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

S protein of SARS-CoV-2 in complex bound with P5A-2F11_3B. Determined by electron microscopy at 3.2 Å resolution. Released 10 Mar 2021.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Chains: 9
Atoms: 34,771
Mol. weight: 665.52 kDa
Ligands: NAG
Released: 10 Mar 2021

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

Secondary structure: helices and β-sheets

7CZZ contains 98 α-helices and 330 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: 28 helices, 77 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	1
β-strand	37	1	2
β-strand	42-43	2	3
β-strand	47-55	9	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
α-helix	308	1
β-strand	309-319	11	10
α-helix	320-322	3
β-strand	323	1	11
β-strand	328	1	11
β-strand	356-358	3	12
β-strand	362	1	13
α-helix	365-369	5
β-strand	376-379	4	12
α-helix	384-389	6
β-strand	391	1	13
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	448-454	7	14
α-helix	460-462	3
β-strand	473-474	2	15
β-strand	485	1	15
β-strand	488-489	2	15
β-strand	492-497	6	14
β-strand	508-516	9	12
β-strand	525	1	13
β-strand	539-543	5	11
β-strand	546-550	5	11
β-strand	551-554	4	16
β-strand	566-568	3	16
β-strand	572-577	6	16
β-strand	584-588	5	16
β-strand	592-601	10	10
β-strand	609-613	5	10
β-strand	642-645	4	10
β-strand	648-651	4	10
β-strand	654-655	2	17
β-strand	664-667	4	17
β-strand	670-674	5	17
β-strand	692-696	5	17
α-helix	697-698	2
β-strand	702-704	3	18
β-strand	711-728	18	19
β-strand	733-736	4	20
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	21
β-strand	797	1	22
β-strand	800	1	22
β-strand	807	1	23
α-helix	812-814	3
β-strand	816	1	23
α-helix	817-825	9
β-strand	858-861	4	20
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	977-981	5
α-helix	986-989	4
α-helix	994-1028	35
α-helix	1029-1033	5
β-strand	1047-1056	10	19
β-strand	1059-1078	20	19
β-strand	1081-1083	3	24
β-strand	1086-1090	5	24
β-strand	1094-1097	4	19
β-strand	1102-1106	5	19
β-strand	1109-1114	6	19
β-strand	1116	1	25
β-strand	1120-1125	6	24
β-strand	1133-1134	2	24
β-strand	1138	1	25
α-helix	1141-1145	5

Chain B: 24 helices, 68 β-strands

Element	Residues	Length	Sheet
β-strand	28-31	4	26
β-strand	36-37	2	27
β-strand	43	1	16
β-strand	48-51	4	28
β-strand	55	1	29
α-helix	56-57	2
β-strand	60-63	4	26
β-strand	90-95	6	30
β-strand	101-107	7	31
β-strand	116-120	5	31
β-strand	127-131	5	31
β-strand	140	1	32
β-strand	158	1	32
β-strand	166-170	5	31
β-strand	188-197	10	30
β-strand	200-209	10	30
β-strand	222-223	2	27
β-strand	224-230	7	30
β-strand	240-242	3	31
β-strand	265-268	4	30
α-helix	269	1
β-strand	271	1	29
β-strand	275-279	5	28
β-strand	285-290	6	28
α-helix	295-302	8
β-strand	311-317	7	33
β-strand	323	1	34
β-strand	328	1	34
β-strand	356-358	3	35
β-strand	362	1	36
α-helix	365-369	5
β-strand	376-379	4	35
α-helix	384-389	6
β-strand	391	1	36
β-strand	394-402	9	35
α-helix	407-409	3
α-helix	417-421	5
β-strand	432-437	6	35
α-helix	439-442	4
β-strand	448-454	7	37
α-helix	460-462	3
β-strand	473-474	2	38
β-strand	485	1	38
β-strand	488-489	2	38
β-strand	492-497	6	37
β-strand	508-516	9	35
β-strand	525	1	36
β-strand	538-543	6	34
β-strand	546-552	7	34
β-strand	565-567	3	39
β-strand	573-577	5	39
β-strand	584-586	3	39
β-strand	587-588	2	34
β-strand	594-599	6	33
β-strand	609-613	5	33
β-strand	642-644	3	33
β-strand	648-651	4	33
β-strand	654-655	2	40
β-strand	664-667	4	40
β-strand	670-673	4	40
β-strand	693-696	4	40
α-helix	697-698	2
β-strand	702-704	3	41
β-strand	711-728	18	42
β-strand	733-736	4	43
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
α-helix	817-822	6
β-strand	858-861	4	43
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	42
β-strand	1059-1078	20	42
β-strand	1081-1083	3	44
β-strand	1086-1090	5	44
β-strand	1094-1097	4	42
β-strand	1102-1105	4	42
β-strand	1113	1	42
β-strand	1116	1	45
β-strand	1120-1122	3	44
β-strand	1133-1134	2	44
β-strand	1138	1	45
α-helix	1141-1144	4

