5XGR: Spike protein S1

Structure of the S1 subunit C-terminal domain from bat-derived coronavirus HKU5 spike protein. Determined by X-ray diffraction at 2.1 Å resolution. Released 10 May 2017.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Bat coronavirus HKU5
Chains: 8
Atoms: 13,125
Mol. weight: 186.54 kDa
Ligands: NAG
Released: 10 May 2017

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

Secondary structure: helices and β-sheets

5XGR contains 77 α-helices and 121 β-strands across 8 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: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
α-helix	6-9	4
β-strand	11	1	2
α-helix	12-15	4
α-helix	16-18	3
β-strand	20-24	5	3
β-strand	27-29	3	1
α-helix	31-35	5
β-strand	39-46	8	3
α-helix	50-55	6
β-strand	58	1	1
β-strand	60-67	8	3
α-helix	70-76	7
α-helix	83-87	5
β-strand	97-103	7	3
β-strand	111	1	2
β-strand	116-126	11	4
β-strand	131-133	3	4
α-helix	135-137	3
α-helix	145-148	4
β-strand	157-160	4	4
β-strand	164-172	9	4
β-strand	178-186	9	3
β-strand	194-196	3	1

Chain B: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
α-helix	6-9	4
β-strand	11	1	6
α-helix	12-15	4
α-helix	16-18	3
β-strand	20-24	5	7
β-strand	27-29	3	5
α-helix	31-35	5
β-strand	39-46	8	7
α-helix	50-55	6
β-strand	58	1	5
β-strand	60-67	8	7
α-helix	70-76	7
α-helix	83-87	5
β-strand	97-103	7	7
β-strand	111	1	6
α-helix	112-114	3
β-strand	116-125	10	8
β-strand	132-133	2	8
α-helix	135-137	3
α-helix	145-148	4
β-strand	157-160	4	8
β-strand	164-172	9	8
β-strand	178-186	9	7
β-strand	194-196	3	5

Chain C: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	9
α-helix	6-9	4
β-strand	11	1	10
α-helix	12-15	4
α-helix	16-18	3
β-strand	20-24	5	3
β-strand	27-29	3	9
α-helix	31-35	5
β-strand	39-46	8	3
β-strand	58	1	9
β-strand	60-67	8	3
α-helix	70-76	7
α-helix	83-87	5
β-strand	97-103	7	3
β-strand	111	1	10
α-helix	112-114	3
β-strand	116-126	11	11
β-strand	131-133	3	11
α-helix	135-137	3
α-helix	140-142	3
α-helix	145-148	4
β-strand	157-160	4	11
β-strand	164-172	9	11
β-strand	178-186	9	3
β-strand	194-196	3	9

Chain D: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	12
α-helix	6-9	4
β-strand	11	1	13
α-helix	12-15	4
α-helix	16-18	3
β-strand	20-24	5	7
β-strand	27-29	3	12
α-helix	31-35	5
β-strand	39-46	8	7
β-strand	58	1	12
β-strand	60-67	8	7
α-helix	70-76	7
α-helix	83-87	5
β-strand	97-103	7	7
β-strand	111	1	13
α-helix	112-114	3
β-strand	116-126	11	14
β-strand	131-133	3	14
α-helix	135-137	3
α-helix	145-148	4
β-strand	157-160	4	14
β-strand	164-172	9	14
β-strand	178-186	9	7
β-strand	194-196	3	12

Chain E: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	15
α-helix	6-9	4
β-strand	11	1	16
α-helix	13-15	3
α-helix	16-18	3
β-strand	20-24	5	17
β-strand	27-29	3	15
α-helix	31-35	5
β-strand	39-46	8	17
α-helix	50-53	4
β-strand	58	1	15
β-strand	60-67	8	17
α-helix	70-76	7
α-helix	83	1
α-helix	84-88	5
β-strand	97-103	7	17
β-strand	111	1	16
β-strand	116-126	11	18
β-strand	131-133	3	18
α-helix	135-137	3
α-helix	145-148	4
β-strand	157-160	4	18
β-strand	164-172	9	18
β-strand	178-186	9	17
β-strand	194-196	3	15

