2024-11-20 REL PDBe PDBe PDBe 2022-06-16 2023-04-05 2023-04-05 2024-11-20 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 1R01AI149297-01 United States cryoEM structure of the catalytically inactive EndoS from S. pyogenes in complex with the Fc region of immunoglobulin G1 Trastoy B Cifuente JO Du JJ Sundberg EJ Guerin ME Endoglycosidase S, EndoS, endo-b-N-acetylglucosaminidase, Fc region, antibody, immunoglobulin G1, Streptococcus pyogenes, N-glycans, HYDROLASE Trastoy B Du JJ Cifuente JO Rudolph L Garcia-Alija M Klontz EH Deredge D Sultana N Huynh CG Flowers MW Li C Sastre DE Wang LX Corzana F Mallagaray A Sundberg EJ Guerin ME Mechanism of antibody-specific deglycosylation and immune evasion by Streptococcal IgG-specific endoglycosidases. Nat Commun UK 14 1705 1705 2023 36973249 doi:10.1038/s41467-023-37215-3 2041-1723 8a64 FULLOVERLAP Complex of the EndoS from S. pyogenes and the Fc region of Immunoglobulin G Complex of the EndoS from S. pyogenes and the Fc region of Immunoglobulin G 0 1 2 Streptococcus pyogenes 0.150 Endo-beta-N-acetylglucosaminidase F2 Streptococcus pyogenes 0.108297039 1 Escherichia coli LEVO EEKTVQVQKGLPSIDSLHYLSENSKKEFKEELSKAGQESQKVKEILAKAQQADKQAQELAKMKIPEKIPMKPLHGPLYGG YFRTWHDKTSDPTEKDKVNSMGELPKEVDLAFIFHDWTKDYSLFWKELATKHVPKLNKQGTRVIRTIPWRFLAGGDNSGI AEDTSKYPNTPEGNKALAKAIVDEYVYKYNLDGLDVDVAHDSIPKVDKKEDTAGVERSIQVFEEIGKLIGPKGVDKSRLF IMDSTYMADKNPLIERGAPYINLLLVQVYGSQGEKGGWEPVSNRPEKTMEERWQGYSKYIRPEQYMIGFSFYEENAQEGN LWYDINSRKDEDKANGINTDITGTRAERYARWQPKTGGVKGGIFSYAIDRDGVAHQPKKYAKQKEFKDATDNIFHSDYSV SKALKTVMLKDKSYDLIDEKDFPDKALREAVMAQVGTRKGDLERFNGTLRLDNPAIQSLEGLNKFKKLAQLDLIGLSRIT KLDRSVLPANMKPGKDTLETVLETYKKDNKEEPATIPPVSLKVSGLTGLKELDLSGFDRETLAGLDAATLTSLEKVDISG NKLDLAPGTENRQIFDTMLSTISNHVGSNEQTVKFDKQKPTGHYPDTYGKTSLRLPVANEKVDLQSQLLFGTVTNQGTLI NSEADYKAYQNHKIAGRSFVDSNYHYNNFKVSYENYTVKVTDSTLGTTTDKTLATDKEETYKVDFFSPADKTKAVHTAKV IVGDEKTMMVNLAEGATVIGGSADPVNARKVFDGQLGSETDNISLGWDSKQSIIFKLKEDGLIKHWRFFNDSARNPETTN KPIQEASLQIFNIKDYNLDNLLENPNKFDDEKYWITVDTYSAQGERATAFSNTLNNITSKYWRVVFDTKGDRYSSPVVPE LQILGYPLPNADTIMKTVTTAKELSQQKDKFSQKMLDELKIKEMALETSLNSKIFDVTAINANAGVLKDCIEKRQLLKKL J7M8R4 Immunoglobulin gamma-1 heavy chain Homo sapiens 0.049386637
TCPPCPAPELLGGP SVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNS TYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDEL TKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQ QGNVFSCSVMHEALHNHYTQKSLSLSPGK
2 Cricetulus griseus LEVO QVQLVQSGGGVVQPGRSLRLSCAASGFTFSRYTIHWVRQAPGKGLEWVAVMSYNGNNKHYADSVNGRFTISRNDSKNTLY LNMNSLRPEDTAVYYCARIRDTAMFFAHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW NSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGP SVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKE YKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVL DSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK singleParticle particle 7.5
Standard PBS
 Quantifoil R1.2/1.3 COPPER 300 GLOW DISCHARGE ETHANE 80 283 FEI VITROBOT MARK II
single blot.
Complex stabilized by glutaraldehyde crosslinking prepared by ultracentrifugation in a fixation glycerol gradient (Grafix) and size exclusion chromatography purified at approximately 0.2 mg/mL
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.3 2.5 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 QUANTUM (4k x 4k) COUNTING 3838 3710 1-60 1 5546 59.4 1 797351
A negatively stained model obtained in RELION.
 C1 4.6 FSC 3 SIGMA CUT-OFF cryoSPARC 339309 MAXIMUM LIKELIHOOD RELION
Classified selected particles in RELION were used for reconstruction and CTFrefinement and Polishing
 MAXIMUM LIKELIHOOD cryoSPARC
Imported selected particles CTFrefined and Polished in RELION were imported in cryoSPARC2 and 2D reclassified for final reconstruction
 200 cryoSPARC emd_15205.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 189.36002 189.36002 189.36002 90.0 90.0 90.0 X Y Z -0.25330344 0.7173578 0.006468186 0.040584818 1.052 1.052 1.052 0.05 AUTHOR Main map cryosparc refine 6EN3 A PDB experimental model 1H3X B PDB experimental model 1H3X C PDB experimental model OTHER
Initial PDB models were rigid-body refined for individual chains. Later, the model was real-space refined removing side chains that couldn't be assigned.
 emd_15205_msk_1.map emd_15205_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 189.36002 189.36002 189.36002 90.0 90.0 90.0 X Y Z -1.5035113 2.1350925 0.006468186 0.07448237 1.052 1.052 1.052 AUTHOR Main map cryosparc refine emd_15205_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 189.36002 189.36002 189.36002 90.0 90.0 90.0 X Y Z -0.28384885 0.76310754 0.0033421672 0.044084653 1.052 1.052 1.052 AUTHOR Half map cryosparc refine emd_15205_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 189.36002 189.36002 189.36002 90.0 90.0 90.0 X Y Z -0.26567912 0.71543944 0.003335954 0.04406144 1.052 1.052 1.052 AUTHOR Half map cryosparc refine