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8tc0

Cryo-EM Structure of Spike Glycoprotein from Bat Coronavirus WIV1 in Closed Conformation

Method: ELECTRON MICROSCOPY Dmax: 166.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike glycoprotein

Bat SARS-like coronavirus WIV1

UniProt U5WI05

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 33 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 19–1127 Chain B； UniProt 19–1127 Chain C； UniProt 19–1127 Not recorded 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 12 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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 EIC LINOLEIC ACID × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 1.88 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 8TC0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7TTY Crystal structure of potent neutralizing antibody 10-40 in complex with bat WIV1 receptor-binding domain Deposited 2022-02-02 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 322–515（194 aa） Fragment：receptor-binding domain (UNP residues 322-515)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M sodium citrate, pH 5.5, 20% propanol, 20% PEG4000
Resolution 3.11 Å R-free 0.329
8WLY Cryo-EM structure of bat WIV1 spike glycoprotein Deposited 2023-10-01 Different construct 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 1–1191（1191 aa）
Chain B 1–1191（1191 aa）
Chain C 1–1191（1191 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
8WLZ Cryo-EM structure of the WIV1 S-hACE2 complex Deposited 2023-10-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–1191（1191 aa）
Chain B 1–1191（1191 aa）
Chain C 1–1191（1191 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.45 Å
8WQ0 Cryo-EM structure of WIV1 spike glycoprotein (the closed state) Deposited 2023-10-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–1191（1191 aa）
Chain B 1–1191（1191 aa）
Chain C 1–1191（1191 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å

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

View Construct and Data Evidence
UniProt name U5WI05_SARS
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1109； UniProt 19–1127 Author chain B； PDBConstruct 1–1109； UniProt 19–1127 Author chain C； PDBConstruct 1–1109； UniProt 19–1127

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 8tc0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8tc0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8tc0
Deposition date deposition_date2023-06-29
Structure title titleCryo-EM Structure of Spike Glycoprotein from Bat Coronavirus WIV1 in Closed Conformation
Keywords keywordsSpike, Glycoprotein, Coronavirus, 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_guinier49.64 Å
Radius of gyration Rg (electron density) rg_electron49.28 Å
Forward intensity I(0) i02039280000.00
Molecular weight molecular_weight379680.0 kDa
Excluded volume excluded_volume475680 ų
Envelope volume envelope_volume652490 ų
Hydration-shell volume shell_volume107100 ų
Envelope diameter envelope_diameter162.3 Å
Shell Rg shell_rg55.29 Å
Envelope Rg envelope_rg48.79 Å
Shape Rg shape_rg49.32 Å
Total Rg total_rg49.33 Å
Total atoms total_atoms50113
Residues n_residues3273
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 dmax166.3 Å
Rg (real space) rg_real49.48 Å
Rg uncertainty (real space) rg_real_error1.36 Å
I(0) (real space) i0_real2.0390e+09
I(0) uncertainty (real space) i0_real_error4.2090e+07
Rg (reciprocal space) rg_reciprocal49.64 Å
I(0) (reciprocal space) i0_reciprocal2040000000.0000
Solution quality estimate total_estimate0.8079
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary57.2 Å
Skewness Skewness skewness0.280
Kurtosis Kurtosis kurtosis-0.433
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha357200000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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8. Citations (1)

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9. Files and Curves (10)