SAXSdb — 8y19

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

Spike glycoprotein

Human coronavirus HKU1 (isolate N2)

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 Homooligomer Protein × 3 其他Polymer 15 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–1290 Chain B； UniProt 1–1290 Chain C； UniProt 1–1290	Not recorded	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 12 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.30 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.

Other PDB	Difference from Current Entry 8Y19	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8Y1A 1up-1 conformation of HKU1-B S protein after incubation of the receptor Deposited 2024-01-24	Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–1290（1290 aa） Chain B 1–1290（1290 aa） Chain C 1–1290（1290 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8Y1B 1up-2 conformation of HKU1-B S protein after incubation of the receptor Deposited 2024-01-24	Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–1290（1290 aa） Chain B 1–1290（1290 aa） Chain C 1–1290（1290 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8Y1C 2up-1 conformation of HKU1-B S protein after incubation of the receptor Deposited 2024-01-24	Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–1290（1290 aa） Chain B 1–1290（1290 aa） Chain C 1–1290（1290 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8Y1D 2up-TM conformation of HKU1-B S protein after incubation of the receptor Deposited 2024-01-24	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–1290（1290 aa） Chain B 1–1290（1290 aa） Chain C 1–1290（1290 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8Y1E 3up-TM conformation of HKU1-B S protein after incubation of the receptor Deposited 2024-01-24	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–1290（1290 aa） Chain B 1–1290（1290 aa） Chain C 1–1290（1290 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8Y1F The closed conformation of the HKU1-B S protein in the apo state Deposited 2024-01-24	Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–1290（1290 aa） Chain B 1–1290（1290 aa） Chain C 1–1290（1290 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8Y1G The 1up conformation of the HKU1-B S protein in the apo state Deposited 2024-01-24	Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–1290（1290 aa） Chain B 1–1290（1290 aa） Chain C 1–1290（1290 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.99 Å
8Y1H The 2up formation of the HKU1-B S protein in the apo state Deposited 2024-01-24	Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–1290（1290 aa） Chain B 1–1290（1290 aa） Chain C 1–1290（1290 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å

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

View Construct and Data Evidence

UniProt name	SPIKE_CVHN2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1290； UniProt 1–1290 Author chain B； PDBConstruct 1–1290； UniProt 1–1290 Author chain C； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8y19
Deposition date deposition_date	2024-01-24
Structure title title	Closed conformation of HKU1-B S protein after incubation of the receptor
Keywords keywords	HCoV-HKU1, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	52.61 Å
Radius of gyration Rg (electron density) rg_electron	52.17 Å
Forward intensity I(0) i0	2511140000.00
Molecular weight molecular_weight	420190.0 kDa
Excluded volume excluded_volume	525360 Å³
Envelope volume envelope_volume	769280 Å³
Hydration-shell volume shell_volume	119260 Å³
Envelope diameter envelope_diameter	167.5 Å
Shell Rg shell_rg	58.26 Å
Envelope Rg envelope_rg	51.29 Å
Shape Rg shape_rg	52.13 Å
Total Rg total_rg	52.47 Å
Total atoms total_atoms	29541
Residues n_residues	3624
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	167.9 Å
Rg (real space) rg_real	52.43 Å
Rg uncertainty (real space) rg_real_error	1.22 Å
I(0) (real space) i0_real	2.5110e+09
I(0) uncertainty (real space) i0_real_error	4.6680e+07
Rg (reciprocal space) rg_reciprocal	52.74 Å
I(0) (reciprocal space) i0_reciprocal	2512000000.0000
Solution quality estimate total_estimate	0.8239
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	61.6 Å
Skewness Skewness skewness	0.190
Kurtosis Kurtosis kurtosis	-0.546
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	358100000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.000

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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	143475.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	29541

MFLIIFILPTTLAVIGDFNCTNSFINDYNKTIPRISEDVVDVSLGLGTYYVLNRVYLNTTLLFTGYFPKSGANFRDLALKGSKYLSTLWYKPPFLSDFNNGIFSKVKNTKLYVNNTLYSEFSTIVIGSVFVNTSYTIVVQPHNGILEITACQYTMCEYPHTVCKSKGSIRNESWHIDSSEPLCLFKKNFTYNVSADWLYFHFYQERGVFYAYYADVGMPTTFLFSLYLGTILSHYYVMPLTCKAISSNTDNETLEYWVTPLSRRQYLLNFDEHGVITNAVDCSSSFLSEIQCKTQSFAPNTGVYDLSGFTVKPVATVYRRIPNLPDCDIDNWLNNVSVPSPLNWERRIFSNCNFNLSTLLRLVHVDSFSCNNLDKSKIFGSCFNSITVDKFAIPNRRRDDLQLGSSGFLQSSNYKIDISSSSCQLYYSLPLVNVTINNFNPSSWNRRYGFGSFNVSSYDVVYSDHCFSVNSDFCPCADPSVVNSCVKSKPLSAICPAGTKYRHCDLDTTLYVNNWCRCSCLPDPISTYSPNTCPQKKVVVGIGEHCPGLGINEEKCGTQLNHSSCSCSPDAFLGWSFDSCISNNRCNIFSNFIFNGINSGTTCSNDLLYSNTEVSTGVCVNYDLYGITGQGIFKEVSAAYYNNWQNLLYDSNGNIIGFKDFLTNKTYTILPCYSGRVSAAFYQNSSSPALLYRNLKCSYVLNNISFISQPFYFDSYLGCVLNAVNLTSYSVSSCDLRMGSGFCIDYALPSSGSASRGISSPYRFVTFEPFNVSFVNDSVETVGGLFEIQIPTNFTIAGHEEFIQTSSPKVTIDCSAFVCSNYAACHDLLSEYGTFCDNINSILNEVNDLLDITQLQVANALMQGVTLSSNLNTNLHSDVDNIDFKSLLGCLGSQCGSSSRSLLEDLLFNKVKLSDVGFVEAYNNCTGGSEIRDLLCVQSFNGIKVLPPILSETQISGYTTAATVAAMFPPWSAAAGVPFSLNVQYRINGLGVTMDVLNKNQKLIANAFNKALLSIQNGFTATNSALAKIQSVVNANAQALNSLLQQLFNKFGAISSSLQEILSRLDPPEAQVQIDRLINGRLTALNAYVSQQLSDITLIKAGASRAIEKVNECVKSQSPRINFCGNGNHILSLVQNAPYGLLFIHFSYKPTSFKTVLVSPGLCLSGDRGIAPKQGYFIKQNDSWMFTGSSYYYPEPISDKNVVFMNSCSVNFTKAPFIYLNNSIPNLSDFEAEFSLWFKNHTSIAPNLTFNSHINATFLDLYYEMNVIQESIKSLNSSFINLKEIGTYEM

来源 Source

来源生物 organism	Human coronavirus HKU1 (isolate N2)
NCBI Class编号 ncbi_taxonomy_id	443240
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 branched

Description description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1073.0 kDa
Source method src_method	man
Copy count entity_count	3

Entity 3 Entity 3 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	12

Entity 4 Entity 4 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	51

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	2.30 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	622548

fit	/app/data/saxs_computation/y1/8y19/8y19.fit
pddf	/app/data/pr_computation/y1/8y19/8y19.pr.out
profile	/app/data/saxs_computation/y1/8y19/8y19.dat

Closed conformation of HKU1-B S protein after incubation of the receptor

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

冷冻电镜 EM 3D