2024-10-23 REL RCSB RCSB RCSB 2021-05-25 2021-06-02 2021-06-02 2024-10-23 CryoEM structure of SARS-CoV-2 spike protein (S-6P, 2-up) in complex with sybodies (Sb45) Jiang J Huang R Margulies D SARS-CoV-2, Spike Protein, S-6P (HexaPro), nanobody, sybody, Sb45, neutralization, VIRAL PROTEIN Ahmad J Jiang J Boyd LF Zeher A Huang R Xia D Natarajan K Margulies DH Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction. J.Biol.Chem. US 297 101202 101202 2021 34537245 doi:10.1016/j.jbc.2021.101202 1083-351X 0071 JBCHA3 EMD-24105 other EM volume
CryoEm structure of SARS-CoV-2 spike protein (S-6P, 1-up) in complex with sybodies (Sb45)
 7n0h FULLOVERLAP Spike protein (S-6P, 2-up) in complex with Synthetic nanobody (Sb45) Spike protein (S-6P, 2-up) in complex with Synthetic nanobody (Sb45) 0 1 2
Synthetic nanobody Sb45 was mixed with freshly purified S-6P in the mole ratio of 3:1, incubated, and subjected to Negative stain and frozen grids for cryoEM data collection.
synthetic construct 0.6 Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.142427438 3 Homo sapiens LEVO MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFD NPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVY SSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRV QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFL PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGS NVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF NFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAG TITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALN TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRV DFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL QELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSA WSHPQFEK P0DTC2 Synthetic nanobody (Sb45) synthetic construct 0.013574048 2 Escherichia coli LEVO QVQLVESGGGLVQAGGSLRLSCAASGFPVYRDRMAWYRQAPGKEREWVAAIYSAGQQTRYADSVKGRFTISRDNAKNTVY LQMNSLKPEDTAVYYCNVKDVGHHYEYYDYWGQGTQVTVSA 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 30 NAG singleParticle particle 0.6 8.0 0.25 TBS Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY 120.0 ETHANE 95 277 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 0.7000000000000001 0.535 2.0 2.431 130000.0 47529.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 78.0 80.0 GATAN K2 QUANTUM (4k x 4k) SUPER-RESOLUTION 2 9725 8.0 56.0 1 1433963
A total of 9,725 micrographs were imported into cryoSPARC. Following patch Motion correction, patch CTF estimation, and curation, the number of micrographs was reduced to 9,237. The blob picker with the particle diameter between 128 and 256 angstroms was used for picking up particles. We used the box size of 400 pixels and extracted 1,433,963 particles initially.
 6XKL
The initial model was built based on 6XKL, but RBD and Sb45 are from 7GKJ and dock on S-6P (6XKL). NTD was replaced by 7B32 with a full sequence.
 18 C1 SIMULTANEOUS ITERATIVE (SIRT) 3.34 FSC 0.143 CUT-OFF cryoSPARC V3.2.0
A series of Ab-initio 3D reconstruction (classification)dividing 2 or 4 subclasses to identify two forms of S-6P, i.e. one RBD up, or two RBD up.
61026 NOT APPLICABLE NOT APPLICABLE 100 cryoSPARC 3.2.0
The best 18 classes were selected with 662,994 particles. 3D classifications further identify two conformations of S-6P: 1-up RBD with 214,171 particles, 2-up RBD with 61,026 particles
 emd_24106.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 420.80002 420.80002 420.80002 90.0 90.0 90.0 X Y Z -0.28980902 0.85205895 -0.0005995958 0.017992163 1.052 1.052 1.052 0.0413 AUTHOR CryoEM map of SARS-Cov-2 Spike protein (S-6P) in complex with sybodies (Sb45) 6XKL A 529-1146 PDB experimental model 6XKL B 529-1146 PDB experimental model 6XKL C 529-1146 PDB experimental model 7KGJ A 334-528 PDB experimental model 7KGJ B 1-121 PDB experimental model 7B32 A 14-289 PDB experimental model RIGID BODY FIT
An initial model for S-6P was generated using PDB 6XKL and rigid body fitted into the map using Chimera. The RBD domain (334-528) and Sb45 are taken from 7KGJ which was superimposed onto the S-6P model in PyMol. The NTD domain (14-289) is taken from 7B32 with full sequence and replace that of 6XKL. We have rebuilt and added more glycans (NAGs). We used the real-space refinement in PHENIX including rigid-body refinement. RBD and NTD are subjected to rigid-body refinement. Simulate annealing (SA) runs once at the initial micro-step, local grid search and ADP refinements were included, using the secondary structure restraints.
Correlation Coefficient REAL 157.0 emd_24106_msk_1.map emd_24106_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 420.80002 420.80002 420.80002 90.0 90.0 90.0 X Y Z 0.0 53.754233999999997 0.16869028 1.1091143 1.052 1.052 1.052 AUTHOR Local resolution map