SAXSdb — 8dao

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

COV44-79 heavy chain constant domain

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	COV44-79 heavy chain variable domain × 1 COV44-79 light chain variable domain × 1 COV44-79 light chain constant domain × 1 （P01834） Spike protein S2 fusion peptide × 1 （P0DTC2）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	COV44-79 heavy chain variable domain × 1 COV44-79 light chain variable domain × 1 COV44-79 light chain constant domain × 1 （P01834） Spike protein S2 fusion peptide × 1 （P0DTC2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IGG1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–103； UniProt 120–222 Author chain G； PDBConstruct 1–103； UniProt 120–222

COV44-79 light chain constant domain

Homo sapiens

UniProt P01834

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	COV44-79 heavy chain variable domain × 1 COV44-79 light chain variable domain × 1 COV44-79 heavy chain constant domain × 1 （P0DOX5） Spike protein S2 fusion peptide × 1 （P0DTC2）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	COV44-79 heavy chain variable domain × 1 COV44-79 light chain variable domain × 1 COV44-79 heavy chain constant domain × 1 （P0DOX5） Spike protein S2 fusion peptide × 1 （P0DTC2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IGKC_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 1–107； UniProt 1–107 Author chain H； PDBConstruct 1–107； UniProt 1–107

Spike protein S2 fusion peptide

OrganismNot specified

UniProt P0DTC2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	COV44-79 heavy chain variable domain × 1 COV44-79 light chain variable domain × 1 COV44-79 heavy chain constant domain × 1 （P0DOX5） COV44-79 light chain constant domain × 1 （P01834）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	COV44-79 heavy chain variable domain × 1 COV44-79 light chain variable domain × 1 COV44-79 heavy chain constant domain × 1 （P0DOX5） COV44-79 light chain constant domain × 1 （P01834）	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	5
Chains and sequence ranges	Author chain I； PDBConstruct 1–15； UniProt 809–823 Author chain J； PDBConstruct 1–15； UniProt 809–823

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	8dao
Deposition date deposition_date	2022-06-13
Structure title title	Crystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV44-79
Keywords keywords	SARS-CoV-2, coronavirus, antibody, fusion peptide, neutralizing antibody, COVID-19, IMMUNE SYSTEM; 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.

8dao__assembly_1__model_1

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

Download this curve (.dat)

8dao__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8dao__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.83 Å
Rg (electron density)	24.99 Å
Total Rg	25.82 Å
Atom count	3457
Residues	456
Excluded volume	61304 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8dao__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8dao__assembly_2__model_1`	pentameric （5）	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 (5)

Entity 1 Entity 1 polymer

Description description	COV44-79 heavy chain variable domain
Molecular weight formula_weight	13673.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,A
Atom count atom_count	6914

QVQLVESGGGVVQPGRSLRLSCAASGLTFSGYAMHWVRQAPGKGLEWVAVISRDARNKYYADSVKGRFTISRDNSKKTVYLEMNSLRVEDTAVYYCAILIIPGITEPGSPDALDIWGQGTMVSVSS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Mus musculus

Entity 2 Entity 2 polymer

Description description	COV44-79 light chain variable domain
Molecular weight formula_weight	11933.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,B

DIQMTQSPSSMSASVGDRVTITCRASQDISKWLAWYQQRPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQASSFPWSITFGQGTRLEIR

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Mus musculus

Entity 3 Entity 3 polymer

Description description	COV44-79 heavy chain constant domain
Molecular weight formula_weight	10585.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,G

ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Mus musculus

Entity 4 Entity 4 polymer

Description description	COV44-79 light chain constant domain
Molecular weight formula_weight	11778.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,H

RTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Mus musculus

Entity 5 Entity 5 polymer

Description description	Spike protein S2 fusion peptide
Molecular weight formula_weight	1767.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J

PSKPSKRSFIEDLLF

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	8daoA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8daoB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8daoC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8daoD01
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	100.368 Å
Unit-cell length b length_b	100.368 Å
Unit-cell length c length_c	229.939 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	16

Space group space_group	P 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	49.880 Å
R factor r_factor	0.2332
R_work r_work	0.2306
R_free r_free	0.2837

Crystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV44-79

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

COV44-79 heavy chain constant domain

State in the Current Structure

Other States of the Same Protein in the Database

COV44-79 light chain constant domain

State in the Current Structure

Other States of the Same Protein in the Database

Spike protein S2 fusion peptide

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

8dao__assembly_1__model_1

8dao__assembly_1__model_1 | I(q)

8dao__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 (5)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV44-79

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

COV44-79 heavy chain constant domain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

COV44-79 light chain constant domain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Spike protein S2 fusion peptide

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

8dao__assembly_1__model_1

8dao__assembly_1__model_1 | I(q)

8dao__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 (5)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)