7CZX: S protein of SARS-CoV-2 in complex

S protein of SARS-CoV-2 in complex bound with P5A-1B9. Determined by electron microscopy at 2.8 Å resolution. Released 10 Mar 2021.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Chains: 9
Atoms: 34,879
Mol. weight: 666.03 kDa
Ligands: NAG
Released: 10 Mar 2021

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

Secondary structure: helices and β-sheets

7CZX contains 99 α-helices and 323 β-strands across 9 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: 24 helices, 69 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	1
β-strand	37	1	2
β-strand	43	1	3
β-strand	49-55	7	4
β-strand	61-65	5	1
β-strand	84-85	2	5
β-strand	90-92	3	6
β-strand	94	1	1
β-strand	95	1	6
β-strand	101	1	7
β-strand	105	1	8
β-strand	106-107	2	5
β-strand	116-121	6	8
β-strand	126-135	10	8
β-strand	141	1	9
β-strand	160-169	10	8
β-strand	189-197	9	6
β-strand	200-208	9	6
α-helix	222	1
β-strand	223	1	2
β-strand	224-230	7	6
β-strand	237-238	2	5
β-strand	242	1	7
β-strand	243	1	9
β-strand	265-267	3	1
β-strand	268-269	2	6
β-strand	271-279	9	4
β-strand	285-290	6	4
α-helix	295-303	9
β-strand	311-319	9	10
β-strand	326-328	3	11
β-strand	356-358	3	12
α-helix	365-369	5
β-strand	376-379	4	12
α-helix	384-389	6
β-strand	394-402	9	12
α-helix	407-409	3
α-helix	417-421	5
β-strand	432-437	6	12
α-helix	439-442	4
β-strand	452-454	3	13
α-helix	460-462	3
β-strand	492-494	3	13
β-strand	508-516	9	12
β-strand	541-543	3	11
β-strand	546-548	3	11
β-strand	551-554	4	14
β-strand	566-567	2	14
β-strand	573-577	5	14
β-strand	584-588	5	14
β-strand	592-599	8	10
β-strand	609-613	5	10
β-strand	642-645	4	10
β-strand	648-651	4	10
β-strand	653-655	3	15
β-strand	664-667	4	15
β-strand	670-674	5	15
β-strand	692-696	5	15
β-strand	711-728	18	16
β-strand	733-736	4	17
α-helix	738-742	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	788-790	3	18
β-strand	797	1	19
β-strand	800	1	19
β-strand	807	1	20
α-helix	812-814	3
β-strand	816	1	20
α-helix	817-825	9
β-strand	858-861	4	17
α-helix	862-863	2
α-helix	867-884	18
α-helix	898-908	11
α-helix	913-917	5
α-helix	920-939	20
α-helix	946-963	18
α-helix	977-980	4
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1056	10	16
β-strand	1059-1078	20	16
β-strand	1081-1083	3	21
β-strand	1086-1090	5	21
β-strand	1094-1097	4	16
β-strand	1102-1106	5	16
β-strand	1109-1114	6	16
β-strand	1116	1	22
β-strand	1120-1125	6	21
β-strand	1133-1134	2	21
β-strand	1138	1	22
α-helix	1141-1145	5