Chain F: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	19
α-helix	6-9	4
β-strand	11	1	20
α-helix	12-14	3
β-strand	15	1	21
α-helix	16-18	3
β-strand	20-24	5	21
β-strand	27-29	3	19
α-helix	31-35	5
β-strand	39-46	8	21
α-helix	50-53	4
β-strand	58	1	19
β-strand	60-67	8	21
α-helix	70-76	7
α-helix	83	1
α-helix	84-88	5
β-strand	97-103	7	21
β-strand	111	1	20
α-helix	112-114	3
β-strand	116-126	11	22
β-strand	131-133	3	22
α-helix	135-137	3
α-helix	145-148	4
β-strand	157-160	4	22
β-strand	164-172	9	22
β-strand	178-186	9	21
β-strand	194-196	3	19

Chain G: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	23
α-helix	6-9	4
β-strand	11	1	24
α-helix	12-15	4
α-helix	16-18	3
β-strand	20-24	5	25
β-strand	27-29	3	23
α-helix	31-35	5
β-strand	39-46	8	25
β-strand	58	1	23
β-strand	60-67	8	25
α-helix	70-76	7
α-helix	83-87	5
β-strand	97-103	7	25
β-strand	111	1	24
β-strand	116-126	11	26
β-strand	131-133	3	26
α-helix	135-137	3
α-helix	145-148	4
β-strand	157-160	4	26
β-strand	164-172	9	26
β-strand	178-186	9	25
β-strand	194-196	3	23

Chain H: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	27
α-helix	6-9	4
β-strand	11	1	28
α-helix	12-15	4
α-helix	16-18	3
β-strand	20-24	5	29
β-strand	27-29	3	27
α-helix	31-35	5
β-strand	39-46	8	29
α-helix	50-53	4
β-strand	58	1	27
β-strand	60-67	8	29
α-helix	70-76	7
α-helix	83-87	5
β-strand	97-103	7	29
β-strand	111	1	28
α-helix	112-114	3
β-strand	116-126	11	30
β-strand	131-133	3	30
α-helix	135-137	3
α-helix	145-148	4
β-strand	158-160	3	30
β-strand	164-172	9	30
β-strand	178-186	9	29
β-strand	194-196	3	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike protein S1	A, B, C, D, E, F, G, H	protein	204	Bat coronavirus HKU5	A3EXD0 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>5XGR_1 Spike protein S1 (chains A, B, C, D, E, F, G, H)
QECDFTPMLTGTPPPIYNFKRLVFTNCNYNLTKLLSLFQVSEFSCHQVSPSSLATGCYSS
LTVDYFAYSTDMSSYLQPGSAGAIVQFNYKQDFSNPTCRVLATVPQNLTTITKPSNYAYL
TECYKTSAYGKNYLYNAPGAYTPCLSLASRGFSTKYQSHSDGELTTTGYIYPVTGNLQMA
FIISVQYGTDTNSVCPMQHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9

Primary citation

Structure of the S1 subunit C-terminal domain from bat-derived coronavirus HKU5 spike protein. Han, X., Qi, J., Song, H. et al. Virology (2017) 507:101-109. DOI 10.1016/j.virol.2017.04.016 · PubMed

Other PDB entries of the same protein (UniProt A3EXD0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9EA0 2.0 Å, Structure of the prefusion HKU5-19s Spike trimer (conformation 1)
9EH8 2.0 Å, Structure of the prefusion HKU5-19s Spike trimer (conformation 2)
9KR8 2.39 Å, Overall structure of HKU5 S protein in closed conformation
9DAK 2.4 Å, Merbecovirus PnNL2018B Spike glycoprotein RBD bound to the P. Nathusii ACE2
9E0I 2.4 Å, Structure of the HKU5-19s RBD bound to the Bos taurus ACE2 receptor
9N7D 2.5 Å, Structure of the Rattus norvegicus ACE2 receptor bound HsItaly2011 RBD complex
9N7E 2.5 Å, Eptesicus fuscus ACE2 peptidase domain bound to VsCoV-a7 RBD complex
9KR9 2.8 Å, Overall structure of HKU5 S protein with S468A/Y463A mutation
9KRA 2.8 Å, The RBD of HKU5 complex with Pipistrellus abramus ACE2
9JJ6 2.94 Å, BtHKU5-CoV-2-441 Spike RBD domain binding to hACE2
9D32 3.1 Å, Structure of the HKU5 RBD bound to the P. abramus ACE2 receptor
9KRB 3.22 Å, The RBD of HKU5 complex with Pitta sordida ACE2

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