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7x27

MERS-CoV spike complex

Method: ELECTRON MICROSCOPY Dmax: 162.1 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 K9N5Q8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain G； UniProt 19–1229 Chain I； UniProt 19–1229 Chain J； UniProt 19–1229 Mutation：H1020Q, V1060P, L1061P No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.49 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 7X27 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4XAK Crystal structure of potent neutralizing antibody m336 in complex with MERS Co-V RBD Deposited 2014-12-15 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 367–601（235 aa） Fragment：Receptor-binding domain (UNP residues 367-601)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% PEG 2000MME, 100 mM HEPES, pH7.5
Resolution 2.45 Å R-free 0.249
4XAK Crystal structure of potent neutralizing antibody m336 in complex with MERS Co-V RBD Deposited 2014-12-15 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 × 3 PDB declaration: trimeric
Chain B 367–601（235 aa） Fragment：Receptor-binding domain (UNP residues 367-601)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% PEG 2000MME, 100 mM HEPES, pH7.5
Resolution 2.45 Å R-free 0.249
4ZPT Structure of MERS-Coronavirus Spike Receptor-binding Domain (England1 Strain) in Complex with Vaccine-Elicited Murine Neutralizing Antibody D12 (Crystal Form 1) Deposited 2015-05-08 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 R 381–588（208 aa） Fragment：receptor-binging domain, UNP residues 381-588
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1 M sodium acetate pH 5.5, 50 mM sodium chloride, 10 % PEG 400, 11 % PEG 8,000
Resolution 2.59 Å R-free 0.244
4ZPT Structure of MERS-Coronavirus Spike Receptor-binding Domain (England1 Strain) in Complex with Vaccine-Elicited Murine Neutralizing Antibody D12 (Crystal Form 1) Deposited 2015-05-08 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 × 3 PDB declaration: trimeric
Chain S 381–588（208 aa） Fragment：receptor-binging domain, UNP residues 381-588
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1 M sodium acetate pH 5.5, 50 mM sodium chloride, 10 % PEG 400, 11 % PEG 8,000
Resolution 2.59 Å R-free 0.244
4ZPV Structure of MERS-Coronavirus Spike Receptor-binding Domain (England1 Strain) in Complex with Vaccine-Elicited Murine Neutralizing Antibody D12 (Crystal Form 2) Deposited 2015-05-08 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 R 381–588（208 aa） Fragment：UNP residues 381-588
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M sodium cacodylate pH 6.5, 80 mM magnesium acetate, 14.5 % PEG 8,000
Resolution 3.20 Å R-free 0.281
4ZPV Structure of MERS-Coronavirus Spike Receptor-binding Domain (England1 Strain) in Complex with Vaccine-Elicited Murine Neutralizing Antibody D12 (Crystal Form 2) Deposited 2015-05-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain S 381–588（208 aa） Fragment：UNP residues 381-588
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M sodium cacodylate pH 6.5, 80 mM magnesium acetate, 14.5 % PEG 8,000
Resolution 3.20 Å R-free 0.281
4ZPW Structure of unbound MERS-CoV spike receptor-binding domain (England1 strain). Deposited 2015-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain R 381–588（208 aa） Fragment：receptor-binding domain, UNP residues 381-588
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M Tris-HCl pH 8.5, 10 % MPD, 29 % PEG 1,500
Resolution 3.02 Å R-free 0.259
4ZPW Structure of unbound MERS-CoV spike receptor-binding domain (England1 strain). Deposited 2015-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain S 381–588（208 aa） Fragment：receptor-binding domain, UNP residues 381-588
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M Tris-HCl pH 8.5, 10 % MPD, 29 % PEG 1,500
Resolution 3.02 Å R-free 0.259
6C6Y Crystal structure of Middle-East Respiratory Syndrome (MERS) coronavirus neutralizing antibody JC57-14 isolated from a vaccinated rhesus macaque in complex with MERS Receptor Binding Domain Deposited 2018-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain S 381–588（208 aa） Fragment：Receptor Binding Domain residues 381-588
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；293 K；90 mM CHES pH 9.5, 18% PEG 8,000
Resolution 3.32 Å R-free 0.267
6C6Y Crystal structure of Middle-East Respiratory Syndrome (MERS) coronavirus neutralizing antibody JC57-14 isolated from a vaccinated rhesus macaque in complex with MERS Receptor Binding Domain Deposited 2018-01-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain R 381–588（208 aa） Fragment：Receptor Binding Domain residues 381-588
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；293 K；90 mM CHES pH 9.5, 18% PEG 8,000
Resolution 3.32 Å R-free 0.267
7M55 B6 Fab fragment bound to the MERS-CoV 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 1230–1244（15 aa） Fragment：residues 1230-1244 of the spike glycoprotein
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Magnesium Chloride and 20% (w/v) PEG3350
Resolution 1.40 Å R-free 0.200
8DGV Crystal structure of MERS-CoV spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC99.103 isolated from a vaccinated COVID-19 convalescent Deposited 2022-06-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1221–1247（27 aa） Fragment：stem helix domain, residues 1221-1247
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；295.15 K；19% (v/v) Isopropanol, 19% (w/v) PEG 4000, 5% (v/v) Glycerol, 0.095 M Sodium citrate pH 5.6
Resolution 2.30 Å R-free 0.249
8DGX Crystal structure of MERS-CoV spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC68.109 isolated from a vaccinated COVID-19 convalescent Deposited 2022-06-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1221–1247（27 aa） Fragment：Stem helix domain, residues 1221-1247
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；0.17 M Sodium acetate, 25.5% (w/v) PEG 4000, 15% (v/v) Glycerol, 0.085 M Tris pH 8.5
Resolution 2.89 Å R-free 0.280
8DGX Crystal structure of MERS-CoV spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC68.109 isolated from a vaccinated COVID-19 convalescent Deposited 2022-06-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1221–1247（27 aa） Fragment：Stem helix domain, residues 1221-1247
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；0.17 M Sodium acetate, 25.5% (w/v) PEG 4000, 15% (v/v) Glycerol, 0.085 M Tris pH 8.5
Resolution 2.89 Å R-free 0.280
8XZ6 MERS-CoV S and radixin complex structure Deposited 2024-01-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1334–1346（13 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M Tris, pH 8.5, and 6% PEG 8000
Resolution 2.12 Å R-free 0.256
8XZ6 MERS-CoV S and radixin complex structure Deposited 2024-01-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1334–1346（13 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M Tris, pH 8.5, and 6% PEG 8000
Resolution 2.12 Å R-free 0.256
8XZ6 MERS-CoV S and radixin complex structure Deposited 2024-01-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1334–1346（13 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M Tris, pH 8.5, and 6% PEG 8000
Resolution 2.12 Å R-free 0.256
8XZ6 MERS-CoV S and radixin complex structure Deposited 2024-01-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1334–1346（13 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M Tris, pH 8.5, and 6% PEG 8000
Resolution 2.12 Å R-free 0.256
8Z4O MERS-CoV post-fusion S ectodomain trimer Deposited 2024-04-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 752–1290（539 aa）
Chain B 752–1290（539 aa）
Chain C 752–1290（539 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
8Z4T MERS-CoV S ectodomain trimer in complex with receptor DPP4-750E Deposited 2024-04-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 19–1224（1206 aa）
Chain B 19–1224（1206 aa）
Chain C 19–1224（1206 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9IXV Cryo-EM structure of MERS-CoV S1-NTD bound with KNIH-88 Fab Deposited 2024-07-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–350（350 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å

