5I08: Spike glycoprotein,Foldon chimera

Prefusion structure of a human coronavirus spike protein. Determined by electron microscopy at 4.04 Å resolution. Released 2 Mar 2016.

Method: Electron microscopy
Resolution: 4.04 Å
Organisms: Human coronavirus HKU1 (isolate N5), Enterobacteria phage T4
Chains: 3
Atoms: 22,683
Mol. weight: 432.89 kDa
Released: 2 Mar 2016

Explore 5I08 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5I08 contains 105 α-helices and 180 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: 35 helices, 60 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	1
α-helix	32-33	2
β-strand	34-39	6	2
β-strand	49	1	3
β-strand	54-55	2	4
β-strand	59-67	9	5
α-helix	68-69	2
α-helix	72	1
β-strand	73-76	4	2
β-strand	80	1	6
β-strand	85-86	2	1
α-helix	87-90	4
β-strand	95-97	3	7
β-strand	101-107	7	2
β-strand	111-112	2	8
β-strand	117-118	2	8
β-strand	124-127	4	7
β-strand	136-142	7	7
β-strand	145-151	7	7
β-strand	161	1	6
β-strand	183-190	8	7
β-strand	197-205	9	2
β-strand	208-214	7	2
β-strand	220	1	3
β-strand	221-227	7	2
β-strand	234-237	4	7
α-helix	238-239	2
β-strand	240	1	6
α-helix	249-251	3
β-strand	256-260	5	2
β-strand	262-270	9	5
β-strand	276-280	5	5
α-helix	282-284	3
α-helix	286-294	9
β-strand	303-306	4	9
β-strand	317-319	3	10
α-helix	329-333	5
β-strand	337-339	3	11
α-helix	341-343	3
β-strand	345-349	5	12
β-strand	353-354	2	13
α-helix	356-361	6
β-strand	364-371	8	12
α-helix	375-380	6
β-strand	386-392	7	12
α-helix	393-394	2
α-helix	398-401	4
α-helix	409-413	5
β-strand	422-430	9	12
β-strand	435-437	3	11
β-strand	456-458	3	14
α-helix	463-464	2
β-strand	577-579	3	14
β-strand	582	1	12
β-strand	585-594	10	12
β-strand	603-604	2	13
β-strand	620-624	5	10
β-strand	627-631	5	10
β-strand	632-635	4	15
β-strand	647-650	4	15
β-strand	653-659	7	15
β-strand	666-670	5	15
α-helix	671-672	2
α-helix	675-676	2
β-strand	677-680	4	9
β-strand	689-693	5	9
α-helix	697-702	6
β-strand	713-714	2	9
β-strand	718-720	3	9
β-strand	724	1	16
β-strand	730	1	16
β-strand	737	1	16
β-strand	742-745	4	16
β-strand	763-766	4	16
β-strand	798-801	4	17
β-strand	809-812	4	18
α-helix	824-832	9
α-helix	836-862	27
α-helix	903-906	4
α-helix	907-909	3
α-helix	915-923	9
α-helix	935-940	6
β-strand	943-946	4	18
α-helix	952-967	16
α-helix	979-987	9
α-helix	996-999	4
α-helix	1003-1016	14
α-helix	1017-1020	4
α-helix	1025-1045	21
α-helix	1046-1048	3
α-helix	1059-1064	6
α-helix	1068-1109	42
α-helix	1110-1114	5
β-strand	1131-1137	7	17
β-strand	1140-1146	7	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein,Foldon chimera	A, B, C	protein	1299	Human coronavirus HKU1 (isolate N5), Enterobacteria phage T4	M1E1E4 (AlphaFold model), Q0ZME7

