SAXSdb — 7y8j

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

;Spike protein S2' ;

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	heavy chain of 3D1 × 1 light chain of 3D1 × 1 water × 3	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	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–7； UniProt 950–956

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	7y8j
Deposition date deposition_date	2022-06-24
Structure title title	3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2
Keywords keywords	human antibody, broad, coronavirus, ANTIMICROBIAL PROTEIN, ANTIMICROBIAL PROTEIN-IMMUNE SYSTEM complex; ANTIMICROBIAL PROTEIN/IMMUNE SYSTEM
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.

7y8j__assembly_1__model_1

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

Download this curve (.dat)

7y8j__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7y8j__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.50 Å
Rg (electron density)	17.42 Å
Total Rg	18.45 Å
Atom count	3476
Residues	242
Excluded volume	31396 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7y8j__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 (4)

Entity 1 Entity 1 polymer

Description description	heavy chain of 3D1
Molecular weight formula_weight	13138.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	4342

QVQLVQSGSELKKPGASVRISCKASGYSFTSLSMNWVRQAPGQGLEWMGWISTKSGDPTYAQAFTGRFVFSLDTSVNTAYLQINSLEAGDTAVYYCARGQPPVGWTFDYWGQGTLVTVSSGG

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	;Spike protein S2' ;
Molecular weight formula_weight	744.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

DVVNQNG

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
Common name common_name	2019-nCoV, SARS-CoV-2
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	synthetic construct

Entity 3 Entity 3 polymer

Description description	light chain of 3D1
Molecular weight formula_weight	11618.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

GSQSALTQPPSASGSPGQSVTISCTGTSSDVGGYNYVSWYQQHPGSAPKLIIYEVSKRPSGVPDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYTSSSTLVFGGGTKLTVLGG

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	430

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7y8jL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	36.965 Å
Unit-cell length b length_b	69.810 Å
Unit-cell length c length_c	51.058 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.46 °
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	1.030 Å
Low-resolution limit resolution_low	24.590 Å
R factor r_factor	0.1338
R_work r_work	0.1335
R_free r_free	0.1446

3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2

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

;Spike protein S2' ;

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

7y8j__assembly_1__model_1

7y8j__assembly_1__model_1 | I(q)

7y8j__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 (4)

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

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2

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

;Spike protein S2' ;

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

7y8j__assembly_1__model_1

7y8j__assembly_1__model_1 | I(q)

7y8j__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 (4)

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

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)