SAXSdb — 7yi6

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

Spike glycoprotein

Human coronavirus 229E

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 835–841	Not recorded	light chain of 3D1 × 1 heavy chain of 3D1 × 1 EDO 1,2-ETHANEDIOL × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Ammonium sulfate, 0.1 M BIS-TRIS buffer at pH 5.5 and 25% (w/v) polyethylene glycol 3350	Resolution 2.28 Å R-free 0.220
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 835–841	Not recorded	light chain of 3D1 × 1 heavy chain of 3D1 × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Ammonium sulfate, 0.1 M BIS-TRIS buffer at pH 5.5 and 25% (w/v) polyethylene glycol 3350	Resolution 2.28 Å R-free 0.220

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 7YI6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5YL9 1.86 Angstrom crystal structure of human Coronavirus 229E fusion core Deposited 2017-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 785–872（88 aa） Fragment：UNP residues 785-872 Chain B 1052–1104（53 aa） Fragment：UNP residues 1052-1104	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；citric acid, BIS-TRIS propane, PEG3350	Resolution 1.86 Å R-free 0.206
5ZHY Structural characterization of the HCoV-229E fusion core Deposited 2018-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 789–856（68 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105 Chain A 1053–1105（53 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105 Chain B 789–856（68 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105 Chain B 1053–1105（53 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105 Chain C 789–856（68 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105 Chain C 1053–1105（53 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.5 M Ammonium sulfate, 12% (v/v) Glycerol, 100 mM Tris/HCl, PH 8.5	Resolution 2.44 Å R-free 0.263
5ZHY Structural characterization of the HCoV-229E fusion core Deposited 2018-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 789–856（68 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105 Chain D 1053–1105（53 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105 Chain E 789–856（68 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105 Chain E 1053–1105（53 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105 Chain F 789–856（68 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105 Chain F 1053–1105（53 aa） Fragment：UNP residues 789-856. UNP residues 1053-1105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.5 M Ammonium sulfate, 12% (v/v) Glycerol, 100 mM Tris/HCl, PH 8.5	Resolution 2.44 Å R-free 0.263
5ZUV Crystal Structure of the Human Coronavirus 229E HR1 motif in complex with pan-CoVs inhibitor EK1 Deposited 2018-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 785–873（89 aa） Fragment：UNP residues 785-873 Chain B 785–873（89 aa） Fragment：UNP residues 785-873 Chain C 785–873（89 aa） Fragment：UNP residues 785-873	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.5；293 K；0.05M MgCl2, 0.1M HEPES, pH 7.5, 30% PEG550MME	Resolution 2.21 Å R-free 0.248
6ATK Crystal structure of the human coronavirus 229E spike protein receptor binding domain in complex with human aminopeptidase N Deposited 2017-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 293–435（143 aa） Fragment：UNP residues 294-432	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；8% PEG 8000, 1mM GSSG, 1mM GSH, 5% Glycerol, 100mM MES, 1ug/mL endo-beta-N-acetylglucosaminidase A	Resolution 3.50 Å R-free 0.267
6ATK Crystal structure of the human coronavirus 229E spike protein receptor binding domain in complex with human aminopeptidase N Deposited 2017-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 293–435（143 aa） Fragment：UNP residues 294-432	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；8% PEG 8000, 1mM GSSG, 1mM GSH, 5% Glycerol, 100mM MES, 1ug/mL endo-beta-N-acetylglucosaminidase A	Resolution 3.50 Å R-free 0.267
6ATK Crystal structure of the human coronavirus 229E spike protein receptor binding domain in complex with human aminopeptidase N Deposited 2017-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 293–435（143 aa） Fragment：UNP residues 294-432	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；8% PEG 8000, 1mM GSSG, 1mM GSH, 5% Glycerol, 100mM MES, 1ug/mL endo-beta-N-acetylglucosaminidase A	Resolution 3.50 Å R-free 0.267
7CYC Cryo-EM structures of Alphacoronavirus spike glycoprotein Deposited 2020-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–1116（1116 aa） Chain B 1–1116（1116 aa） Chain C 1–1116（1116 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
7CYD Cryo-EM structures of Alphacoronavirus spike glycoprotein Deposited 2020-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–1116（1116 aa） Chain B 1–1116（1116 aa） Chain C 1–1116（1116 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.55 Å
7VN9 Crystal structure of human coronavirus 229E spike protein receptor-binding domain in complex with C04 Fab Deposited 2021-10-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 294–435（142 aa） Fragment：receptor-binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；1.6M AmSO4, 0.1M Critic Acid pH 5.0	Resolution 4.49 Å R-free 0.288
7VN9 Crystal structure of human coronavirus 229E spike protein receptor-binding domain in complex with C04 Fab Deposited 2021-10-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 294–435（142 aa） Fragment：receptor-binding domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；1.6M AmSO4, 0.1M Critic Acid pH 5.0	Resolution 4.49 Å R-free 0.288
7VNG Crystal structure of human coronavirus 229E spike protein receptor-binding domain in complex with S11 Fab Deposited 2021-10-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 294–435（142 aa） Fragment：receptor binding domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；3.6M Sodium Formate, 10% Glycerol	Resolution 3.80 Å R-free 0.318

