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9ueb

Prefusion structure of 2014-422 spike glycoprotein

Method: ELECTRON MICROSCOPY Dmax: 161.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike glycoprotein

Middle East respiratory syndrome-related coronavirus

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 Homooligomer Protein × 3 其他Polymer 9 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–1288 Chain B； UniProt 1–1288 Chain C； UniProt 1–1288 Not recorded 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 9 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

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 9UEB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8SAK BtCoV-422 in complex with neutralizing antibody JC57-11 Deposited 2023-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–1289（1289 aa）
Chain B 1–1289（1289 aa）
Chain C 1–1289（1289 aa）
Mutation：A885P, A1056P, V1057P Mutation：A885P, A1056P, V1057P Mutation：A885P, A1056P, V1057P 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
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
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 Different structure-quality metrics 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 1–1288； UniProt 1–1288 Author chain B； PDBConstruct 1–1288； UniProt 1–1288 Author chain C； PDBConstruct 1–1288； UniProt 1–1288

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 9ueb

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9ueb
Deposition date deposition_date2025-04-08
Structure title titlePrefusion structure of 2014-422 spike glycoprotein
Keywords keywords2014-422, 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_guinier50.48 Å
Radius of gyration Rg (electron density) rg_electron50.03 Å
Forward intensity I(0) i02251250000.00
Molecular weight molecular_weight393190.0 kDa
Excluded volume excluded_volume490040 ų
Envelope volume envelope_volume682550 ų
Hydration-shell volume shell_volume110740 ų
Envelope diameter envelope_diameter162.3 Å
Shell Rg shell_rg56.00 Å
Envelope Rg envelope_rg49.28 Å
Shape Rg shape_rg50.04 Å
Total Rg total_rg50.16 Å
Total atoms total_atoms27649
Residues n_residues3507
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 dmax161.4 Å
Rg (real space) rg_real50.35 Å
Rg uncertainty (real space) rg_real_error1.09 Å
I(0) (real space) i0_real2.2510e+09
I(0) uncertainty (real space) i0_real_error4.1990e+07
Rg (reciprocal space) rg_reciprocal50.58 Å
I(0) (reciprocal space) i0_reciprocal2252000000.0000
Solution quality estimate total_estimate0.8815
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary57.3 Å
Skewness Skewness skewness0.221
Kurtosis Kurtosis kurtosis-0.521
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha362400000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.727
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)