SAXSdb — 7tty

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

Spike protein S1

Bat SARS-like coronavirus WIV1

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 1 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 322–515	Fragment：receptor-binding domain (UNP residues 322-515)	1040 heavy chain × 1 1040 light chain × 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, SITTING DROP；295 K；0.1 M sodium citrate, pH 5.5, 20% propanol, 20% PEG4000	Resolution 3.11 Å R-free 0.329

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 7TTY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8TC0 Cryo-EM Structure of Spike Glycoprotein from Bat Coronavirus WIV1 in Closed Conformation Deposited 2023-06-29	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 19–1127（1109 aa） Chain B 19–1127（1109 aa） Chain C 19–1127（1109 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 EIC LINOLEIC ACID × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 1.88 Å
8WLY Cryo-EM structure of bat WIV1 spike glycoprotein Deposited 2023-10-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–1191（1191 aa） Chain B 1–1191（1191 aa） Chain C 1–1191（1191 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.96 Å
8WLZ Cryo-EM structure of the WIV1 S-hACE2 complex Deposited 2023-10-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–1191（1191 aa） Chain B 1–1191（1191 aa） Chain C 1–1191（1191 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.45 Å
8WQ0 Cryo-EM structure of WIV1 spike glycoprotein (the closed state) Deposited 2023-10-10	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 1–1191（1191 aa） Chain B 1–1191（1191 aa） Chain C 1–1191（1191 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.78 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	U5WI05_SARS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–194； UniProt 322–515

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	7tty
Deposition date deposition_date	2022-02-02
Structure title title	Crystal structure of potent neutralizing antibody 10-40 in complex with bat WIV1 receptor-binding domain
Keywords keywords	;COVID-19, SarbecoVirus, WIV1 RBD, Viral protein, Spike glycoprotein, Receptor Binding Protein, Neutralizing antibody, potent, 10-40, Fab, 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	29.75 Å
Radius of gyration Rg (electron density) rg_electron	29.24 Å
Forward intensity I(0) i0	78415600.00
Molecular weight molecular_weight	69255.0 kDa
Excluded volume excluded_volume	86318 Å³
Envelope volume envelope_volume	110740 Å³
Hydration-shell volume shell_volume	32469 Å³
Envelope diameter envelope_diameter	106.9 Å
Shell Rg shell_rg	35.67 Å
Envelope Rg envelope_rg	29.02 Å
Shape Rg shape_rg	29.18 Å
Total Rg total_rg	30.01 Å
Total atoms total_atoms	9569
Residues n_residues	613
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	103.2 Å
Rg (real space) rg_real	29.82 Å
Rg uncertainty (real space) rg_real_error	1.07 Å
I(0) (real space) i0_real	7.8420e+07
I(0) uncertainty (real space) i0_real_error	1.2650e+06
Rg (reciprocal space) rg_reciprocal	29.79 Å
I(0) (reciprocal space) i0_reciprocal	78410000.0000
Solution quality estimate total_estimate	0.8709
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.1 Å
Skewness Skewness skewness	0.425
Kurtosis Kurtosis kurtosis	-0.210
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11670000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.953

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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 protein S1
Molecular weight formula_weight	21979.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9600

NLCPFGEVFNATTFPSVYAWERKRISNCVADYSVLYNSTSFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFTGCVLAWNTRNIDATQTGNYNYKYRSLRHGKLRPFERDISNVPFSPDGKPCTPPAFNCYWPLNDYGFYITNGIGYQPYRVVVLSFELLNAPATVCGPKK

来源 Source

来源生物 organism	Bat SARS-like coronavirus WIV1
NCBI Class编号 ncbi_taxonomy_id	1415852
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	1040 heavy chain
Molecular weight formula_weight	24794.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QLQLQESGPGLVKPSETLSLTCTVSGGSISSSNFYWGWIRQPPGKGLEWIASITYSGRTFYNPSLKSRVAISVDTSKNQFSLKLSSVTAADTAVYYCARTFPSYYDRSGYHYLNYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSXXXSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

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	Homo sapiens

Entity 3 Entity 3 polymer

Description description	1040 light chain
Molecular weight formula_weight	22938.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

NFMLTQPHSMSESPGKTVTISCTRSSGSIASNYVQWYQQRPGSSPTTVIYEDNQRPSGVPDRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDSSSWVFGGGTKLTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT

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	Homo sapiens

Entity 4 Entity 4 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

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7ttyH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7ttyH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7ttyL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7ttyL02
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	51.311 Å
Unit-cell length b length_b	69.546 Å
Unit-cell length c length_c	95.215 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.63 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	3.110 Å
Low-resolution limit resolution_low	91.690 Å
R factor r_factor	0.2440
R_work r_work	0.2346
R_free r_free	0.3293

fit	/app/data/saxs_computation/tt/7tty/7tty.fit
pddf	/app/data/pr_computation/tt/7tty/7tty.pr.out
profile	/app/data/saxs_computation/tt/7tty/7tty.dat

Crystal structure of potent neutralizing antibody 10-40 in complex with bat WIV1 receptor-binding domain

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

Spike protein 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 (4)

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

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)