SAXSdb — 8qh1

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

Spike glycoprotein

Severe acute respiratory syndrome coronavirus 2

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 E； UniProt 328–527	Not recorded	Cv2.3194 heavy chain × 1 IGK@ protein × 1 （Q6PJF2） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350, 0.2 M sodium malonate	Resolution 2.65 Å R-free 0.232

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 8QH1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9SSM Crystal structure of 084-7D Fab bound to SARS-CoV-2 Beta RBD Deposited 2025-09-26	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain R 318–538（221 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；8.25% PEG 3350 4.95% MPD 0.2 M Lithium sulfate 0.1 M imidazole/hydrochloric acid pH 6.5 20% Ethylene glycol added after crystallization	Resolution 2.70 Å R-free 0.269

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A8A5XRG7_SARS2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 1–200； UniProt 328–527

IGK@ protein

Homo sapiens

UniProt Q6PJF2

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 L； UniProt 21–235	Not recorded	Spike glycoprotein × 1 （A0A8A5XRG7） Cv2.3194 heavy chain × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350, 0.2 M sodium malonate	Resolution 2.65 Å R-free 0.232

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 8QH1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2AGJ Crystal Structure of a glycosylated Fab from an IgM cryoglobulin with properties of a natural proteolytic antibody Deposited 2005-07-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 21–235（215 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 15000-20000, sodium chloride, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.60 Å R-free 0.279
4YPG Structural Insights Into the Neutralization Properties of a Human Anti-Interferon Monoclonal Antibody Deposited 2015-03-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 21–235（215 aa）	Not recorded	NI NICKEL (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.01 M NiCl2, 0.1 M Tris HCl	Resolution 3.00 Å R-free 0.272
4YPG Structural Insights Into the Neutralization Properties of a Human Anti-Interferon Monoclonal Antibody Deposited 2015-03-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 21–235（215 aa）	Not recorded	NI NICKEL (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.01 M NiCl2, 0.1 M Tris HCl	Resolution 3.00 Å R-free 0.272
6MYY Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs bound, sharpened map Deposited 2018-11-02	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 Heteromer；Protein × 9 PDB declaration: nonameric	Chain C 127–235（109 aa） Fragment：germline VK3-11 with the mature CDR L3 of VRC01 Chain F 127–235（109 aa） Fragment：germline VK3-11 with the mature CDR L3 of VRC01 Chain L 127–235（109 aa） Fragment：germline VK3-11 with the mature CDR L3 of VRC01	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6MZJ Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 2 Fabs bound, sharpened map Deposited 2018-11-05	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 Heteromer；Protein × 7 PDB declaration: heptameric	Chain C 127–235（109 aa） Fragment：germline VK3-11 with the mature CDRL3 of VRC01 Chain L 127–235（109 aa） Fragment：germline VK3-11 with the mature CDRL3 of VRC01	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
6UDK HIV-1 bNAb 1-55 in complex with modified BG505 SOSIP-based immunogen RC1 and 10-1074 Deposited 2019-09-19	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 Heteromer；Protein × 18 PDB declaration: octadecameric	Chain E 122–235（114 aa） Chain L 122–235（114 aa） Chain N 122–235（114 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；0 blot force, 3.5 second blot time, 3 uL sample added to freshly glow-discharged grids	Resolution 3.90 Å
8QH0 Crystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194 Deposited 2023-09-06	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 L 21–234（214 aa）	Not recorded	PRO PROLINE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；20% PEG 3350, 0.2 M lithium citrate	Resolution 1.87 Å R-free 0.209

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q6PJF2_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain L； PDBConstruct 1–211； UniProt 21–235

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	8qh1
Deposition date deposition_date	2023-09-06
Structure title title	Crystal structure of the SARS-CoV-2 RBD from the Omicron BA4 variant with the antibody Cv2.3194
Keywords keywords	Coronavirus Neutralizing Antibody, 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	31.87 Å
Radius of gyration Rg (electron density) rg_electron	31.87 Å
Forward intensity I(0) i0	73096100.00
Molecular weight molecular_weight	67290.0 kDa
Excluded volume excluded_volume	83988 Å³
Envelope volume envelope_volume	109510 Å³
Hydration-shell volume shell_volume	30788 Å³
Envelope diameter envelope_diameter	118.0 Å
Shell Rg shell_rg	36.18 Å
Envelope Rg envelope_rg	31.83 Å
Shape Rg shape_rg	31.82 Å
Total Rg total_rg	32.38 Å
Total atoms total_atoms	4742
Residues n_residues	619
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	110.8 Å
Rg (real space) rg_real	32.22 Å
Rg uncertainty (real space) rg_real_error	1.20 Å
I(0) (real space) i0_real	7.3100e+07
I(0) uncertainty (real space) i0_real_error	1.3080e+06
Rg (reciprocal space) rg_reciprocal	32.07 Å
I(0) (reciprocal space) i0_reciprocal	73090000.0000
Solution quality estimate total_estimate	0.8390
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.0 Å
Skewness Skewness skewness	0.567
Kurtosis Kurtosis kurtosis	-0.197
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8985000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.766; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.820; Smooth: 0.784

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Spike glycoprotein
Molecular weight formula_weight	27508.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E
Atom count atom_count	4753

NITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKGSGLVPRGSHHHHHHHHSAWSHPQFEKGTGGLNDIFEAQKIEWHE

来源 Source

来源生物 organism	Severe acute respiratory syndrome coronavirus 2
NCBI Class编号 ncbi_taxonomy_id	2697049
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Cv2.3194 heavy chain
Molecular weight formula_weight	24379.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQLVESGGGLIQPGGSLRLSCAASGITVTSNYMSWVRQAPGKGLEWVSVIYPGGSTFYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDLVVYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH

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	IGK@ protein
Molecular weight formula_weight	22810.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPGRFSGSGSGTDFTLTISRLEPEDFAIYYCQQGVTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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 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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

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8. Citations (1)

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Unit-cell length a length_a	57.793 Å
Unit-cell length b length_b	85.348 Å
Unit-cell length c length_c	193.987 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.48 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	39.010 Å
R factor r_factor	0.1994
R_work r_work	0.1976
R_free r_free	0.2323

fit	/app/data/saxs_computation/qh/8qh1/8qh1.fit
pddf	/app/data/pr_computation/qh/8qh1/8qh1.pr.out
profile	/app/data/saxs_computation/qh/8qh1/8qh1.dat

Crystal structure of the SARS-CoV-2 RBD from the Omicron BA4 variant with the antibody Cv2.3194

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

IGK@ protein

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 (5)

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 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)