7KRQ: Spike glycoprotein

Structural impact on SARS-CoV-2 spike protein by D614G substitution. Determined by electron microscopy at 3.4 Å resolution. Released 31 Mar 2021.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 27,819
Mol. weight: 457.73 kDa
Ligands: NAG
Released: 31 Mar 2021

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

Secondary structure: helices and β-sheets

7KRQ contains 133 α-helices and 242 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: 44 helices, 81 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
β-strand	27-31	5	1
β-strand	37	1	2
β-strand	42-43	2	3
β-strand	47-55	9	4
α-helix	56-57	2
β-strand	60-68	9	1
β-strand	78-79	2	1
β-strand	83-85	3	5
β-strand	90-96	7	1
β-strand	101-107	7	5
β-strand	111	1	6
β-strand	116-121	6	5
β-strand	126-131	6	5
β-strand	133-144	12	6
β-strand	153-163	11	6
β-strand	168-171	4	5
α-helix	172-174	3
β-strand	186-197	12	1
β-strand	200-212	13	1
α-helix	216-218	3
α-helix	222	1
β-strand	223	1	2
β-strand	224-229	6	1
β-strand	237-242	6	5
β-strand	243	1	6
α-helix	260-262	3
β-strand	263-269	7	1
β-strand	271-279	9	4
β-strand	285-290	6	4
α-helix	295-302	8
β-strand	311-319	9	7
β-strand	320	1	8
α-helix	321-322	2
β-strand	325	1	9
β-strand	328	1	9
β-strand	335	1	10
α-helix	336	1
α-helix	338-342	5
α-helix	347-348	2
β-strand	349	1	11
α-helix	350-352	3
β-strand	354-358	5	11
β-strand	361-362	2	10
α-helix	365-369	5
β-strand	376-379	4	11
α-helix	384-389	6
β-strand	391-392	2	10
β-strand	395-403	9	11
α-helix	404-409	6
α-helix	417-421	5
β-strand	432-437	6	11
α-helix	439-442	4
β-strand	452-454	3	12
α-helix	460-462	3
β-strand	473-474	2	13
β-strand	485	1	13
β-strand	488-489	2	13
β-strand	492-494	3	12
α-helix	502	1
β-strand	507-513	7	11
β-strand	517	1	10
β-strand	524-525	2	10
α-helix	528-532	5
β-strand	538-543	6	9
β-strand	546-554	9	9
β-strand	565-567	3	9
β-strand	573-577	5	9
β-strand	584-588	5	9
α-helix	589-591	3
β-strand	592-599	8	7
β-strand	609-613	5	7
β-strand	615	1	14
α-helix	619-623	5
β-strand	629	1	8
α-helix	635-638	4
β-strand	643-645	3	7
β-strand	648-651	4	7
β-strand	654-655	2	15
β-strand	664-667	4	15
β-strand	670-675	6	15
β-strand	691-696	6	15
α-helix	697-698	2
β-strand	701-704	4	16
β-strand	711-715	5	17
β-strand	718-728	11	18
β-strand	733-736	4	19
α-helix	738-742	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	787-790	4	20
α-helix	802-804	3
β-strand	807	1	21
β-strand	816	1	21
α-helix	817-825	9
α-helix	843-846	4
α-helix	849-854	6
β-strand	858-861	4	19
α-helix	862-863	2
α-helix	867-884	18
α-helix	887-890	4
α-helix	898-908	11
α-helix	913-917	5
α-helix	920-940	21
α-helix	946-964	19
α-helix	965-967	3
α-helix	977-981	5
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1042	1	22
β-strand	1044	1	22
β-strand	1047-1056	10	18
β-strand	1059-1069	11	18
β-strand	1072-1078	7	17
β-strand	1081-1082	2	23
β-strand	1086-1090	5	23
β-strand	1094-1097	4	17
β-strand	1102-1105	4	17
β-strand	1113-1114	2	17
β-strand	1116	1	24
β-strand	1120-1125	6	23
β-strand	1133-1134	2	23
β-strand	1138	1	24
α-helix	1142-1159	18

