8UPX: Omicron-S-MERS-RBD

Omicron-S-MERS-RBD. Determined by electron microscopy at 3.4 Å resolution. Released 21 Aug 2024.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 23,232
Mol. weight: 422.71 kDa
Ligands: NAG
Released: 21 Aug 2024

Explore 8UPX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8UPX contains 80 α-helices and 175 β-strands across 3 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: 21 helices, 54 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
β-strand	29-31	3	1
β-strand	42-43	2	2
β-strand	47-53	7	3
α-helix	56-57	2
β-strand	60-62	3	1
β-strand	63-67	5	4
β-strand	81-83	3	5
β-strand	87-94	8	4
β-strand	99-105	7	5
β-strand	114-119	6	5
β-strand	124-129	6	5
β-strand	131	1	6
β-strand	138-139	2	5
β-strand	152-153	2	5
β-strand	158	1	6
β-strand	163-166	4	5
β-strand	183-192	10	4
β-strand	195-203	9	4
β-strand	221-226	6	4
β-strand	234-240	7	5
β-strand	242	1	7
β-strand	256	1	7
β-strand	260-266	7	4
β-strand	270-276	7	3
β-strand	282-287	6	3
α-helix	292-300	9
β-strand	307-313	7	8
α-helix	316-318	3
β-strand	322-323	2	9
β-strand	553-557	5	9
β-strand	562-569	8	9
β-strand	590-592	3	9
β-strand	599-603	5	9
β-strand	610-615	6	8
β-strand	624-627	4	8
α-helix	649-652	4
β-strand	657-660	4	8
β-strand	663-666	4	8
β-strand	669-670	2	10
β-strand	679-682	4	10
β-strand	685-690	6	10
β-strand	706-711	6	10
β-strand	716-717	2	11
β-strand	726-730	5	12
β-strand	733-743	11	13
β-strand	749-750	2	14
α-helix	753	1
α-helix	754-758	5
α-helix	763-769	7
α-helix	774-797	24
β-strand	802-803	2	15
α-helix	832-839	8
α-helix	864-869	6
β-strand	874-875	2	14
α-helix	876-878	3
α-helix	884-898	15
α-helix	902-904	3
α-helix	913-923	11
α-helix	929-954	26
α-helix	961-979	19
α-helix	992-998	7
α-helix	1001-1043	43
α-helix	1044-1048	5
β-strand	1062-1071	10	13
β-strand	1074-1084	11	13
β-strand	1087-1093	7	12
β-strand	1096-1097	2	16
β-strand	1102-1105	4	16
β-strand	1109-1112	4	12
β-strand	1117-1120	4	12
β-strand	1128	1	12
β-strand	1135-1137	3	16
β-strand	1148-1149	2	16
α-helix	1157-1160	4

Chain B: 36 helices, 65 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
β-strand	27-30	4	17
β-strand	36-37	2	18
β-strand	47-55	9	19
α-helix	56-57	2
β-strand	61-67	7	17
β-strand	82-83	2	20
β-strand	88-94	7	17
β-strand	102-105	4	20
β-strand	114-119	6	20
β-strand	124-129	6	20
β-strand	131-133	3	21
β-strand	143	1	22
β-strand	147	1	22
β-strand	155-158	4	21
β-strand	163-166	4	20
β-strand	183-192	10	17
β-strand	195-203	9	17
α-helix	205-206	2
β-strand	219-220	2	18
β-strand	221-226	6	17
β-strand	234-237	4	20
β-strand	242	1	23
β-strand	256	1	23
β-strand	260-266	7	17
β-strand	268-276	9	19
β-strand	282-287	6	19
α-helix	292-300	9
β-strand	308-316	9	24
α-helix	317-319	3
β-strand	322	1	25
α-helix	337-340	4
α-helix	347-349	3
β-strand	351-355	5	26
α-helix	362-368	7
β-strand	370-377	8	26
α-helix	381-384	4
β-strand	392-398	7	26
α-helix	401-406	6
α-helix	414	1
α-helix	415-419	5
β-strand	428-435	8	26
α-helix	443-444	2
β-strand	448-457	10	27
β-strand	464-466	3	27
α-helix	468-470	3
α-helix	476-479	4
β-strand	490-495	6	27
α-helix	496-497	2
β-strand	504-512	9	27
β-strand	518-526	9	26
β-strand	554-556	3	25
α-helix	558-560	3
β-strand	563-565	3	25
β-strand	566	1	28
β-strand	580	1	29
β-strand	590-592	3	29
β-strand	599-601	3	29
β-strand	603	1	28
α-helix	604-606	3
β-strand	607-614	8	24
β-strand	624-627	4	24
β-strand	657-660	4	24
β-strand	663-666	4	24
β-strand	669-670	2	30
β-strand	679-682	4	30
β-strand	685-690	6	30
β-strand	706-711	6	30
β-strand	716-719	4	31
β-strand	726-743	18	32
β-strand	749-751	3	33
α-helix	753-756	4
α-helix	762-768	7
α-helix	769-771	3
α-helix	775-797	23
β-strand	802-803	2	11
β-strand	812	1	34
β-strand	815	1	34
α-helix	832-840	9
α-helix	864-869	6
β-strand	873-875	3	33
α-helix	876-878	3
α-helix	882-898	17
α-helix	902-904	3
α-helix	913-924	12
α-helix	929-933	5
α-helix	935-954	20
α-helix	961-979	19
α-helix	980-982	3
α-helix	992-996	5
α-helix	1001-1043	43
α-helix	1044-1048	5
β-strand	1062-1071	10	32
β-strand	1074-1091	18	32
β-strand	1096-1097	2	35
β-strand	1101-1105	5	35
β-strand	1109-1112	4	32
β-strand	1117-1120	4	32
β-strand	1135-1140	6	35
β-strand	1148-1149	2	35
α-helix	1157-1160	4

