SAXSdb — 8y8i

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike glycoprotein

Human coronavirus HKU1 (isolate N5)

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 14–1276 Chain B； UniProt 14–1276 Chain C； UniProt 14–1276	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.58 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8Y8I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5I08 Prefusion structure of a human coronavirus spike protein Deposited 2016-02-03	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1276（1263 aa） Chain B 14–1276（1263 aa） Chain C 14–1276（1263 aa）	Mutation：R751G, R752G, K753S, R754G, R755S,R751G, R752G, K753S, R754G, R755S Mutation：R751G, R752G, K753S, R754G, R755S,R751G, R752G, K753S, R754G, R755S Mutation：R751G, R752G, K753S, R754G, R755S,R751G, R752G, K753S, R754G, R755S	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；3 uL sample was applied to grid, blotted, and plunged into liquid ethane.	Resolution 4.04 Å
8S0M Crystal structure of the HKU1 receptor binding domain in complex with TMPRSS2 and the nanobody A01 Deposited 2024-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 307–672（366 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.35 M NaH2PO4, 0.65 M K2HPO4	Resolution 3.55 Å R-free 0.221
8S0M Crystal structure of the HKU1 receptor binding domain in complex with TMPRSS2 and the nanobody A01 Deposited 2024-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 307–672（366 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.35 M NaH2PO4, 0.65 M K2HPO4	Resolution 3.55 Å R-free 0.221
8Y87 Structure of HCoV-HKU1C spike in the functionally anchored-1up conformation with 1TMPRSS2 Deposited 2024-02-06	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 14–1276（1263 aa） Chain B 14–1276（1263 aa） Chain C 14–1276（1263 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.26 Å
8Y88 Structure of HCoV-HKU1C spike in the functionally anchored-2up conformation with 2TMPRSS2 Deposited 2024-02-06	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 14–1276（1263 aa） Chain B 14–1276（1263 aa） Chain C 14–1276（1263 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.03 Å
8Y89 Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 2TMPRSS2 Deposited 2024-02-06	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 14–1276（1263 aa） Chain B 14–1276（1263 aa） Chain C 14–1276（1263 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.32 Å
8Y8A Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 3TMPRSS2 Deposited 2024-02-06	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 14–1276（1263 aa） Chain B 14–1276（1263 aa） Chain C 14–1276（1263 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.19 Å
8Y8B Local structure of HCoV-HKU1C spike in complex with TMPRSS2 and glycan Deposited 2024-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 14–1276（1263 aa） Chain B 14–1276（1263 aa）	Not recorded	MJJ methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
8Y8C Structure of HCoV-HKU1C spike in the inactive-closed conformation Deposited 2024-02-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1276（1263 aa） Chain B 14–1276（1263 aa） Chain C 14–1276（1263 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
8Y8D Structure of HCoV-HKU1C spike in the inactive-1up conformation Deposited 2024-02-06	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1276（1263 aa） Chain B 14–1276（1263 aa） Chain C 14–1276（1263 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.41 Å
8Y8E Structure of HCoV-HKU1C spike in the inactive-2up conformation Deposited 2024-02-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1276（1263 aa） Chain B 14–1276（1263 aa） Chain C 14–1276（1263 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å
8Y8F Structure of HCoV-HKU1C spike in the glycan-activated-closed conformation Deposited 2024-02-06	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1276（1263 aa） Chain B 14–1276（1263 aa） Chain C 14–1276（1263 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å
8Y8G Structure of HCoV-HKU1C spike in the glycan-activated-1up conformation Deposited 2024-02-06	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1276（1263 aa） Chain B 14–1276（1263 aa） Chain C 14–1276（1263 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
8Y8H Structure of HCoV-HKU1C spike in the glycan-activated-2up conformation Deposited 2024-02-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 14–1276（1263 aa） Chain B 14–1276（1263 aa） Chain C 14–1276（1263 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å
8Y8J Local structure of HCoV-HKU1C spike in complex with glycan Deposited 2024-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 14–1276（1263 aa） Chain B 14–1276（1263 aa）	Not recorded	MJJ methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.57 Å
8YQQ Structure of HKU1B RBD with TMPRSS2 Deposited 2024-03-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 323–607（285 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.95 Å

15 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPIKE_CVHN5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1263； UniProt 14–1276 Author chain B； PDBConstruct 1–1263； UniProt 14–1276 Author chain C； PDBConstruct 1–1263； UniProt 14–1276

