SAXSdb — 8wyr

▼

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

Interleukin-2,Isoform 1 of Immunoglobulin heavy constant mu

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 12 其他Polymer 1	Immunoglobulin J chain × 1 （P01591） Interleukin-2,CD5 antigen-like × 1 （O43866,P60568） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 CALCIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IGHM_HUMAN
Isoform	P01871-1
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 56–403； UniProt 106–453 Author chain B； PDBConstruct 56–403； UniProt 106–453 Author chain C； PDBConstruct 56–403； UniProt 106–453 Author chain D； PDBConstruct 56–403； UniProt 106–453 Author chain E； PDBConstruct 56–403； UniProt 106–453 Author chain F； PDBConstruct 56–403； UniProt 106–453 Author chain G； PDBConstruct 56–403； UniProt 106–453 Author chain H； PDBConstruct 56–403； UniProt 106–453 Author chain K； PDBConstruct 56–403； UniProt 106–453 Author chain L； PDBConstruct 56–403； UniProt 106–453

Interleukin-2,Isoform 1 of Immunoglobulin heavy constant mu

Homo sapiens

UniProt P60568

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 12 其他Polymer 1	Immunoglobulin J chain × 1 （P01591） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 CALCIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IL2_HUMAN
Isoform	—
PDB entities	1, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–21； UniProt 1–21 Author chain B； PDBConstruct 1–21； UniProt 1–21 Author chain C； PDBConstruct 1–21； UniProt 1–21 Author chain D； PDBConstruct 1–21； UniProt 1–21 Author chain E； PDBConstruct 1–21； UniProt 1–21 Author chain F； PDBConstruct 1–21； UniProt 1–21 Author chain G； PDBConstruct 1–21； UniProt 1–21 Author chain H； PDBConstruct 1–21； UniProt 1–21 Author chain K； PDBConstruct 1–21； UniProt 1–21 Author chain L； PDBConstruct 1–21； UniProt 1–21 Author chain M； PDBConstruct 1–21； UniProt 1–21

Immunoglobulin J chain

Homo sapiens

UniProt P01591

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 12 其他Polymer 1	Interleukin-2,Isoform 1 of Immunoglobulin heavy constant mu × 10 （P01871,P60568） Interleukin-2,CD5 antigen-like × 1 （O43866,P60568） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 CALCIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IGJ_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain J； PDBConstruct 1–159； UniProt 1–159

Interleukin-2,CD5 antigen-like

Homo sapiens

UniProt O43866

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 12 其他Polymer 1	Interleukin-2,Isoform 1 of Immunoglobulin heavy constant mu × 10 （P01871,P60568） Immunoglobulin J chain × 1 （P01591） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 CALCIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CD5L_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain M； PDBConstruct 32–359； UniProt 20–347

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8wyr
Deposition date deposition_date	2023-10-31
Structure title title	Cryo-EM structure of human CD5L bound to IgM-Fc/J
Keywords keywords	immunoglobulin, CD5 antigen-like, pentamer, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

8wyr__assembly_1__model_1

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

Download this curve (.dat)

8wyr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8wyr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	55.37 Å
Rg (electron density)	55.33 Å
Total Rg	55.27 Å
Atom count	20612
Residues	2629
Excluded volume	364880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8wyr__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Interleukin-2,Isoform 1 of Immunoglobulin heavy constant mu
Molecular weight formula_weight	44086.5 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,K,L
Atom count atom_count	20612

MYRMQLLSCIALSLALVTNSASAWSHPQFEKGGGSGGGSGGSAWSHPQFEKIDTTIAELPPKVSVFVPPRDGFFGNPRKSKLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVQAEAKESGPTTYKVTSTLTIKESDWLGQSMFTCRVDHRGLTFQQNASSMCVPDQDTAIRVFAIPPSFASIFLTKSTKLTCLVTDLTTYDSVTISWTRQNGEAVKTHTNISESHPNATFSAVGEASICEDDWNSGERFTCTVTHTDLPSPLKQTISRPKGVALHRPDVYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSAPMPEPQAPGRYFAHSILTVSEEEWNTGETYTCVVAHEALPNRVTERTVDKSTGKPTLYNVSLVMSDTAGTCY

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 polymer

Description description	Immunoglobulin J chain
Molecular weight formula_weight	19204.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MKNHLLFWGVLAVFIKAVHVKAQEDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNIRIIVPLNNRENISDPTSPLRTRFVYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSATETCYTYDRNKCYTAVVPLVYGGETKMVETALTPDACYPDYPYDVPDYA

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 3 Entity 3 polymer

Description description	Interleukin-2,CD5 antigen-like
Molecular weight formula_weight	39757.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MYRMQLLSCIALSLALVTNSARIHHHHHHHHSPSGVRLVGGLHRCEGRVEVEQKGQWGTVCDDGWDIKDVAVLCRELGCGAASGTPSGILYEPPAEKEQKVLIQSVSCTGTEDTLAQCEQEEVYDCSHDEDAGASCENPESSFSPVPEGVRLADGPGHCKGRVEVKHQNQWYTVCQTGWSLRAAKVVCRQLGCGRAVLTQKRCNKHAYGRKPIWLSQMSCSGREATLQDCPSGPWGKNTCNHDEDTWVECEDPFDLRLVGGDNLCSGRLEVLHKGVWGSVCDDNWGEKEDQVVCKQLGCGKSLSPSFRDRKCYGPGVGRIWLDNVRCSGEEQSLEQCQHRFWGFHDCTHQEDVAVICSG

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 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	1

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	10

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

▶

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	3.39 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	381470

Cryo-EM structure of human CD5L bound to IgM-Fc/J

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

Interleukin-2,Isoform 1 of Immunoglobulin heavy constant mu

State in the Current Structure

Other States of the Same Protein in the Database

Interleukin-2,Isoform 1 of Immunoglobulin heavy constant mu

State in the Current Structure

Other States of the Same Protein in the Database

Immunoglobulin J chain

State in the Current Structure

Other States of the Same Protein in the Database

Interleukin-2,CD5 antigen-like

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

8wyr__assembly_1__model_1

8wyr__assembly_1__model_1 | I(q)

8wyr__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 (6)

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

Entity 6 Entity 6 non-polymer

7. Citations (1)

Cryo-EM structure of human CD5L bound to IgM-Fc/J

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

Interleukin-2,Isoform 1 of Immunoglobulin heavy constant mu

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Interleukin-2,Isoform 1 of Immunoglobulin heavy constant mu

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Immunoglobulin J chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Interleukin-2,CD5 antigen-like

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

8wyr__assembly_1__model_1

8wyr__assembly_1__model_1 | I(q)

8wyr__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 (6)

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

Entity 6 Entity 6 non-polymer

7. Citations (1)