SAXSdb — 8x5o

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

spike protein S2

Coronavirus HKU15

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 983–1058 Chain B； UniProt 983–1058 Chain C； UniProt 983–1058	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；289 K；2.8M Sodium Acetate, HCl pH 7.0	Resolution 2.67 Å R-free 0.291

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 8X5O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4QZV Bat-derived coronavirus HKU4 uses MERS-CoV receptor human CD26 for cell entry Deposited 2014-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 372–611（240 aa） Fragment：receptor binding domain (UNP RESIDUES 372-611)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M sodium citrate, pH 5.5, 15% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.59 Å R-free 0.224
4QZV Bat-derived coronavirus HKU4 uses MERS-CoV receptor human CD26 for cell entry Deposited 2014-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 372–611（240 aa） Fragment：receptor binding domain (UNP RESIDUES 372-611)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M sodium citrate, pH 5.5, 15% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.59 Å R-free 0.224
7M52 B6 Fab fragment bound to the HKU4 spike stem helix peptide Deposited 2021-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1231–1245（15 aa） Fragment：Residues 1231-1245 of the spike glycoprotein	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.6 M Sodium Chloride, 0.1 M MES-NaOH, and 20% (w/v) PEG 4000	Resolution 1.50 Å R-free 0.197
9LZH Prefusion structure of HKU4 spike glycoprotein Deposited 2025-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–1291（1291 aa） Chain B 1–1291（1291 aa） Chain C 1–1291（1291 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPIKE_BCHK4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 983–1058 Author chain B； PDBConstruct 1–76； UniProt 983–1058 Author chain C； PDBConstruct 1–76； UniProt 983–1058

spike protein S2

Coronavirus HKU15

UniProt S4WYD6

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1247–1290 Chain B； UniProt 1247–1290 Chain C； UniProt 1247–1290	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；289 K；2.8M Sodium Acetate, HCl pH 7.0	Resolution 2.67 Å R-free 0.291

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	S4WYD6_BCHK4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 83–126； UniProt 1247–1290 Author chain B； PDBConstruct 83–126； UniProt 1247–1290 Author chain C； PDBConstruct 83–126； UniProt 1247–1290

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	8x5o
Deposition date deposition_date	2023-11-17
最后修订 last_revision	2025-05-21
Structure title title	Crystal structure of the post-fusion core of MjHKUr-CoV spike protein.
Keywords keywords	MjHKUr-CoV, spike protein, postfusion, VIRUS, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	29.70 Å
Radius of gyration Rg (electron density) rg_electron	30.34 Å
Forward intensity I(0) i0	21266100.00
Molecular weight molecular_weight	35439.0 kDa
Excluded volume excluded_volume	44397 Å³
Envelope volume envelope_volume	60393 Å³
Hydration-shell volume shell_volume	19480 Å³
Envelope diameter envelope_diameter	113.5 Å
Shell Rg shell_rg	31.60 Å
Envelope Rg envelope_rg	32.50 Å
Shape Rg shape_rg	30.32 Å
Total Rg total_rg	30.53 Å
Total atoms total_atoms	2487
Residues n_residues	329
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	114.4 Å
Rg (real space) rg_real	30.42 Å
Rg uncertainty (real space) rg_real_error	1.47 Å
I(0) (real space) i0_real	2.1270e+07
I(0) uncertainty (real space) i0_real_error	3.5850e+05
Rg (reciprocal space) rg_reciprocal	30.11 Å
I(0) (reciprocal space) i0_reciprocal	21260000.0000
Solution quality estimate total_estimate	0.6552
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.780
Kurtosis Kurtosis kurtosis	-0.055
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7034000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.177; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.048; Smooth: 0.938

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	198.736 Å
Unit-cell length b length_b	198.736 Å
Unit-cell length c length_c	64.130 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	2.670 Å
Low-resolution limit resolution_low	34.420 Å
R factor r_factor	0.2433
R_work r_work	0.2407
R_free r_free	0.2915

Description description	spike protein S2
Molecular weight formula_weight	13405.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2612

Crystal structure of the post-fusion core of MjHKUr-CoV spike protein.

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

spike protein S2

State in the Current Structure

Other States of the Same Protein in the Database

spike protein S2

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Coronavirus HKU15
NCBI Class编号 ncbi_taxonomy_id	1965089
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	125

fit	/app/data/saxs_computation/x5/8x5o/8x5o.fit
pddf	/app/data/pr_computation/x5/8x5o/8x5o.pr.out
profile	/app/data/saxs_computation/x5/8x5o/8x5o.dat