7ZRV

cryo-EM structure of omicron spike in complex with de novo designed binder, full map

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,Envelope glycoprotein	polymer	1285	142558.1	3	UniProt (P0DTC2) UniProt (M1E1E4) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) Pfam (PF07921)	Severe acute respiratory syndrome coronavirus 2	S glycoprotein,E2,Peplomer protein
2	D, E (E, F)	de novo designed binder	polymer	79	8829.9	2	Pfam (PF21528) UniProt (by SIFTS) (Q9VKJ9)	Drosophila melanogaster (fruit fly)
3	DA, EA, F, FA, GA... (d, e, D, f, g...)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	18	In PDB GlyTouCan (G42666HT)
4	AA, BA, CA, G, I... (a, b, c, G, I...)	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		586.5	12	In PDB GlyTouCan (G15407YE)
5	JA, KA, LA, MA, NA... (A, B, C)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	16	Chemie (NAG)

Sequence modifications

A, B, C: 4 - 1208 (UniProt: P0DTC2)

PDB	External Database	Details
Val 70	Ala 67	conflict
-	His 69	deletion
-	Val 70	deletion
Ile 96	Thr 95	conflict
-	Gly 142	deletion
-	Val 143	deletion
-	Tyr 144	deletion
Asp 143	Tyr 145	conflict
Ile 209	-	insertion
Val 210	-	insertion
Arg 211	Asn 211	conflict
Glu 212	Leu 212	conflict
Pro 213	Val 213	conflict
Glu 214	Arg 214	conflict
Asp 339	Gly 339	conflict
Leu 371	Ser 371	conflict
Pro 373	Ser 373	conflict
Phe 375	Ser 375	conflict
Asn 417	Lys 417	conflict
Lys 440	Asn 440	conflict
Ser 446	Gly 446	conflict
Asn 477	Ser 477	conflict
Lys 478	Thr 478	conflict
Ala 484	Glu 484	conflict
Arg 493	Gln 493	conflict
Ser 496	Gly 496	conflict
Arg 498	Gln 498	conflict
Tyr 501	Asn 501	conflict
His 505	Tyr 505	conflict
Lys 547	Thr 547	conflict
Gly 614	Asp 614	conflict
Tyr 655	His 655	conflict
Lys 679	Asn 679	conflict
His 681	Pro 681	conflict
Gly 682	Arg 682	conflict
Ser 683	Arg 683	conflict
Ser 685	Arg 685	conflict
Lys 764	Asn 764	conflict
Tyr 796	Asp 796	conflict
Lys 856	Asn 856	conflict
His 954	Gln 954	conflict
Lys 969	Asn 969	conflict
Phe 981	Leu 981	conflict
Pro 986	Lys 986	conflict
Pro 987	Val 987	conflict
Gly 1209	-	linker
Ser 1210	-	linker

A, B, C: 1211 - 1240 (UniProt: M1E1E4)

PDB	External Database	Details
Arg 1239	Ser 29	conflict
Leu 1241	-	expression tag
Glu 1242	-	expression tag
Val 1243	-	expression tag
Leu 1244	-	expression tag
Phe 1245	-	expression tag
Gln 1246	-	expression tag
Gly 1247	-	expression tag
Pro 1248	-	expression tag
Gly 1249	-	expression tag
His 1250	-	expression tag
His 1251	-	expression tag
His 1252	-	expression tag
His 1253	-	expression tag
His 1254	-	expression tag
His 1255	-	expression tag
His 1256	-	expression tag
His 1257	-	expression tag
Ser 1258	-	expression tag
Ala 1259	-	expression tag
Trp 1260	-	expression tag
Ser 1261	-	expression tag
His 1262	-	expression tag
Pro 1263	-	expression tag
Gln 1264	-	expression tag
Phe 1265	-	expression tag
Glu 1266	-	expression tag
Lys 1267	-	expression tag
Gly 1268	-	expression tag
Gly 1269	-	expression tag
Gly 1270	-	expression tag
Ser 1271	-	expression tag
Gly 1272	-	expression tag
Gly 1273	-	expression tag
Gly 1274	-	expression tag
Gly 1275	-	expression tag
Ser 1276	-	expression tag
Gly 1277	-	expression tag
Gly 1278	-	expression tag
Ser 1279	-	expression tag
Ala 1280	-	expression tag
Trp 1281	-	expression tag
Ser 1282	-	expression tag
His 1283	-	expression tag
Pro 1284	-	expression tag
Gln 1285	-	expression tag
Phe 1286	-	expression tag
Glu 1287	-	expression tag
Lys 1288	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	5
	Total formula weight	445334.1
Branched	Number of molecules	30
	Total formula weight	14677.7
Non-Polymers*	Number of molecules	16
	Total formula weight	3539.3
All*	Total formula weight	463551.1

*Water molecules are not included.