9ELM

Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11 spike protein (closed state)

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, B, C (A, B, C)	Spike glycoprotein	polymer	1200	133300.1	3	UniProt (A0A6N0C4S6) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) UniProt (by SIFTS) (A0A6V7ALX9)	Severe acute respiratory syndrome coronavirus 2	S glycoprotein,E2,Peplomer protein
2	D, H, I, M, N... (D, H, I, M, N...)	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		586.5	6	In PDB GlyTouCan (G15407YE)
3	E, F, G, J, K... (E, F, G, J, K...)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	9	In PDB GlyTouCan (G42666HT)
4	AA, BA, CA, DA, EA... (B, C, A)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	21	Chemie (NAG)

Sequence modifications

A, B, C: 4 - 1208 (UniProt: A0A6N0C4S6)

PDB	External Database	Details
Ile 22	Thr 19	variant
Thr 24	Arg 21	variant
-	Leu 24	deletion
-	Pro 25	deletion
-	Pro 26	deletion
Ser 27	Ala 27	variant
Leu 50	Ser 50	variant
-	His 69	deletion
-	Val 70	deletion
Phe 127	Val 127	variant
Asp 143	Gly 142	variant
-	Tyr 145	deletion
Ser 157	Phe 157	variant
Gly 158	Arg 158	variant
-	Asn 211	deletion
Ile 212	Leu 212	variant
Gly 213	Val 213	variant
Phe 216	Leu 216	variant
Asn 245	His 245	variant
Asp 264	Ala 264	variant
Val 332	Ile 332	variant
His 339	Gly 339	variant
Thr 356	Lys 356	variant
Phe 371	Ser 371	variant
Pro 373	Ser 373	variant
Phe 375	Ser 375	variant
Ala 376	Thr 376	variant
Lys 403	Arg 403	variant
Asn 405	Asp 405	variant
Ser 408	Arg 408	variant
Asn 417	Lys 417	variant
Lys 440	Asn 440	variant
His 445	Val 445	variant
Ser 446	Gly 446	variant
Asp 450	Asn 450	variant
Trp 452	Leu 452	variant
Ser 455	Leu 455	variant
Lys 460	Asn 460	variant
Asn 478	Ser 477	variant
Lys 479	Thr 478	variant
Lys 482	Asn 481	variant
-	Val 483	deletion
Lys 484	Glu 484	variant
Pro 486	Phe 486	variant
Arg 498	Gln 498	variant
Tyr 501	Asn 501	variant
His 505	Tyr 505	variant
Lys 554	Glu 554	variant
Val 570	Ala 570	variant
Ser 621	Pro 621	variant
Tyr 655	His 655	variant
Lys 679	Asn 679	variant
Arg 681	Pro 681	variant
Gly 682	Arg 682	variant
Ser 683	Arg 683	variant
Ser 685	Arg 685	variant
Lys 764	Asn 764	variant
Tyr 796	Asp 796	variant
Pro 817	Phe 817	variant
Pro 892	Ala 892	variant
Pro 899	Ala 899	variant
Phe 939	Ser 939	variant
Pro 942	Ala 942	variant
His 954	Gln 954	variant
Lys 969	Asn 969	variant
Pro 986	Lys 986	variant
Pro 987	Val 987	variant
Leu 1143	Pro 1143	variant

Contents of the asymmetric unit

Polymers	Number of chains	3
	Total formula weight	399900.4
Branched	Number of molecules	15
	Total formula weight	7338.9
Non-Polymers*	Number of molecules	21
	Total formula weight	4645.4
All*	Total formula weight	411884.6

*Water molecules are not included.