0 0 150 150 150 231.0 231.0 231.0 90.0 90.0 90.0 X Y Z -0.014650891 0.05266803 0.0003644281 0.0035579717 1.54 1.54 1.54 0.007 AUTHOR Unmasked dimer component of alpha-1 antitrypsin heat-induced polymers generated from purified plasma wild-type M variant; subunits rotated ~60 degrees around dimer axis. emd_4620_msk_1.map emd_4620_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 150 150 150 0 0 0 150 150 150 231.0 231.0 231.0 90.0 90.0 90.0 X Y Z -0.013337048 0.05266803 0.00047739857 0.0032145737 1.54 1.54 1.54 AUTHOR Tightly masked dimer component of alpha-1 antitrypsin heat-induced polymers generated from purified plasma wild-type M variant; subunits rotated ~60 degrees around dimer axis.