12 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPIKE_MERS1
Isoform —
PDB entities 1
Chains and sequence ranges Author chain G； PDBConstruct 2–1212； UniProt 19–1229 Author chain I； PDBConstruct 2–1212； UniProt 19–1229 Author chain J； PDBConstruct 2–1212； UniProt 19–1229

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 7x27

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7x27
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7x27
Deposition date deposition_date2022-02-25
Structure title titleMERS-CoV spike complex
Keywords keywordsreceptor binding domain, antibody, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier51.00 Å
Radius of gyration Rg (electron density) rg_electron50.66 Å
Forward intensity I(0) i01528590000.00
Molecular weight molecular_weight323350.0 kDa
Excluded volume excluded_volume403400 ų
Envelope volume envelope_volume563860 ų
Hydration-shell volume shell_volume93982 ų
Envelope diameter envelope_diameter165.7 Å
Shell Rg shell_rg52.97 Å
Envelope Rg envelope_rg49.91 Å
Shape Rg shape_rg50.68 Å
Total Rg total_rg50.67 Å
Total atoms total_atoms22770
Residues n_residues2949
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 dmax162.1 Å
Rg (real space) rg_real50.88 Å
Rg uncertainty (real space) rg_real_error1.53 Å
I(0) (real space) i0_real1.5290e+09
I(0) uncertainty (real space) i0_real_error2.9040e+07
Rg (reciprocal space) rg_reciprocal51.08 Å
I(0) (reciprocal space) i0_reciprocal1529000000.0000
Solution quality estimate total_estimate0.8867
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary57.5 Å
Skewness Skewness skewness0.187
Kurtosis Kurtosis kurtosis-0.570
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha126900000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.944; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.698
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (2)

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9. Files and Curves (10)