Chain B: 26 helices, 67 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	23
β-strand	37	1	24
β-strand	49-55	7	25
β-strand	61-65	5	23
β-strand	84-85	2	26
β-strand	90-92	3	27
β-strand	94	1	23
β-strand	95	1	27
β-strand	101	1	28
β-strand	105	1	29
β-strand	106-107	2	26
β-strand	116-121	6	29
β-strand	126-135	10	29
β-strand	141	1	30
β-strand	160-169	10	29
β-strand	189-197	9	27
β-strand	200-208	9	27
α-helix	222	1
β-strand	223	1	24
β-strand	224-230	7	27
β-strand	237-238	2	26
β-strand	242	1	28
β-strand	243	1	30
β-strand	265-267	3	23
β-strand	268-269	2	27
β-strand	271-279	9	25
β-strand	285-290	6	25
α-helix	295-303	9
β-strand	309-319	11	31
α-helix	320-322	3
β-strand	327-328	2	32
β-strand	335	1	33
β-strand	356-358	3	34
β-strand	362	1	33
α-helix	365-369	5
β-strand	376-379	4	34
α-helix	384-386	3
β-strand	395-398	4	34
β-strand	402	1	34
α-helix	407-409	3
α-helix	417-421	5
β-strand	432-437	6	34
α-helix	439-442	4
β-strand	452-454	3	35
α-helix	460-462	3
β-strand	492-494	3	35
β-strand	508-515	8	34
α-helix	532-534	3
β-strand	539-543	5	32
β-strand	546-550	5	32
β-strand	551-554	4	36
β-strand	565-567	3	36
β-strand	573-577	5	36
β-strand	584-588	5	36
α-helix	589-590	2
β-strand	592-601	10	31
β-strand	609-613	5	31
β-strand	642-645	4	31
β-strand	648-651	4	31
β-strand	654-655	2	37
β-strand	664-667	4	37
β-strand	670-673	4	37
β-strand	693-696	4	37
α-helix	697-698	2
β-strand	702-704	3	38
β-strand	711-728	18	39
β-strand	733-736	4	40
α-helix	738-742	5
α-helix	748-753	6
α-helix	754-756	3
α-helix	759-782	24
α-helix	817-822	6
β-strand	858-861	4	40
α-helix	862-863	2
α-helix	867-884	18
α-helix	898-908	11
α-helix	914-917	4
α-helix	920-938	19
α-helix	946-964	19
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1056	10	39
β-strand	1059-1078	20	39
β-strand	1081-1083	3	41
β-strand	1086-1090	5	41
β-strand	1094-1097	4	39
β-strand	1102-1105	4	39
β-strand	1113	1	39
β-strand	1116	1	42
β-strand	1120-1122	3	41
β-strand	1133-1134	2	41
β-strand	1138	1	42
α-helix	1141-1144	4

Chain C: 25 helices, 67 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	43
β-strand	37	1	44
β-strand	49-55	7	45
β-strand	61-65	5	43
β-strand	84-85	2	46
β-strand	90-92	3	47
β-strand	94	1	43
β-strand	95	1	47
β-strand	101	1	48
β-strand	105	1	49
β-strand	106-107	2	46
β-strand	116-121	6	49
β-strand	126-135	10	49
β-strand	141	1	50
β-strand	160-169	10	49
β-strand	189-197	9	47
β-strand	200-208	9	47
α-helix	222	1
β-strand	223	1	44
β-strand	224-230	7	47
β-strand	237-238	2	46
β-strand	242	1	48
β-strand	243	1	50
β-strand	265-267	3	43
β-strand	268-269	2	47
β-strand	271-279	9	45
β-strand	285-290	6	45
α-helix	295-303	9
α-helix	308-309	2
β-strand	311-314	4	51
β-strand	318-319	2	52
β-strand	325-328	4	53
β-strand	356-358	3	54
α-helix	365-369	5
β-strand	376-379	4	54
α-helix	384-389	6
β-strand	394-402	9	54
α-helix	407-409	3
α-helix	417-421	5
β-strand	432-437	6	54
α-helix	439-442	4
β-strand	452-454	3	55
α-helix	460-462	3
β-strand	492-494	3	55
β-strand	508-516	9	54
β-strand	539-543	5	53
β-strand	546-550	5	53
β-strand	551-554	4	3
β-strand	566-567	2	3
β-strand	573-577	5	3
β-strand	584-588	5	3
β-strand	592-593	2	52
β-strand	596-599	4	51
β-strand	609-613	5	51
β-strand	642-645	4	51
β-strand	648-651	4	51
β-strand	654-655	2	56
β-strand	664-667	4	56
β-strand	670-673	4	56
β-strand	693-696	4	56
β-strand	702-704	3	18
β-strand	711-728	18	57
β-strand	733-736	4	58
α-helix	738-742	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	788-790	3	38
α-helix	817-825	9
β-strand	858-861	4	58
α-helix	862-863	2
α-helix	867-884	18
α-helix	898-907	10
α-helix	914-917	4
α-helix	920-938	19
α-helix	946-964	19
α-helix	965-967	3
α-helix	978-981	4
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1056	10	57
β-strand	1059-1078	20	57
β-strand	1081-1083	3	59
β-strand	1086-1090	5	59
β-strand	1094-1097	4	57
β-strand	1102-1105	4	57
β-strand	1113	1	57
β-strand	1116	1	60
β-strand	1120-1122	3	59
β-strand	1133-1134	2	59
β-strand	1138	1	60
α-helix	1141-1145	5

