9ixv

Cryo-EM structure of MERS-CoV S1-NTD bound with KNIH-88 Fab

Method: ELECTRON MICROSCOPY Dmax: 116.4 Å Quality: GOOD

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–350 Not recorded Heavy chain from KNIH-88, monoclonal antibody × 1 Light chain from KNIH-88, monoclonal antibody × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.11 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.

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 A; PDBConstruct 1–350; UniProt 1–350

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 9ixv

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9ixv
Deposition date deposition_date2024-07-29
Structure title titleCryo-EM structure of MERS-CoV S1-NTD bound with KNIH-88 Fab
Keywords keywordsmonoclonal antibody, MERS-CoV S1-NTD, KNIH-88, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier32.32
Radius of gyration Rg (electron density) rg_electron32.77
Forward intensity I(0) i080761300.00
Molecular weight molecular_weight71916.0 kDa
Excluded volume excluded_volume90154 ų
Envelope volume envelope_volume120650 ų
Hydration-shell volume shell_volume32827 ų
Envelope diameter envelope_diameter122.6
Shell Rg shell_rg36.64
Envelope Rg envelope_rg33.31
Shape Rg shape_rg32.77
Total Rg total_rg33.10
Total atoms total_atoms5074
Residues n_residues657
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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 dmax116.4
Rg (real space) rg_real32.76
Rg uncertainty (real space) rg_real_error1.35
I(0) (real space) i0_real8.0760e+07
I(0) uncertainty (real space) i0_real_error1.5450e+06
Rg (reciprocal space) rg_reciprocal32.57
I(0) (reciprocal space) i0_reciprocal80750000.0000
Solution quality estimate total_estimate0.8068
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary30.9
Skewness Skewness skewness0.644
Kurtosis Kurtosis kurtosis-0.061
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14590000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.613; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.719; Smooth: 0.927

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)