SAXSdb — 9z3k

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

SPIKE PROTEIN

Severe acute respiratory syndrome coronavirus 2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 3	2-acetamido-2-deoxy-beta-D-glucopyranose × 18	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 180–397； UniProt 914–1131 Author chain A； PDBConstruct 399–524； UniProt 703–828 Author chain B； PDBConstruct 180–397； UniProt 914–1131 Author chain B； PDBConstruct 399–524； UniProt 703–828 Author chain C； PDBConstruct 180–397； UniProt 914–1131 Author chain C； PDBConstruct 399–524； UniProt 703–828

SPIKE PROTEIN

Severe acute respiratory syndrome coronavirus 2

UniProt Q12306

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 3	2-acetamido-2-deoxy-beta-D-glucopyranose × 18	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SUMO_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–114； UniProt 1–94 Author chain B； PDBConstruct 21–114； UniProt 1–94 Author chain C； PDBConstruct 21–114； UniProt 1–94

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	9z3k
Deposition date deposition_date	2025-11-07
Structure title title	SARS-CoV-2 S2 trimer stabilized in the early fusion intermediate conformation by circular permutation and clamping by gp41 (E-FICs-v1)
Keywords keywords	;S2prime, coronavirus, SARS-CoV-2, spike, fusion, entry, antiviral, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID, 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.

9z3k__assembly_1__model_1

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

Download this curve (.dat)

9z3k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9z3k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	82.38 Å
Rg (electron density)	84.33 Å
Total Rg	82.53 Å
Atom count	8448
Residues	1212
Excluded volume	147640 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9z3k__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 (2)

Entity 1 Entity 1 polymer

Description description	SPIKE PROTEIN
Molecular weight formula_weight	68016.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	8448

MTRLTVLALLAGLLASSRASMSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHRENDDDDKTGTGSTVQVRKLLSGIVQQQSNLLRAIEAQQHLLKLTVWGIKQLQAQVEERINAIETAINVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLAKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGTNSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLPDPGSNEEWLQWDKEISNYTHIIYELIEESQKQQEKNEQELLELDKSSGGTDDDDKTGSLNDIFEAQKIEWHEQGSHHHHHHHH

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 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	18

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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	3.30 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	114104

SARS-CoV-2 S2 trimer stabilized in the early fusion intermediate conformation by circular permutation and clamping by gp41 (E-FICs-v1)

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

SPIKE PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

SPIKE PROTEIN

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

9z3k__assembly_1__model_1

9z3k__assembly_1__model_1 | I(q)

9z3k__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

7. Citations (1)

SARS-CoV-2 S2 trimer stabilized in the early fusion intermediate conformation by circular permutation and clamping by gp41 (E-FICs-v1)

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

SPIKE PROTEIN

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

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

9z3k__assembly_1__model_1

9z3k__assembly_1__model_1 | I(q)

9z3k__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

7. Citations (1)