Chains H, I and J: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	61
β-strand	17-25	9	61
β-strand	33-39	7	62
β-strand	46-52	7	62
β-strand	58-59	2	62
β-strand	67-72	6	61
β-strand	77-83	7	61
β-strand	91-97	7	62
β-strand	117-118	2	62
β-strand	122-124	3	62
β-strand	135-139	5	63
β-strand	147	1	63
β-strand	150-160	11	63
β-strand	165-169	5	64
α-helix	170-172	3
β-strand	179-180	2	63
α-helix	181-183	3
β-strand	184-185	2	63
β-strand	191-200	10	63
α-helix	201-203	3
β-strand	210-215	6	64
β-strand	220-225	6	64

Chains K, M and N: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	65
β-strand	11	1	66
β-strand	20-23	4	65
β-strand	39	1	67
β-strand	41-44	4	68
β-strand	51-54	4	68
β-strand	60	1	68
β-strand	69-73	5	65
β-strand	76-80	5	65
β-strand	91-93	3	68
β-strand	96	1	67
β-strand	109	1	68
β-strand	110	1	66
α-helix	118-119	2
β-strand	120-124	5	69
α-helix	125-127	3
α-helix	128-133	6
β-strand	135-143	9	69
β-strand	151-156	6	70
β-strand	159-160	2	70
β-strand	165-169	5	69
α-helix	170-173	4
β-strand	181-188	8	69
α-helix	189-192	4
β-strand	197-203	7	70
β-strand	211-216	6	70

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1283	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
Immunoglobulin heavy variable 4-59,chain H of P5A-1B9,IGH@ protein	H, I, J	protein	458	Homo sapiens	P01825 (AlphaFold model), Q6GMX6 (AlphaFold model)
IG c168_light_IGKV4-1_IGKJ4,Uncharacterized protein	K, M, N	protein	220	Homo sapiens	A0A5C2G1U0 (AlphaFold model), Q8TCD0

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

>7CZX_1 Spike glycoprotein (chains A, B, C)
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE
GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN
CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD
YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC
NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN
FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY
ECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI
SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQE
VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC
LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM
QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN
TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA
SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA
ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP
LQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDD
SEPVLKGVKLHYTLEDYKDDDDK

Sequence of entity 2 (H, I, J), FASTA

>7CZX_2 Immunoglobulin heavy variable 4-59,chain H of P5A-1B9,IGH@ protein (chains H, I, J)
QVQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPPGKGLEWIGYISYSGSTNYN
PSLKSRVTISLDTSKNQFSLKLSSVTAADTAVYYCASNGQYYDILTGQPPDYWYFDLWGR
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPC
PAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKT
KPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVY
TLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSK
LTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Sequence of entity 3 (K, M, N), FASTA

>7CZX_3 IG c168_light_IGKV4-1_IGKJ4,Uncharacterized protein (chains K, M, N)
DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTR
ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTPLTFGGGTKVEIKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	33

Primary citation

Structural basis for bivalent binding and inhibition of SARS-CoV-2 infection by human potent neutralizing antibodies. Yan, R., Wang, R., Ju, B. et al. Cell Res (2021) 31:517-525. DOI 10.1038/s41422-021-00487-9 · PubMed

Other PDB entries of the same protein (UniProt P0DTC2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z8O 0.96 Å, Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide
7Y8J 1.03 Å, 3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2
9FC2 1.21 Å, The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the…
7EK6 1.24 Å, Structure of viral peptides IPB19/N52
7EAM 1.4 Å, immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 7D6
7M53 1.4 Å, B6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
7M8U 1.45 Å, Crystal Structure of HLA-B*35:01 in complex with IPFAMQMAY, an 9-mer epitope from…
7ZR2 1.45 Å, Crystal structure of a chimeric protein mimic of SARS-CoV-2 Spike HR1 in complex with HR2
8D36 1.45 Å, Crystal structure of SARS-CoV-2 fusion peptide in complex with neutralizing antibody…
8ENS 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 spike tail…
8ENW 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 clientized spike…

Browse structure collections

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