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

>5I08_1 Spike glycoprotein,Foldon chimera (chains A, B, C)
VIGDFNCTNSFINDYNKTIPRISEDVVDVSLGLGTYYVLNRVYLNTTLLFTGYFPKSGAN
FRDLALKGSIYLSTLWYKPPFLSDFNNGIFSKVKNTKLYVNNTLYSEFSTIVIGSVFVNT
SYTIVVQPHNGILEITACQYTMCEYPHTVCKSKGSIRNESWHIDSSEPLCLFKKNFTYNV
SADWLYFHFYQERGVFYAYYADVGMPTTFLFSLYLGTILSHYYVMPLTCNAISSNTDNET
LEYWVTPLSRRQYLLNFDEHGVITNAVDCSSSFLSEIQCKTQSFAPNTGVYDLSGFTVKP
VATVYRRIPNLPDCDIDNWLNNVSVPSPLNWERRIFSNCNFNLSTLLRLVHVDSFSCNNL
DKSKIFGSCFNSITVDKFAIPNRRRDDLQLGSSGFLQSSNYKIDISSSSCQLYYSLPLVN
VTINNFNPSSWNRRYGFGSFNLSSYDVVYSDHCFSVNSDFCPCADPSVVNSCAKSKPPSA
ICPAGTKYRHCDLDTTLYVKNWCRCSCLPDPISTYSPNTCPQKKVVVGIGEHCPGLGINE
EKCGTQLNHSSCFCSPDAFLGWSFDSCISNNRCNIFSNFIFNGINSGTTCSNDLLYSNTE
ISTGVCVNYDLYGITGQGIFKEVSAAYYNNWQNLLYDSNGNIIGFKDFLTNKTYTILPCY
SGRVSAAFYQNSSSPALLYRNLKCSYVLNNISFISQPFYFDSYLGCVLNAVNLTSYSVSS
CDLRMGSGFCIDYALPSSGGSGSGISSPYRFVTFEPFNVSFVNDSVETVGGLFEIQIPTN
FTIAGHEEFIQTSSPKVTIDCSAFVCSNYAACHDLLSEYGTFCDNINSILNEVNDLLDIT
QLQVANALMQGVTLSSNLNTNLHSDVDNIDFKSLLGCLGSQCGSSSRSLLEDLLFNKVKL
SDVGFVEAYNNCTGGSEIRDLLCVQSFNGIKVLPPILSETQISGYTTAATVAAMFPPWSA
AAGVPFSLNVQYRINGLGVTMDVLNKNQKLIANAFNKALLSIQNGFTATNSALAKIQSVV
NANAQALNSLLQQLFNKFGAISSSLQEILSRLDNLEAQVQIDRLINGRLTALNAYVSQQL
SDITLIKAGASRAIEKVNECVKSQSPRINFCGNGNHILSLVQNAPYGLLFIHFSYKPTSF
KTVLVSPGLCLSGDRGIAPKQGYFIKQNDSWMFTGSSYYYPEPISDKNVVFMNSCSVNFT
KAPFIYLNNSIPNLSDFEAELSLWFKNHTSIAPNLTFNSHINATFLDLYYEMNVIQESIK
SLNGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGLEVLFQ

Primary citation

Pre-fusion structure of a human coronavirus spike protein. Kirchdoerfer, R.N., Cottrell, C.A., Wang, N. et al. Nature (2016) 531:118-121. DOI 10.1038/nature17200 · PubMed

Other PDB entries of the same protein (UniProt M1E1E4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BJM 2.07 Å, Crystal Structure of Inhibitor 5c in Complex with Prefusion RSV F Glycoprotein
6VKE 2.1 Å, Crystal Structure of Inhibitor JNJ-40012665 in Complex with Prefusion RSV F Glycoprotein
6A0Z 2.33 Å, Crystal structure of broadly neutralizing antibody 13D4 bound to H5N1 influenza…
5KWW 2.5 Å, Crystal Structure of Inhibitor JNJ-53718678 In Complex with Prefusion RSV F Glycoprotein
6VKD 2.5 Å, Crystal Structure of Inhibitor JNJ-36689282 in Complex with Prefusion RSV F Glycoprotein
6VKC 2.6 Å, Crystal Structure of Inhibitor JNJ-36811054 in Complex with Prefusion RSV F Glycoprotein
7ZRV 2.8 Å, cryo-EM structure of omicron spike in complex with de novo designed binder, full map
7AD1 2.92 Å, Cryo-EM structure of a prefusion stabilized SARS-CoV-2 Spike (D614N, R682S, R685G,…
7QTI 3.04 Å, SARS-CoV-2 S Omicron Spike B.1.1.529 - 3-P2G3 and 1-P5C3 Fabs (Global)
5U68 3.08 Å, Structural basis for antibody cross-neutralization of respiratory syncytial virus and…
6W16 3.1 Å, Crystal structure of a human metapneumovirus monomeric fusion protein complexed with 458…
7FJN 3.25 Å, Cryo-EM structure of South African (B.1.351) SARS-CoV-2 spike glycoprotein in complex…

Browse structure collections

About this viewer

MolViewer shows 5I08 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.