Chain C: 23 helices, 56 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
β-strand	27-30	4	36
β-strand	36-37	2	37
β-strand	47-55	9	38
α-helix	56-57	2
β-strand	61-67	7	36
β-strand	83	1	39
β-strand	87-94	8	36
β-strand	101-105	5	39
β-strand	109	1	40
β-strand	114-119	6	39
β-strand	124-129	6	39
β-strand	132	1	40
β-strand	139-143	5	41
β-strand	147-152	6	41
β-strand	161-166	6	39
β-strand	183-192	10	36
β-strand	195-204	10	36
β-strand	219-220	2	37
β-strand	221-226	6	36
β-strand	234-238	5	39
β-strand	241-243	3	41
β-strand	260-266	7	36
β-strand	268-276	9	38
β-strand	282-287	6	38
α-helix	292-299	8
β-strand	308-314	7	42
α-helix	317-319	3
β-strand	322	1	2
β-strand	553-558	6	2
β-strand	561-569	9	2
β-strand	580-582	3	2
β-strand	588-593	6	2
β-strand	598-603	6	2
β-strand	609-614	6	42
β-strand	624-627	4	42
β-strand	657-660	4	42
β-strand	663-666	4	42
β-strand	669-670	2	43
β-strand	679-682	4	43
β-strand	685-690	6	43
β-strand	706-711	6	43
β-strand	716-717	2	15
β-strand	726-730	5	44
β-strand	733-743	11	45
β-strand	749-750	2	46
α-helix	753	1
α-helix	754-758	5
α-helix	762-769	8
α-helix	776-797	22
β-strand	802-805	4	31
β-strand	812	1	47
β-strand	815	1	47
α-helix	834-839	6
α-helix	857-859	3
α-helix	864-869	6
β-strand	874-875	2	46
α-helix	876-878	3
α-helix	882-898	17
α-helix	902-904	3
α-helix	913-924	12
α-helix	929-933	5
α-helix	935-952	18
α-helix	961-979	19
α-helix	980-982	3
α-helix	992-994	3
α-helix	1001-1043	43
α-helix	1044-1048	5
β-strand	1062-1071	10	45
β-strand	1074-1084	11	45
β-strand	1087-1091	5	44
β-strand	1096-1097	2	48
β-strand	1102-1105	4	48
β-strand	1109-1112	4	49
β-strand	1117-1120	4	49
β-strand	1128	1	49
β-strand	1135-1137	3	48
β-strand	1148-1149	2	48
α-helix	1157-1160	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein,SARS-CoV-2 omicron spike with MERS RBD	A, B, C	protein	1249	Severe acute respiratory syndrome coronavirus 2	A0A0U2MMB6, A0A7T8KZF1, A0A8B1J577

Sequence of entity 1 (A, B, C), FASTA

>8UPX_1 Spike glycoprotein,SARS-CoV-2 omicron spike with MERS RBD (chains A, B, C)
QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNG
TKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQF
CNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNID
GYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS
GWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTS
NFRVQPTESIVRFPQAEGVECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVND
FTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILA
TVPHNLTTITKPLKYSYINKCSRLLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYR
KQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKLCGPKKSTNLVKNKC
VNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVI
TPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNN
SYECDIPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNF
TISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNT
QEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYG
DCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPF
PMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQA
LNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEI
RASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTA
PAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVY
DPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLI
DLQELGKYEQYIKGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	14

Primary citation

Pan-beta-coronavirus subunit vaccine prevents SARS-CoV-2 Omicron, SARS-CoV, and MERS-CoV challenge. Wang, G., Verma, A.K., Guan, X. et al. J Virol (2024) 98:e0037624-e0037624. DOI 10.1128/jvi.00376-24 · PubMed

Browse structure collections

About this viewer

MolViewer shows 8UPX directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.