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8y8i
Deposition date deposition_date	2024-02-06
Structure title title	Structure of HCoV-HKU1C spike in the glycan-activated-3up conformation
Keywords keywords	HKU1C, spike, TMPRSS2, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	59.07 Å
Radius of gyration Rg (electron density) rg_electron	58.73 Å
Forward intensity I(0) i0	2183400000.00
Molecular weight molecular_weight	393800.0 kDa
Excluded volume excluded_volume	492780 Å³
Envelope volume envelope_volume	757010 Å³
Hydration-shell volume shell_volume	110280 Å³
Envelope diameter envelope_diameter	212.4 Å
Shell Rg shell_rg	58.65 Å
Envelope Rg envelope_rg	58.12 Å
Shape Rg shape_rg	58.68 Å
Total Rg total_rg	58.89 Å
Total atoms total_atoms	27728
Residues n_residues	3567
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	196.2 Å
Rg (real space) rg_real	59.09 Å
Rg uncertainty (real space) rg_real_error	1.40 Å
I(0) (real space) i0_real	2.1830e+09
I(0) uncertainty (real space) i0_real_error	4.1110e+07
Rg (reciprocal space) rg_reciprocal	59.03 Å
I(0) (reciprocal space) i0_reciprocal	2183000000.0000
Solution quality estimate total_estimate	0.8624
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	72.7 Å
Skewness Skewness skewness	0.354
Kurtosis Kurtosis kurtosis	-0.205
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	175400000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.540

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Spike glycoprotein
Molecular weight formula_weight	140242.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,B
Atom count atom_count	27728

VIGDFNCTNSFINDYNKTIPRISEDVVDVSLGLGTYYVLNRVYLNTTLLFTGYFPKSGANFRDLALKGSIYLSTLWYKPPFLSDFNNGIFSKVKNTKLYVNNTLYSEFSTIVIGSVFVNTSYTIVVQPHNGILEITACQYTMCEYPHTVCKSKGSIRNESWHIDSSEPLCLFKKNFTYNVSADWLYFHFYQERGVFYAYYADVGMPTTFLFSLYLGTILSHYYVMPLTCNAISSNTDNETLEYWVTPLSRRQYLLNFDEHGVITNAVDCSSSFLSEIQCKTQSFAPNTGVYDLSGFTVKPVATVYRRIPNLPDCDIDNWLNNVSVPSPLNWERRIFSNCNFNLSTLLRLVHVDSFSCNNLDKSKIFGSCFNSITVDKFAIPNRRRDDLQLGSSGFLQSSNYKIDISSSSCQLYYSLPLVNVTINNFNPSSWNRRYGFGSFNLSSYDVVYSDHCFSVNSDFCPCADPSVVNSCAKSKPPSAICPAGTKYRHCDLDTTLYVKNWCRCSCLPDPISTYSPNTCPQKKVVVGIGEHCPGLGINEEKCGTQLNHSSCFCSPDAFLGWSFDSCISNNRCNIFSNFIFNGINSGTTCSNDLLYSNTEISTGVCVNYDLYGITGQGIFKEVSAAYYNNWQNLLYDSNGNIIGFKDFLTNKTYTILPCYSGRVSAAFYQNSSSPALLYRNLKCSYVLNNISFISQPFYFDSYLGCVLNAVNLTSYSVSSCDLRMGSGFCIDYALPSSGGSGSGISSPYRFVTFEPFNVSFVNDSVETVGGLFEIQIPTNFTIAGHEEFIQTSSPKVTIDCSAFVCSNYAACHDLLSEYGTFCDNINSILNEVNDLLDITQLQVANALMQGVTLSSNLNTNLHSDVDNIDFKSLLGCLGSQCGSSSRSPLEDLLFNKVKLSDVGFVEAYNNCTGGSEIRDLLCVQSFNGIKVLPPILSETQISGYTTAATVAAMFPPWSAAAGVPFPLNVQYRINGLGVTMDVLNKNQKLIANAFNKALLSIQNGFTATPSALAKIQSVVNANAQALNSLLQQLFNKFGAISSSLQEILSRLDPPEAQVQIDRLINGRLTALNAYVSQQLSDITLIKAGASRAIEKVNECVKSQSPRINFCGNGNHILSLVQNAPYGLLFIHFSYKPTSFKTVLVSPGLCLSGDRGIAPKQGYFIKQNDSWMFTGSSYYYPEPISDKNVVFMNSCSVNFTKAPFIYLNNSIPNLSDFEAELSLWFKNHTSIAPNLTFNSHINATFLDLYYEMNVIQESIKSLN

来源 Source

来源生物 organism	Human coronavirus HKU1 (isolate N5)
NCBI Class编号 ncbi_taxonomy_id	443241
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	6

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.58 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	89689

fit	/app/data/saxs_computation/y8/8y8i/8y8i.fit
pddf	/app/data/pr_computation/y8/8y8i/8y8i.pr.out
profile	/app/data/saxs_computation/y8/8y8i/8y8i.dat

Structure of HCoV-HKU1C spike in the glycan-activated-3up conformation

1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike glycoprotein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)