Chain B: 45 helices, 81 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
β-strand	27-31	5	25
β-strand	37	1	26
β-strand	42-43	2	9
β-strand	47-55	9	27
α-helix	56-57	2
β-strand	60-68	9	25
β-strand	78-79	2	25
β-strand	83-85	3	28
β-strand	90-96	7	25
β-strand	101-107	7	28
β-strand	111	1	29
β-strand	116-121	6	28
β-strand	126-131	6	28
β-strand	133-144	12	29
β-strand	153-163	11	29
β-strand	168-171	4	28
α-helix	172-174	3
β-strand	186-197	12	25
β-strand	200-212	13	25
α-helix	216-218	3
α-helix	222	1
β-strand	223	1	26
β-strand	224-229	6	25
β-strand	237-242	6	28
β-strand	243	1	29
α-helix	260-262	3
β-strand	263-269	7	25
β-strand	271-279	9	27
β-strand	285-290	6	27
α-helix	295-302	8
β-strand	311-319	9	30
β-strand	320	1	31
α-helix	321-322	2
β-strand	325	1	32
β-strand	328	1	32
β-strand	335	1	33
α-helix	336	1
α-helix	338-342	5
α-helix	347-348	2
β-strand	349	1	34
α-helix	350-352	3
β-strand	354-358	5	34
β-strand	361-362	2	33
α-helix	365-369	5
β-strand	376-379	4	34
α-helix	384-389	6
β-strand	391-392	2	33
β-strand	395-403	9	34
α-helix	404-406	3
α-helix	407-410	4
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	473-474	2	36
β-strand	485	1	36
β-strand	488-489	2	36
β-strand	492-494	3	35
α-helix	502	1
β-strand	507-513	7	34
β-strand	517	1	33
β-strand	524-525	2	33
α-helix	528-532	5
β-strand	538-543	6	32
β-strand	546-554	9	32
β-strand	565-567	3	32
β-strand	573-577	5	32
β-strand	584-588	5	32
α-helix	589-591	3
β-strand	592-599	8	30
β-strand	609-613	5	30
α-helix	619-622	4
β-strand	629	1	31
α-helix	635-638	4
β-strand	643-645	3	30
β-strand	648-651	4	30
β-strand	654-655	2	37
β-strand	664-667	4	37
β-strand	670-675	6	37
β-strand	691-696	6	37
α-helix	697-698	2
β-strand	701-704	4	38
β-strand	711-715	5	39
β-strand	718-728	11	40
β-strand	733-736	4	41
α-helix	738-742	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	787-790	4	16
α-helix	802-804	3
β-strand	807	1	42
β-strand	816	1	42
α-helix	817-825	9
β-strand	835	1	14
α-helix	843-846	4
α-helix	849-854	6
β-strand	858-861	4	41
α-helix	862-863	2
α-helix	867-884	18
α-helix	887-890	4
α-helix	898-908	11
α-helix	913-917	5
α-helix	920-940	21
α-helix	946-964	19
α-helix	965-967	3
α-helix	977-981	5
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1042	1	43
β-strand	1044	1	43
β-strand	1047-1056	10	40
β-strand	1059-1069	11	40
β-strand	1072-1078	7	39
β-strand	1081-1082	2	44
β-strand	1086-1090	5	44
β-strand	1094-1097	4	39
β-strand	1102-1105	4	39
β-strand	1112-1114	3	39
β-strand	1116	1	45
β-strand	1120-1125	6	44
β-strand	1133-1134	2	44
β-strand	1138	1	45
α-helix	1142-1159	18

