SAXSdb — 4zpw

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

Spike glycoprotein

Human coronavirus EMC (isolate United Kingdom/H123990006/2012)

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain R； UniProt 381–588	Fragment：receptor-binding domain, UNP residues 381-588	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain S； UniProt 381–588	Fragment：receptor-binding domain, UNP residues 381-588	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

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 4ZPW	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 oligomeric state Different ligand/ion 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 oligomeric state 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state 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 oligomeric state Different ligand/ion 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
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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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
7X27 MERS-CoV spike complex Deposited 2022-02-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain G 19–1229（1211 aa） Chain I 19–1229（1211 aa） Chain J 19–1229（1211 aa）	Mutation：H1020Q, V1060P, L1061P Mutation：H1020Q, V1060P, L1061P Mutation：H1020Q, V1060P, L1061P	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.49 Å
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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 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 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 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPIKE_CVEMC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain R； PDBConstruct 1–208； UniProt 381–588 Author chain S； PDBConstruct 1–208； UniProt 381–588

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4zpw
Deposition date deposition_date	2015-05-08
Structure title title	Structure of unbound MERS-CoV spike receptor-binding domain (England1 strain).
Keywords keywords	Vaccine, Immunogen, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	27.13 Å
Radius of gyration Rg (electron density) rg_electron	26.63 Å
Forward intensity I(0) i0	35795600.00
Molecular weight molecular_weight	46776.0 kDa
Excluded volume excluded_volume	58687 Å³
Envelope volume envelope_volume	72396 Å³
Hydration-shell volume shell_volume	23960 Å³
Envelope diameter envelope_diameter	93.5 Å
Shell Rg shell_rg	32.15 Å
Envelope Rg envelope_rg	26.66 Å
Shape Rg shape_rg	26.57 Å
Total Rg total_rg	27.43 Å
Total atoms total_atoms	3283
Residues n_residues	416
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	90.9 Å
Rg (real space) rg_real	27.27 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	3.5800e+07
I(0) uncertainty (real space) i0_real_error	6.3290e+05
Rg (reciprocal space) rg_reciprocal	27.23 Å
I(0) (reciprocal space) i0_reciprocal	35790000.0000
Solution quality estimate total_estimate	0.8771
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.2 Å
Skewness Skewness skewness	0.459
Kurtosis Kurtosis kurtosis	-0.279
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4541000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.926; Smooth: 0.852

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Spike glycoprotein
Molecular weight formula_weight	22964.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R,S
Atom count atom_count	3388

VECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRFLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKL

来源 Source

来源生物 organism	Human coronavirus EMC (isolate United Kingdom/H123990006/2012)
通用名 common_name	HCoV-EMC
NCBI Class编号 ncbi_taxonomy_id	1263720
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	105

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4zpwR01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1840 — Spike protein, C-terminal core receptor binding subdomain

Domain ID domain_id	4zpwR02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	210 — ubp-family deubiquitinating enzyme fold
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4zpwS01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1840 — Spike protein, C-terminal core receptor binding subdomain

Domain ID domain_id	4zpwS02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	210 — ubp-family deubiquitinating enzyme fold
Homologous superfamily homologous superfamily	30 —

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8. Citations (1)

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Unit-cell length a length_a	46.667 Å
Unit-cell length b length_b	109.887 Å
Unit-cell length c length_c	125.279 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.023 Å
Low-resolution limit resolution_low	43.731 Å
R factor r_factor	0.2195
R_work r_work	0.2173
R_free r_free	0.2589

fit	/app/data/saxs_computation/zp/4zpw/4zpw.fit
pddf	/app/data/pr_computation/zp/4zpw/4zpw.pr.out
profile	/app/data/saxs_computation/zp/4zpw/4zpw.dat

Structure of unbound MERS-CoV spike receptor-binding domain (England1 strain).

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

Spike glycoprotein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction