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A 3.4 Angstrom cryo-EM structure of the human coronavirus spike trimer computationally derived from vitrified NL63 virus particles

Method: ELECTRON MICROSCOPY Dmax: 172.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike glycoprotein

OrganismNot specified

UniProt Q6Q1S2

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 63 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–1356 Chain B； UniProt 1–1356 Chain C； UniProt 1–1356 Not recorded ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 33 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 6 ;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 ELECTRON MICROSCOPY cryo-EM buffer：pH 8；20 mM Tris, pH 8.0, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.39 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 7KIP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2IEQ Core Structure of S2 from the Human Coronavirus NL63 Spike Glycoprotein Deposited 2006-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 981–1037（57 aa） Fragment：residues 981-1038, 1242-1283 connected by 10-mer link
Chain A 1242–1283（42 aa） Fragment：residues 981-1038, 1242-1283 connected by 10-mer link
Chain B 981–1037（57 aa） Fragment：residues 981-1038, 1242-1283 connected by 10-mer link
Chain B 1242–1283（42 aa） Fragment：residues 981-1038, 1242-1283 connected by 10-mer link
Chain C 981–1037（57 aa） Fragment：residues 981-1038, 1242-1283 connected by 10-mer link
Chain C 1242–1283（42 aa） Fragment：residues 981-1038, 1242-1283 connected by 10-mer link
Not recorded NA SODIUM ION × 3 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；PEG 400, sodium acetate, Imidazole, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.75 Å R-free 0.240
3KBH Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor Deposited 2009-10-20 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 × 4 PDB declaration: tetrameric
Chain E 481–616（136 aa） Fragment：residues 481-616
Chain G 481–616（136 aa） Fragment：residues 481-616
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；285 K；20% PEG 6000, 100 mM Na citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 285K
Resolution 3.31 Å R-free 0.300
3KBH Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor Deposited 2009-10-20 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 × 4 PDB declaration: tetrameric
Chain F 481–616（136 aa） Fragment：residues 481-616
Chain H 481–616（136 aa） Fragment：residues 481-616
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；285 K；20% PEG 6000, 100 mM Na citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 285K
Resolution 3.31 Å R-free 0.300
5SZS Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy Deposited 2016-08-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 16–1291（1276 aa）
Chain B 16–1291（1276 aa）
Chain C 16–1291（1276 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7FC3 structure of NL63 receptor-binding domain complexed with horse ACE2 Deposited 2021-07-13 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 E 481–611（131 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；1.8M Ammonium sulfate, 0.1M BIS-TRIS pH6.5, 2% v/v polyethylene glycol monomethylether 550
Resolution 3.19 Å R-free 0.283
8FR7 A hinge glycan regulates spike bending and impacts coronavirus infectivity Deposited 2023-01-06 Different oligomeric state Different ligand/ion Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–1356（1356 aa）
Chain B 1–1356（1356 aa）
Chain C 1–1356（1356 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris, pH 8.0, 120 mM NaCl, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9OPQ TMPRSS2 (S441A) bound to the HCoV-NL63 S2'region genetically fused to the HCoV-HKU1 RBD Deposited 2025-05-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 867–877（11 aa）
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 3.30 Å
9Z3J HCoV-NL63 S2' peptide bound to TMPRSS2 S441A (complexed with the H1H7 Fab and an anti-kappa-nanobody) Deposited 2025-11-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 866–880（15 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPIKE_CVHNL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1356； UniProt 1–1356 Author chain B； PDBConstruct 1–1356； UniProt 1–1356 Author chain C； PDBConstruct 1–1356； UniProt 1–1356

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 7kip

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7kip
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7kip
Deposition date deposition_date2020-10-24
Structure title titleA 3.4 Angstrom cryo-EM structure of the human coronavirus spike trimer computationally derived from vitrified NL63 virus particles
Keywords keywordsNL63, in situ, Spike trimer, glycosylation sites, single particle cryo-EM, 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_guinier52.94 Å
Radius of gyration Rg (electron density) rg_electron52.50 Å
Forward intensity I(0) i02697800000.00
Molecular weight molecular_weight435690.0 kDa
Excluded volume excluded_volume545110 ų
Envelope volume envelope_volume851060 ų
Hydration-shell volume shell_volume129470 ų
Envelope diameter envelope_diameter176.2 Å
Shell Rg shell_rg60.07 Å
Envelope Rg envelope_rg51.53 Å
Shape Rg shape_rg52.50 Å
Total Rg total_rg52.75 Å
Total atoms total_atoms30612
Residues n_residues3576
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 dmax172.1 Å
Rg (real space) rg_real52.73 Å
Rg uncertainty (real space) rg_real_error1.06 Å
I(0) (real space) i0_real2.6980e+09
I(0) uncertainty (real space) i0_real_error4.7080e+07
Rg (reciprocal space) rg_reciprocal53.10 Å
I(0) (reciprocal space) i0_reciprocal2699000000.0000
Solution quality estimate total_estimate0.8781
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary63.1 Å
Skewness Skewness skewness0.180
Kurtosis Kurtosis kurtosis-0.453
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha856900000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.848
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

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8. Citations (1)

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9. Files and Curves (10)