SAXSdb — 7vn9

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

Spike glycoprotein S1

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	Other combination Heteromer Protein × 3 其他Polymer 2 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 294–435	Fragment：receptor-binding domain	C04 Fab heavy chain × 1 C04 Fab light chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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
2	Other combination Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 294–435	Fragment：receptor-binding domain	C04 Fab heavy chain × 1 C04 Fab light chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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

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 7VN9	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 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 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 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
7VNG Crystal structure of human coronavirus 229E spike protein receptor-binding domain in complex with S11 Fab Deposited 2021-10-11	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 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
7YI6 bnAb 3D1 in complex with 6-mer HR1 peptide from HCoV-229E S protein Deposited 2022-07-15	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 835–841（7 aa）	Not recorded	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
7YI6 bnAb 3D1 in complex with 6-mer HR1 peptide from HCoV-229E S protein Deposited 2022-07-15	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 C 835–841（7 aa）	Not recorded	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

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	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–142； UniProt 294–435 Author chain E； PDBConstruct 1–142； UniProt 294–435

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	7vn9
Deposition date deposition_date	2021-10-10
Structure title title	Crystal structure of human coronavirus 229E spike protein receptor-binding domain in complex with C04 Fab
Keywords keywords	Neutralizing antibody, human coronavirus 229E, C04 Fab., IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL 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	39.98 Å
Radius of gyration Rg (electron density) rg_electron	39.69 Å
Forward intensity I(0) i0	221678000.00
Molecular weight molecular_weight	121140.0 kDa
Excluded volume excluded_volume	151530 Å³
Envelope volume envelope_volume	222270 Å³
Hydration-shell volume shell_volume	46857 Å³
Envelope diameter envelope_diameter	129.9 Å
Shell Rg shell_rg	44.92 Å
Envelope Rg envelope_rg	39.13 Å
Shape Rg shape_rg	39.65 Å
Total Rg total_rg	40.11 Å
Total atoms total_atoms	8541
Residues n_residues	1113
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	124.9 Å
Rg (real space) rg_real	39.93 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	2.2170e+08
I(0) uncertainty (real space) i0_real_error	3.8670e+06
Rg (reciprocal space) rg_reciprocal	39.97 Å
I(0) (reciprocal space) i0_reciprocal	221700000.0000
Solution quality estimate total_estimate	0.8980
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	40.6 Å
Skewness Skewness skewness	0.161
Kurtosis Kurtosis kurtosis	-0.754
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21900000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.782

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	C04 Fab heavy chain
Molecular weight formula_weight	24304.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,A
Atom count atom_count	8541

EVQLVESGGGLVQPGGSLRLSCAASGFNISSSYIHWVRQAPGKGLEWVASIYSSYGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWWASVGGAGGGLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	C04 Fab light chain
Molecular weight formula_weight	23343.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQGYGWLITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 Entity 3 polymer

Description description	Spike glycoprotein S1
Molecular weight formula_weight	16194.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

PVYHKHTFIVLYVDFKPQSGGGKCFNCYPAGVNITLANFNETKGPLCVDTSHFTTKYVAVYANVGRWSASINTGNCPFSFGKVNNFVKFGSVCFSLKDIPGGCAMPIVANWAYSKYYTIGSLYVSWSDGDGITGVPQPVEGVENLYFQ

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	Trichoplusia ni

Entity 4 Entity 4 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	183.732 Å
Unit-cell length b length_b	183.732 Å
Unit-cell length c length_c	255.988 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 62 2 2
Space-group number int_tables_number	180
Crystal system crystal_system	—

Resolution resolution	4.490 Å
Low-resolution limit resolution_low	42.660 Å
R factor r_factor	0.2742
R_work r_work	0.2734
R_free r_free	0.2885

fit	/app/data/saxs_computation/vn/7vn9/7vn9.fit
pddf	/app/data/pr_computation/vn/7vn9/7vn9.pr.out
profile	/app/data/saxs_computation/vn/7vn9/7vn9.dat

Crystal structure of human coronavirus 229E spike protein receptor-binding domain in complex with C04 Fab

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

Spike glycoprotein S1

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 (6)

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 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)