Structure of SARS-CoV-2 spike at pH 5.5, all RBDs down

Summary for 6XM5

Related6XLU 6XM0 6XM3 6XM4
EMDB information22251 22253 22254 22255 22256
DescriptorSpike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose (3 entities in total)
Functional Keywordssars-cov-2 spike, covid19, viral protein
Biological sourceSevere acute respiratory syndrome coronavirus 2 (2019-nCoV)
Total number of polymer chains3
Total molecular weight435399.42
Zhou, T.,Tsybovsky, Y.,Olia, A.,Kwong, P.D. (deposition date: 2020-06-29, release date: 2020-07-29, Last modification date: 2020-08-12)
Primary citation
Zhou, T.,Tsybovsky, Y.,Olia, A.S.,Gorman, J.,Rapp, M.A.,Cerutti, G.,Chuang, G.-Y.,Katsamba, P.S.,Nazzari, A.,Sampson, J.M.,Schon, A.,Wang, P.D.,Bimela, J.,Shi, W.,Teng, I.T.,Zhang, B.,Boyington, J.C.,Sastry, M.,Stephens, T.,Stuckey, J.,Wang, S.,Friesner, R.A.,Ho, D.D.,Mascola, J.R.,Shapiro, L.,Kwong, P.D.
Cryo-EM Structures Delineate a pH-Dependent Switch that Mediates Endosomal Positioning of SARS-CoV-2 Spike Receptor-Binding Domains
Biorxiv, 2020
PubMed: 32637958 (PDB entries with the same primary citation)
DOI: 10.1101/2020.07.04.187989
MImport into Mendeley
Experimental method

Structure validation

ClashscoreRamachandran outliersSidechain outliers40 0.5%MetricValuePercentile RanksWorseBetterPercentile relative to all structuresPercentile relative to all EM structures
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PDB entries from 2020-08-12