Chain C: 44 helices, 80 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
β-strand	27-31	5	46
β-strand	37	1	47
β-strand	42-43	2	32
β-strand	47-55	9	48
α-helix	56-57	2
β-strand	60-68	9	46
β-strand	78-79	2	46
β-strand	83-85	3	49
β-strand	90-96	7	46
β-strand	101-107	7	49
β-strand	111	1	50
β-strand	116-121	6	49
β-strand	126-131	6	49
β-strand	133-144	12	50
β-strand	153-163	11	50
β-strand	168-171	4	49
α-helix	172-174	3
β-strand	186-197	12	46
β-strand	200-212	13	46
α-helix	216-218	3
α-helix	222	1
β-strand	223	1	47
β-strand	224-229	6	46
β-strand	237-242	6	49
β-strand	243	1	50
α-helix	260-262	3
β-strand	263-269	7	46
β-strand	271-279	9	48
β-strand	285-290	6	48
α-helix	295-302	8
β-strand	311-319	9	51
β-strand	320	1	52
α-helix	321-322	2
β-strand	325	1	3
β-strand	328	1	3
β-strand	335	1	53
α-helix	336	1
α-helix	338-342	5
α-helix	347-348	2
β-strand	349	1	54
α-helix	350-352	3
β-strand	354-358	5	54
β-strand	361-362	2	53
α-helix	365-369	5
β-strand	376-379	4	54
α-helix	384-389	6
β-strand	391-392	2	53
β-strand	395-403	9	54
α-helix	404-409	6
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	473-474	2	56
β-strand	485	1	56
β-strand	488-489	2	56
β-strand	492-494	3	55
α-helix	502	1
β-strand	507-513	7	54
β-strand	517	1	53
β-strand	524-525	2	53
α-helix	528-532	5
β-strand	538-543	6	3
β-strand	546-554	9	3
β-strand	565-567	3	3
β-strand	573-577	5	3
β-strand	584-588	5	3
α-helix	589-591	3
β-strand	592-599	8	51
β-strand	609-613	5	51
α-helix	619-622	4
β-strand	629	1	52
α-helix	635-638	4
β-strand	643-645	3	51
β-strand	648-651	4	51
β-strand	654-655	2	57
β-strand	664-667	4	57
β-strand	670-675	6	57
β-strand	691-696	6	57
α-helix	697-698	2
β-strand	701-704	4	20
β-strand	711-715	5	58
β-strand	718-728	11	59
β-strand	733-736	4	60
α-helix	738-742	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	787-790	4	38
α-helix	802-804	3
β-strand	807	1	61
β-strand	816	1	61
α-helix	817-825	9
α-helix	849-854	6
β-strand	858-861	4	60
α-helix	862-863	2
α-helix	867-884	18
α-helix	887-890	4
α-helix	893-895	3
α-helix	898-908	11
α-helix	913-917	5
α-helix	920-940	21
α-helix	946-964	19
α-helix	965-967	3
α-helix	977-981	5
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1042	1	62
β-strand	1044	1	62
β-strand	1047-1056	10	59
β-strand	1059-1069	11	59
β-strand	1072-1078	7	58
β-strand	1081-1082	2	63
β-strand	1086-1090	5	63
β-strand	1094-1097	4	58
β-strand	1102-1105	4	58
β-strand	1113-1114	2	58
β-strand	1116	1	64
β-strand	1120-1125	6	63
β-strand	1133-1134	2	63
β-strand	1138	1	64
α-helix	1142-1159	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1310	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

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

>7KRQ_1 Spike glycoprotein (chains A, B, C)
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE
GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN
CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD
YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC
NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN
FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
GTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY
ECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI
SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQE
VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC
LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM
QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN
TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA
SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA
ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP
LQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDD
SEPVLKGVKLHYTLESGGGSAWSHPQFEKGGGSGGGSGGSSAWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	24

Primary citation

Structural impact on SARS-CoV-2 spike protein by D614G substitution. Zhang, J., Cai, Y., Xiao, T. et al. Science (2021) 372:525-530. DOI 10.1126/science.abf2303 · 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 more

7KRQ is part of these collections:

SARS-CoV-2 and COVID-19

About this viewer

MolViewer shows 7KRQ 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.