SAXSdb — 8v5v

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

Spike protein S2,Fibritin

Tequatrovirus T4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 9 其他Polymer 3	Variable domain of the light chain from the human antibody 6C10 × 3 Variable domain of the heavy chain from the human antibody 6C10 × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 15	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 E； PDBConstruct 1–521； UniProt 691–1211 Author chain F； PDBConstruct 1–521； UniProt 691–1211 Author chain G； PDBConstruct 1–521； UniProt 691–1211

Spike protein S2,Fibritin

Tequatrovirus T4

UniProt P10104

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 9 其他Polymer 3	Variable domain of the light chain from the human antibody 6C10 × 3 Variable domain of the heavy chain from the human antibody 6C10 × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 15	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	WAC_BPT4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 524–550； UniProt 458–484 Author chain F； PDBConstruct 524–550； UniProt 458–484 Author chain G； PDBConstruct 524–550； UniProt 458–484

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	8v5v
Deposition date deposition_date	2023-12-01
Structure title title	Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation
Keywords keywords	SARS-CoV-2, Spike, S2, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

8v5v__assembly_1__model_1

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

Download this curve (.dat)

8v5v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8v5v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.88 Å
Rg (electron density)	43.20 Å
Total Rg	43.55 Å
Atom count	15882
Residues	2025
Excluded volume	282160 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8v5v__assembly_1__model_1`	nonameric （9）	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	Spike protein S2,Fibritin
Molecular weight formula_weight	64292.5 kDa
Mutation mutation	F817P,A892P,A899P,A942P,V987P,Y707C,T883C,Y788C,A876C
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,E,F
Atom count atom_count	15882

SIIAYTMSLGAENSVACSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQCYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSCLLAGTICSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKGSGYIPEAPRDGQAYVRKDGEWVLLSTFLLEVLFQGPAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Source Source

Source organism organism	Tequatrovirus T4
NCBI taxonomy ID ncbi_taxonomy_id	10665
Host organism host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	Variable domain of the light chain from the human antibody 6C10
Molecular weight formula_weight	11697.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	d,g,e

AIRMTQSPSTLSVSPGERATLSCRASQSVSSYLAWYQHKPGQAPRLLVYGASTRATGIPARFSGSGSGTEFTLTISSLQSEDFAVYYCQQYNNWPPPFTFGPGTKVDI

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	Variable domain of the heavy chain from the human antibody 6C10
Molecular weight formula_weight	13913.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	f,c,b

QVQLVQSGAEVRKPGASVKVSCKASGYTFTGYYIHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGWVIMTRDTSISTAYMELSRLTSDDTAVYYCARCGARSYYYDSGDYCAFDIWGQGTVVTV

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

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	3

Entity 5 Entity 5 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	15

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	2.93 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	408064

Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation

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

Spike protein S2,Fibritin

State in the Current Structure

Other States of the Same Protein in the Database

Spike protein S2,Fibritin

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

8v5v__assembly_1__model_1

8v5v__assembly_1__model_1 | I(q)

8v5v__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

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 branched

Entity 5 Entity 5 non-polymer

7. Citations (1)

Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation

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

Spike protein S2,Fibritin

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,Fibritin

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

8v5v__assembly_1__model_1

8v5v__assembly_1__model_1 | I(q)

8v5v__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

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 branched

Entity 5 Entity 5 non-polymer

7. Citations (1)