Chain C: 25 helices, 80 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	46
β-strand	31	1	47
β-strand	37	1	48
β-strand	54-55	2	49
β-strand	60	1	47
β-strand	63	1	46
β-strand	65	1	50
β-strand	84-85	2	51
β-strand	90-94	5	50
β-strand	95-96	2	52
β-strand	101-102	2	53
β-strand	104-107	4	51
β-strand	116-119	4	51
β-strand	127	1	54
β-strand	128-130	3	51
β-strand	132-135	4	55
β-strand	160-164	5	55
β-strand	171	1	54
β-strand	188-189	2	52
β-strand	193-194	2	50
β-strand	198	1	56
β-strand	200	1	56
β-strand	201-205	5	50
β-strand	208-209	2	52
β-strand	223	1	48
β-strand	224-229	6	50
β-strand	237-238	2	51
β-strand	241-242	2	53
β-strand	265-269	5	50
β-strand	271-272	2	49
β-strand	275-279	5	57
β-strand	285-290	6	57
α-helix	295-303	9
β-strand	311-319	9	58
α-helix	320-322	3
β-strand	325	1	59
β-strand	328	1	59
β-strand	356-358	3	60
β-strand	362	1	61
α-helix	365-369	5
β-strand	376-379	4	60
α-helix	384-389	6
β-strand	391	1	61
β-strand	394-402	9	60
α-helix	407-409	3
α-helix	417-421	5
β-strand	432-437	6	60
α-helix	439-442	4
β-strand	448-454	7	62
α-helix	460-462	3
β-strand	473-474	2	63
β-strand	485	1	63
β-strand	488-489	2	63
β-strand	492-497	6	62
β-strand	508-516	9	60
β-strand	525	1	61
β-strand	539-543	5	59
β-strand	546-550	5	59
β-strand	551-554	4	64
β-strand	565-566	2	3
β-strand	567	1	65
β-strand	573	1	65
β-strand	575-577	3	64
β-strand	584-588	5	64
β-strand	592-599	8	58
β-strand	609-613	5	58
α-helix	617-619	3
β-strand	642-644	3	58
β-strand	648-651	4	58
β-strand	654-655	2	66
β-strand	664-667	4	66
β-strand	670-675	6	66
β-strand	691-696	6	66
β-strand	702-704	3	21
β-strand	711-728	18	67
β-strand	733-736	4	68
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	41
α-helix	817-825	9
β-strand	858-861	4	68
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	67
β-strand	1059-1078	20	67
β-strand	1081-1083	3	69
β-strand	1086-1090	5	69
β-strand	1094-1097	4	67
β-strand	1102-1105	4	67
β-strand	1113	1	67
β-strand	1116	1	70
β-strand	1120-1122	3	69
β-strand	1133-1134	2	69
β-strand	1138	1	70
α-helix	1141-1145	5

Chains H, I and J: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	71
β-strand	10-12	3	72
β-strand	17-25	9	71
β-strand	35	1	73
β-strand	38-39	2	72
β-strand	68-69	2	71
β-strand	72-73	2	71
β-strand	78-84	7	71
β-strand	92-94	3	72
β-strand	97	1	73
β-strand	116-120	5	72
β-strand	129-133	5	74
β-strand	141	1	74
β-strand	144-154	11	74
β-strand	159-163	5	75
α-helix	164-166	3
β-strand	173-174	2	74
α-helix	175-177	3
β-strand	178-179	2	74
β-strand	185-194	10	74
α-helix	195-197	3
β-strand	204-209	6	75
β-strand	214-219	6	75

Chains K, M and N: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	76
β-strand	21-24	4	76
β-strand	42-44	3	77
β-strand	50-52	3	77
β-strand	76-79	4	76
β-strand	91	1	77
β-strand	107	1	77
β-strand	120-124	5	78
α-helix	125-127	3
α-helix	128-133	6
β-strand	135-143	9	78
β-strand	151-156	6	79
β-strand	159-160	2	79
β-strand	165-169	5	78
α-helix	170-173	4
β-strand	181-188	8	78
α-helix	189-192	4
β-strand	197-203	7	79
β-strand	211-216	6	79

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 1-8,Immunoglobulin heavy variable 1-8,chain H of…	H, I, J	protein	452	Homo sapiens	P0DP01 (AlphaFold model), V9HW68 (AlphaFold model)
IG c168_light_IGKV4-1_IGKJ4,Immunoglobulin kappa constant	K, M, N	protein	220	Homo sapiens	A0A5C2G1U0 (AlphaFold model), P01834

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

>7CZZ_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

>7CZZ_2 Immunoglobulin heavy variable 1-8,Immunoglobulin heavy variable 1-8,chain H of P5A-2F11_3B,Epididymis luminal protein 214,Epididymis luminal protein 214 (chains H, I, J)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYDINWVRQATGQGLEWMGWMNPNSGNTGY
AQKFQGRVTMTRNTSISTAYMELSSLRSEDTAVYYCARYIVVVPAAKGFDPWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELL
GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQ
YNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSR
DELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKS
RWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

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

>7CZZ_3 IG c168_light_IGKV4-1_IGKJ4,Immunoglobulin kappa constant (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	27

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…

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