SAXSdb — 9rn6

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

;Spike protein S2',Chimeric protein mimic of SARS-CoV-2 Spike HR1 ;

Severe acute respiratory syndrome coronavirus 2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Nanobody NB278 × 1 Nanobody NB184 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPIKE_SARS2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–76； UniProt 915–988 Author chain A； PDBConstruct 157–230； UniProt 915–988

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	9rn6
Deposition date deposition_date	2025-06-19
Last revision last_revision	2026-01-21
Structure title title	Crystal structure of a protein mimic of SARS-CoV-2 spike's HR1 domain in complex with two nanobodies bound to different epitopes
Keywords keywords	Neutralizing nanobodies; SARS-Cov-2; Spike S2 subunit, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9rn6__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9rn6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9rn6__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	37.68 Å
Rg (electron density)	38.35 Å
Total Rg	38.24 Å
Atom count	6959
Residues	454
Excluded volume	61700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9rn6__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	;Spike protein S2',Chimeric protein mimic of SARS-CoV-2 Spike HR1 ;
Molecular weight formula_weight	26577.7 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	6959

MDVLYENQKLIANKFNSAIGKIQDSLSSTASELGKLQDEVNQNAQDLNTLVKQLSSNFGRISSELNDILSRLDKGEPAKDLRSDIDNLESKIAGFNSSLQKVLTNLAQKNQNVEDKLKGLESRTSSLEKQIKGIASNFQNEILKQREYLVNKGSGNVLYENQKLIENQFNSAIGKIQDSLSSTKSALGKLKDVVNQNKQALNTLVKQLSSNFGAISSVLNDIKSRLDKVEGGGGSHHHHHH

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nanobody NB278
Molecular weight formula_weight	13597.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QVQLQESGGGLVQAGGSLRLSCAASGIAFSNNAMGWYRQAPGKQRELVANIITFGNTYYTDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCHTYGDSPERGYWGQGTQVTVSSHHHHHH

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Nanobody NB184
Molecular weight formula_weight	15294.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

QVQLQESGGGLVHPGQSLTLSCAPSGRTFSNYDIGWFRQAPGKEREFVADIRLNSGSTYYADSVKGRFTISRDNVKNTVYLQMNSLKPEDTAVYYCAARSPGGILYDYWGQGTQVTVSSAAAYPYDVPDYGSHHHHHH

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

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Unit-cell length a length_a	47.560 Å
Unit-cell length b length_b	67.340 Å
Unit-cell length c length_c	230.780 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	4

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	orthorhombic

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.2474
R_work r_work	0.2466
R_free r_free	0.2631

Crystal structure of a protein mimic of SARS-CoV-2 spike's HR1 domain in complex with two nanobodies bound to different epitopes

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

;Spike protein S2',Chimeric protein mimic of SARS-CoV-2 Spike HR1 ;

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9rn6__assembly_1__model_1

9rn6__assembly_1__model_1 | I(q)

9rn6__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

7. Citations (1)

Crystal structure of a protein mimic of SARS-CoV-2 spike's HR1 domain in complex with two nanobodies bound to different epitopes

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

;Spike protein S2',Chimeric protein mimic of SARS-CoV-2 Spike HR1 ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9rn6__assembly_1__model_1

9rn6__assembly_1__model_1 | I(q)

9rn6__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

7. Citations (1)