6ZGF: Spike glycoprotein

Spike Protein of RaTG13 Bat Coronavirus in Closed Conformation. Determined by electron microscopy at 3.1 Å resolution. Released 1 Jul 2020.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Bat coronavirus RaTG13
Chains: 3
Atoms: 26,163
Mol. weight: 445.09 kDa
Ligands: NAG
Released: 1 Jul 2020

Explore 6ZGF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZGF contains 102 α-helices and 207 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.

Chains A, B and C: 34 helices, 69 β-strands

Element	Residues	Length	Sheet
β-strand	27-31	5	1
β-strand	33-37	5	2
β-strand	48-55	8	3
β-strand	60-64	5	1
β-strand	84-85	2	4
β-strand	90-96	7	1
β-strand	101-107	7	4
β-strand	116-120	5	4
β-strand	127-131	5	4
β-strand	133-143	11	4
β-strand	155-163	9	4
β-strand	168-170	3	4
β-strand	188-197	10	1
β-strand	200-209	10	1
α-helix	216-218	3
β-strand	220-223	4	2
β-strand	224-229	6	1
β-strand	237-245	9	4
β-strand	264-269	6	1
β-strand	271-279	9	3
β-strand	285-290	6	3
α-helix	295-303	9
β-strand	311	1	5
β-strand	314	1	6
β-strand	324-328	5	7
β-strand	335	1	8
α-helix	336	1
β-strand	349	1	9
α-helix	350-352	3
β-strand	354-358	5	9
β-strand	361-362	2	8
α-helix	365-368	4
β-strand	376-379	4	9
α-helix	384-386	3
β-strand	391-392	2	8
β-strand	394-403	10	9
α-helix	404-409	6
α-helix	418-421	4
β-strand	431-437	7	9
α-helix	439-442	4
β-strand	452-454	3	10
β-strand	473-474	2	11
β-strand	488-489	2	11
β-strand	492-494	3	10
α-helix	503-505	3
β-strand	507-516	10	9
β-strand	524-525	2	8
β-strand	538-543	6	7
β-strand	546-554	9	7
β-strand	565-567	3	7
β-strand	573-577	5	7
β-strand	584-588	5	7
β-strand	595-598	4	6
β-strand	599	1	5
β-strand	609-612	4	6
α-helix	620-623	4
α-helix	633-635	3
β-strand	643-645	3	6
β-strand	648-651	4	6
β-strand	654-655	2	12
α-helix	656	1
β-strand	664-667	4	12
β-strand	670-675	6	12
β-strand	687-692	6	12
α-helix	693-694	2
β-strand	697-699	3	13
β-strand	707-711	5	14
β-strand	714-724	11	15
β-strand	729-732	4	16
α-helix	734-738	5
α-helix	757-767	11
α-helix	769-778	10
β-strand	783-785	3	17
α-helix	787-789	3
α-helix	803-804	2
α-helix	808-810	3
α-helix	813-821	9
α-helix	833-836	4
α-helix	846-850	5
β-strand	854-857	4	16
α-helix	858-859	2
α-helix	863-876	14
α-helix	883-885	3
α-helix	894-903	10
α-helix	909-914	6
α-helix	916-935	20
α-helix	938-940	3
α-helix	946-960	15
α-helix	961-963	3
α-helix	982-1024	43
α-helix	1025-1029	5
β-strand	1043-1052	10	15
β-strand	1055-1065	11	15
β-strand	1068-1074	7	14
β-strand	1077-1078	2	18
β-strand	1083-1086	4	18
β-strand	1090-1093	4	14
β-strand	1098-1102	5	14
β-strand	1105-1110	6	14
β-strand	1112	1	19
β-strand	1116-1118	3	18
β-strand	1129-1130	2	18
β-strand	1134	1	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1283	Bat coronavirus RaTG13	A0ABF7PLN6

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

>6ZGF_1 Spike glycoprotein (chains A, B, C)
MGILPSPGMPALLSLVSLLSVLLMGCVAETGMFVFLVLLPLVSSQCVNLTTRTQLPPAYT
NSSTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHAIHVSGTNGIKRFDNPVLPFNDG
VYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNN
KSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTP
INLVRDLPPGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGY
LQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTDSIVRF
PNITNLCPFGEVFNATTFASVYAWNRKRISNCVADYSVLYNSTSFSTFKCYGVSPTKLND
LCFTNVYADSFVITGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSKHIDAKEGGNF
NYLYRLFRKANLKPFERDISTEIYQAGSKPCNGQTGLNCYYPLYRYGFYPTDGVGHQPYR
VVVLSFELLNAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDI
ADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQL
TPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSRSVASQSII
AYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLL
LQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPS
KRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQY
TSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGK
IQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQI
DRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFP
QSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQ
IITTDNTFVSGSCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGIN
ASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQSGRENLYFQGGGGSGYIPEAPRDGQ
AYVRKDGEWVLLSTFLGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	27

Primary citation

SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects. Wrobel, A.G., Benton, D.J., Xu, P. et al. Nat Struct Mol Biol (2020) 27:763-767. DOI 10.1038/s41594-020-0468-7 · PubMed

Other PDB entries of the same protein (UniProt A0ABF7PLN6), best resolution first:

7W6R 2.6 Å, Structure of Bat coronavirus RaTG13 spike receptor-binding domain complexed with its…
9JR4 2.76 Å, Crystal structure of RaTG13 receptor-binding domain complexed with squirrel ACE2
7TTX 2.8 Å, Crystal structure of potent neutralizing antibody 10-40 in complex with Sarbecovirus bat…
7DRV 3.09 Å, Structural basis of SARS-CoV-2-closely-related bat coronavirus RaTG13 to hACE2
9KOS 3.74 Å, Crystal structure of RaTG13 RBD complexed with sheep ACE2
9KOW 3.98 Å, Crystal structure of RaTG13 RBD complexed with cattle ACE2
7P8I 4.5 Å, Receptor-binding domain (RBD) of the spike protein of the bat coronavirus RaTG13 virus…
7P8J 6.58 Å, Receptor-binding domain (RBD) of the spike protein of the bat coronavirus RaTG13 virus…

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