7x28

MERS-CoV spike complex with S41 neutralizing antibody Fab Class3 (2u1d RBD with 2Fab)

Method: ELECTRON MICROSCOPY Dmax: 222.8 Å Quality: GOOD

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

Spike glycoprotein

Middle East respiratory syndrome-related coronavirus

UniProt K0BRG7

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain F; UniProt 1–1290 Chain G; UniProt 1–1290 Chain I; UniProt 1–1290 Not recorded antibody S41 heavy chain × 2 antibody S41 light chain × 2 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.

22 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name K0BRG7_MERS
Isoform
PDB entities 3
Chains and sequence ranges Author chain F; PDBConstruct 1–1290; UniProt 1–1290 Author chain G; PDBConstruct 1–1290; UniProt 1–1290 Author chain I; PDBConstruct 1–1290; UniProt 1–1290

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 7x28

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7x28
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7x28
Deposition date deposition_date2022-02-25
Structure title titleMERS-CoV spike complex with S41 neutralizing antibody Fab Class3 (2u1d RBD with 2Fab)
Keywords keywordsreceptor binding domain, 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_guinier72.15
Radius of gyration Rg (electron density) rg_electron72.63
Forward intensity I(0) i02829650000.00
Molecular weight molecular_weight448260.0 kDa
Excluded volume excluded_volume560010 ų
Envelope volume envelope_volume866230 ų
Hydration-shell volume shell_volume108050 ų
Envelope diameter envelope_diameter252.8
Shell Rg shell_rg63.72
Envelope Rg envelope_rg72.04
Shape Rg shape_rg72.61
Total Rg total_rg72.53
Total atoms total_atoms31571
Residues n_residues4119
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 dmax222.8
Rg (real space) rg_real72.19
Rg uncertainty (real space) rg_real_error1.28
I(0) (real space) i0_real2.8240e+09
I(0) uncertainty (real space) i0_real_error5.8640e+07
Rg (reciprocal space) rg_reciprocal70.85
I(0) (reciprocal space) i0_reciprocal2820000000.0000
Solution quality estimate total_estimate0.8418
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary70.9
Skewness Skewness skewness0.406
Kurtosis Kurtosis kurtosis-0.510
Angular range angular_range— – 0.1100 −1
Current regularization parameter α current_alpha0.0573
Highest regularization parameter α highest_alpha118300000.0000
Real-space data points n_real_points23
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.033

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id7x28C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7x28C02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7x28D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7x28D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7x28H01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7x28H02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7x28K01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7x28K02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)