SAXSdb — 5m3d

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

CD81 antigen

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 4 PHOSPHATE ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 2 PHOSPHATE ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CD81_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–92； UniProt 112–201 Author chain B； PDBConstruct 3–92； UniProt 112–201 Author chain C； PDBConstruct 3–92； UniProt 112–201 Author chain D； PDBConstruct 3–92； UniProt 112–201

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	5m3d
Deposition date deposition_date	2016-10-14
Structure title title	Structural tuning of CD81LEL (space group P31)
Keywords keywords	human cellular receptor for Hepatitis C virus, cell adhesion; CELL ADHESION
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.

5m3d__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5m3d__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5m3d__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	17.26 Å
Rg (electron density)	16.58 Å
Total Rg	17.54 Å
Atom count	2739
Residues	180
Excluded volume	24466 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5m3d__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5m3d__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 (4)

Entity 1 Entity 1 polymer

Description description	CD81 antigen
Molecular weight formula_weight	11182.4 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	5490

ETGFVNKDQIAKDVKQFYDQALQQAVVDDDANNAKAVVKTFHETLDCCGSSTLTALTTSVLKNNLCPSGSNIISNLFKEDCHQKIDDLFSGKGTKHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	10

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5m3da1
Class class	a — All alpha proteins
Fold Fold fold	a.135 — Tetraspanin
Superfamily Superfamily superfamily	a.135.1 — Tetraspanin
Family Family family	a.135.1.1 — Tetraspanin

Domain ID domain_id	d5m3da2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5m3db1
Class class	a — All alpha proteins
Fold Fold fold	a.135 — Tetraspanin
Superfamily Superfamily superfamily	a.135.1 — Tetraspanin
Family Family family	a.135.1.1 — Tetraspanin

Domain ID domain_id	d5m3db2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5m3dc1
Class class	a — All alpha proteins
Fold Fold fold	a.135 — Tetraspanin
Superfamily Superfamily superfamily	a.135.1 — Tetraspanin
Family Family family	a.135.1.1 — Tetraspanin

Domain ID domain_id	d5m3dc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5m3dd1
Class class	a — All alpha proteins
Fold Fold fold	a.135 — Tetraspanin
Superfamily Superfamily superfamily	a.135.1 — Tetraspanin
Family Family family	a.135.1.1 — Tetraspanin

Domain ID domain_id	d5m3dd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	5m3dA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1450 — Cd81 Antigen, Extracellular Domain; Chain: A
Homologous superfamily homologous superfamily	10 — Tetraspanin

Domain ID domain_id	5m3dB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1450 — Cd81 Antigen, Extracellular Domain; Chain: A
Homologous superfamily homologous superfamily	10 — Tetraspanin

Domain ID domain_id	5m3dC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1450 — Cd81 Antigen, Extracellular Domain; Chain: A
Homologous superfamily homologous superfamily	10 — Tetraspanin

Domain ID domain_id	5m3dD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1450 — Cd81 Antigen, Extracellular Domain; Chain: A
Homologous superfamily homologous superfamily	10 — Tetraspanin

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Unit-cell length a length_a	97.948 Å
Unit-cell length b length_b	97.948 Å
Unit-cell length c length_c	34.409 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.380 Å
Low-resolution limit resolution_low	48.974 Å
R factor r_factor	0.1763
R_work r_work	0.1738
R_free r_free	0.2222

Structural tuning of CD81LEL (space group P31)

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

CD81 antigen

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

5m3d__assembly_2__model_1

5m3d__assembly_2__model_1 | I(q)

5m3d__assembly_2__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (3)

Structural tuning of CD81LEL (space group P31)

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

CD81 antigen

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

5m3d__assembly_2__model_1

5m3d__assembly_2__model_1 | I(q)

5m3d__assembly_2__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (3)