7UFK: Chimeric omicron RBD

Crystal structure of chimeric omicron RBD (strain BA.2) complexed with human ACE2. Determined by X-ray diffraction at 2.38 Å resolution. Released 19 Oct 2022.

Method

X-ray diffraction

Resolution

2.38 Å

Organisms

Homo sapiens, Severe acute respiratory syndrome coronavirus 2

Chains

4

Atoms

13,092

Mol. weight

192.5 kDa

Ligands

ZN, NAG

Released

19 Oct 2022

Explore 7UFK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UFK contains 102 α-helices and 56 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 43 helices, 11 β-strands

Molecules and chains

>7UFK_1 Angiotensin-converting enzyme 2 (chains A, B)
STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQST
LAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNP
QECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYED
YGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISP
IGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSV
GLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGH
IQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINF
LLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYC
DPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNML
RLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYAD

>7UFK_2 Spike protein S1 (chains E, F)
RVVPSGDVVRFPNITNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFK
CYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNT
RNIDATSTGNYNYKYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFR
PTYGVGHQPYRVVVLSFELLNAPATVCGPKLSTDLIK

Ligands and cofactors

Water and common crystallization additives (CL, NA, EDO) are not listed.

Primary citation

Structural basis for mouse receptor recognition by SARS-CoV-2 omicron variant. Zhang, W., Shi, K., Geng, Q. et al. Proc Natl Acad Sci U S A (2022) 119:e2206509119-e2206509119. DOI 10.1073/pnas.2206509119 · PubMed

Related structures

Other PDB entries of the same protein (UniProt Q9BYF1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

• 9SPA 1.79 Å, Apo ACE2 extracellular domain
• 28KD 2.02 Å, ACE2 extracellular domain in complex with the macrocyclic peptide GR3.1.2
• 8BYJ 2.07 Å, The structures of Ace2 in complex with bicyclic peptide inhibitor
• 8B9P 2.11 Å, ACE2 in complex with bicyclic peptide inhibitor
• 8XSF 2.16 Å, SARS-CoV-2 rbd + imcas-364 + hACE2
• 1R42 2.2 Å, Native Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2)
• 7JVO 2.2 Å, Importin alpha bound to the C-terminus of ACE2
• 8TOR 2.2 Å, ACE2-peptide 2 complex
• 9RVA 2.2 Å, Crystal structure of the extracellular part of human ACE2 in complex with the…
• 9UE7 2.27 Å, Cryo-EM structure of SARS-CoV-2 KP.2 spike in complex with ACE2
• 8TOQ 2.3 Å, ACE2-peptide 1 complex
• 8BFW 2.33 Å, The structures of Ace2 in complex with bicyclic peptide inhibitor

Browse structure collections

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