SAXSdb — 7y9b

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

Membrane protein

Pipistrellus bat coronavirus HKU5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	3,6,9,12,15-PENTAOXATRICOSAN-1-OL × 2 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	3,6,9,12,15-PENTAOXATRICOSAN-1-OL × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VME1_BCHK5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–220； UniProt 1–220 Author chain B； PDBConstruct 1–220； UniProt 1–220 Author chain C； PDBConstruct 1–220； UniProt 1–220 Author chain D； PDBConstruct 1–220； UniProt 1–220

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	7y9b
Deposition date deposition_date	2022-06-24
Structure title title	Crystal structure of the membrane (M) protein of a SARS-COV-2-related coronavirus
Keywords keywords	M protein, SARS-COV-2 related, MEMBRANE PROTEIN; MEMBRANE 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.

7y9b__assembly_1__model_1

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

Download this curve (.dat)

7y9b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7y9b__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.90 Å
Rg (electron density)	24.47 Å
Total Rg	25.37 Å
Atom count	3012
Residues	374
Excluded volume	55219 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7y9b__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7y9b__assembly_2__model_1`	dimeric （2）	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	Membrane protein
Molecular weight formula_weight	24730.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6039

MASSNVTLSNDEVLRLVKDWNFTWSVVFLLITIVLQYGYPSRSMFVYVIKMFVLWLLWPASMALSIFCAVYPIDLASQIISGILAATSCAMWISYFVQSIRLFMRTGSWWSFNPESNCLLNVPIGGTTVVRPLVEDSTSVTAVVTDGYLKMAGMHFGACDFQRLPSEVTVAKPNVLIALKMIKRQAYGTNSGVAIYHRYKAGNYRRPPIIQDQELALLRA

Source Source

Source organism organism	Pipistrellus bat coronavirus HKU5
NCBI taxonomy ID ncbi_taxonomy_id	694008
Host organism host_organism	Komagataella pastoris

Entity 2 Entity 2 non-polymer

Description description	3,6,9,12,15-PENTAOXATRICOSAN-1-OL
Molecular weight formula_weight	350.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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Unit-cell length a length_a	76.569 Å
Unit-cell length b length_b	66.571 Å
Unit-cell length c length_c	112.628 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.83 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.214 Å
Low-resolution limit resolution_low	37.090 Å
R factor r_factor	0.2719
R_work r_work	0.2709
R_free r_free	0.2931

Crystal structure of the membrane (M) protein of a SARS-COV-2-related coronavirus

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

Membrane 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

7y9b__assembly_1__model_1

7y9b__assembly_1__model_1 | I(q)

7y9b__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 non-polymer

Entity 3 Entity 3 water

7. Citations (1)

Crystal structure of the membrane (M) protein of a SARS-COV-2-related coronavirus

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

Membrane 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

7y9b__assembly_1__model_1

7y9b__assembly_1__model_1 | I(q)

7y9b__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 non-polymer

Entity 3 Entity 3 water

7. Citations (1)