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9lzh

Prefusion structure of HKU4 spike glycoprotein

Method: ELECTRON MICROSCOPY Dmax: 157.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike glycoprotein

Bat coronavirus HKU4

UniProt A3EX94

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 3 其他Polymer 10 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–1291 Chain B； UniProt 1–1291 Chain C； UniProt 1–1291 Not recorded 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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

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 9LZH 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 method 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 method 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 method 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
8X5O Crystal structure of the post-fusion core of MjHKUr-CoV spike protein. Deposited 2023-11-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 983–1058（76 aa）
Chain B 983–1058（76 aa）
Chain C 983–1058（76 aa）
Not recorded No recorded non-water small molecule 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

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 1–1291； UniProt 1–1291 Author chain B； PDBConstruct 1–1291； UniProt 1–1291 Author chain C； PDBConstruct 1–1291； UniProt 1–1291

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9lzh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9lzh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9lzh
Deposition date deposition_date2025-02-21
Structure title titlePrefusion structure of HKU4 spike glycoprotein
Keywords keywordsHKU4, spike, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier50.08 Å
Radius of gyration Rg (electron density) rg_electron49.70 Å
Forward intensity I(0) i02213850000.00
Molecular weight molecular_weight392860.0 kDa
Excluded volume excluded_volume490960 ų
Envelope volume envelope_volume686670 ų
Hydration-shell volume shell_volume111360 ų
Envelope diameter envelope_diameter164.8 Å
Shell Rg shell_rg55.83 Å
Envelope Rg envelope_rg49.41 Å
Shape Rg shape_rg49.72 Å
Total Rg total_rg49.86 Å
Total atoms total_atoms27644
Residues n_residues3495
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax157.7 Å
Rg (real space) rg_real49.96 Å
Rg uncertainty (real space) rg_real_error1.46 Å
I(0) (real space) i0_real2.2140e+09
I(0) uncertainty (real space) i0_real_error4.3640e+07
Rg (reciprocal space) rg_reciprocal50.16 Å
I(0) (reciprocal space) i0_reciprocal2214000000.0000
Solution quality estimate total_estimate0.8720
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary61.0 Å
Skewness Skewness skewness0.242
Kurtosis Kurtosis kurtosis-0.486
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha405300000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.924; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.582
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)