← Back to search
8sak

BtCoV-422 in complex with neutralizing antibody JC57-11

Method: ELECTRON MICROSCOPY Dmax: 179.0 Å Quality: GOOD
▼

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

Spike glycoprotein

unclassified Merbecovirus

UniProt A0A2R4KP93

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 Heteromer Protein × 5 其他Polymer 16 PDB declaration: pentameric（5） Consistent with protein copy count Chain A； UniProt 1–1289 Chain B； UniProt 1–1289 Chain C； UniProt 1–1289 Mutation：A885P, A1056P, V1057P JC57-11 Fab heavy chain × 1 JC57-11 Fab light chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 12 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]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 ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.00 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 8SAK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9JMJ Cryo-EM structure of the GD-BatCoV (BtCoV/Ii/GD/2014-422) RBD in complex with human DPP4 Deposited 2024-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 371–610（240 aa） Fragment：RBD,RBD
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9JMP Cryo-EM structure of GD-BatCoV (BtCoV/Ii/GD/2014-422) S-trimer Deposited 2024-09-20 Different construct 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 1–1294（1294 aa）
Chain B 1–1294（1294 aa）
Chain C 1–1294（1294 aa）
Mutation：A885P,S962P,A969P,N1012P,A1056P,V1057P Mutation：A885P,S962P,A969P,N1012P,A1056P,V1057P Mutation：A885P,S962P,A969P,N1012P,A1056P,V1057P NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 EIC LINOLEIC ACID × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9UEB Prefusion structure of 2014-422 spike glycoprotein Deposited 2025-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–1288（1288 aa）
Chain B 1–1288（1288 aa）
Chain C 1–1288（1288 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.59 Å
9V2L Complex structure of 2014-422 spike RBD bound to human DPP4 Deposited 2025-05-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 371–593（223 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

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

View Construct and Data Evidence
UniProt name A0A2R4KP93_MERS
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1289； UniProt 1–1289 Author chain B； PDBConstruct 1–1289； UniProt 1–1289 Author chain C； PDBConstruct 1–1289； UniProt 1–1289

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 8sak

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8sak
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id8sak
Deposition date deposition_date2023-04-01
Structure title titleBtCoV-422 in complex with neutralizing antibody JC57-11
Keywords keywords;coronavirus, MERS, neutralizing, antibody, MERS-like, merbecovirus, bat, virus, CDRH3, RBD, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex ;; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier51.50 Å
Radius of gyration Rg (electron density) rg_electron51.26 Å
Forward intensity I(0) i02362100000.00
Molecular weight molecular_weight405480.0 kDa
Excluded volume excluded_volume506350 ų
Envelope volume envelope_volume709070 ų
Hydration-shell volume shell_volume112970 ų
Envelope diameter envelope_diameter193.2 Å
Shell Rg shell_rg56.41 Å
Envelope Rg envelope_rg50.80 Å
Shape Rg shape_rg51.27 Å
Total Rg total_rg51.37 Å
Total atoms total_atoms28520
Residues n_residues3580
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
▼

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

Maximum dimension Dmax dmax179.0 Å
Rg (real space) rg_real51.45 Å
Rg uncertainty (real space) rg_real_error1.80 Å
I(0) (real space) i0_real2.3620e+09
I(0) uncertainty (real space) i0_real_error4.8840e+07
Rg (reciprocal space) rg_reciprocal51.54 Å
I(0) (reciprocal space) i0_reciprocal2362000000.0000
Solution quality estimate total_estimate0.7935
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary57.8 Å
Skewness Skewness skewness0.352
Kurtosis Kurtosis kurtosis-0.223
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha385000000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.771; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (7)

▶

8. Citations (1)

▶

9. Files and Curves (10)