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

View Construct and Data Evidence

UniProt name	SPIKE_CVH22
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–7； UniProt 835–841 Author chain C； PDBConstruct 1–7； UniProt 835–841

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	7yi6
Deposition date deposition_date	2022-07-15
Structure title title	bnAb 3D1 in complex with 6-mer HR1 peptide from HCoV-229E S protein
Keywords keywords	bnAb, HR1, 6-mer, ANTIVIRAL PROTEIN, ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex; ANTIVIRAL PROTEIN/IMMUNE SYSTEM
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	32.56 Å
Radius of gyration Rg (electron density) rg_electron	32.06 Å
Forward intensity I(0) i0	134826000.00
Molecular weight molecular_weight	91690.0 kDa
Excluded volume excluded_volume	114390 Å³
Envelope volume envelope_volume	148140 Å³
Hydration-shell volume shell_volume	39993 Å³
Envelope diameter envelope_diameter	115.5 Å
Shell Rg shell_rg	37.67 Å
Envelope Rg envelope_rg	31.47 Å
Shape Rg shape_rg	32.04 Å
Total Rg total_rg	32.57 Å
Total atoms total_atoms	6459
Residues n_residues	867
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	109.9 Å
Rg (real space) rg_real	32.61 Å
Rg uncertainty (real space) rg_real_error	0.95 Å
I(0) (real space) i0_real	1.3480e+08
I(0) uncertainty (real space) i0_real_error	2.0490e+06
Rg (reciprocal space) rg_reciprocal	32.59 Å
I(0) (reciprocal space) i0_reciprocal	134800000.0000
Solution quality estimate total_estimate	0.8608
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	40.4 Å
Skewness Skewness skewness	0.430
Kurtosis Kurtosis kurtosis	-0.085
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16300000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.757

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Spike glycoprotein
Molecular weight formula_weight	758.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	6923

DVVNQQG

来源 Source

来源生物 organism	Human coronavirus 229E
通用名 common_name	HCoV-229E
NCBI Class编号 ncbi_taxonomy_id	11137
宿主生物 host_organism	chemical production metagenome

Entity 2 Entity 2 polymer

Description description	light chain of 3D1
Molecular weight formula_weight	22473.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

ALTQPPSASGSPGQSVTISCTGTSSDVGGYNYVSWYQQHPGKAPKLIIYEVSKRPSGVPDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYTSSSTLVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	heavy chain of 3D1
Molecular weight formula_weight	23370.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F

QVQLVQSGSELKKPGASVRISCKASGYSFTSLSMNWVRQAPGQGLEWMGWISTKSGDPTYAQAFTGRFVFSLDTSVNTAYLQINSLEAGDTAVYYCARGQPPVGWTFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPP

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	458

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7yi6B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7yi6B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7yi6E01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7yi6E02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	73.906 Å
Unit-cell length b length_b	72.703 Å
Unit-cell length c length_c	86.264 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.280 Å
Low-resolution limit resolution_low	45.860 Å
R factor r_factor	0.1941
R_work r_work	0.1927
R_free r_free	0.2204

fit	/app/data/saxs_computation/yi/7yi6/7yi6.fit
pddf	/app/data/pr_computation/yi/7yi6/7yi6.pr.out
profile	/app/data/saxs_computation/yi/7yi6/7yi6.dat

bnAb 3D1 in complex with 6-mer HR1 peptide from HCoV-229E S protein

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

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)