SAXSdb — 8e4c

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

Isoform 2 of Immunoglobulin heavy constant mu

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 105–475 Chain B； UniProt 105–475	Not recorded	B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein × 1 （P11911,P21578） B-cell antigen receptor complex-associated protein beta chain × 1 （P15530） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8E4C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4BA8 High resolution NMR structure of the C mu3 domain from IgM Deposited 2012-09-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 222–321（100 aa） Fragment：C MU3, RESIDUES 222-321	Mutation：YES	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 50 NMR sample composition 90% H20/10% D20, 20MM PHOSHATE BUFFER, 50MM NACL	Resolution not provided
4JVW IgM C4-domain from mouse Deposited 2013-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 324–436（113 aa） Fragment：uno residues 324-436 Chain D 324–436（113 aa） Fragment：uno residues 324-436	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；0.1 M HEPES, 15% PEG 8000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.234
4JVW IgM C4-domain from mouse Deposited 2013-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 324–436（113 aa） Fragment：uno residues 324-436 Chain C 324–436（113 aa） Fragment：uno residues 324-436	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；0.1 M HEPES, 15% PEG 8000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.234

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IGHM_MOUSE
Isoform	P01872-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 47–417； UniProt 105–475 Author chain B； PDBConstruct 47–417； UniProt 105–475

B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein

Mus musculus

UniProt P11911

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–169	Not recorded	Isoform 2 of Immunoglobulin heavy constant mu × 2 （P01872） B-cell antigen receptor complex-associated protein beta chain × 1 （P15530） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8E4C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8EMA mouse full length B cell receptor Deposited 2022-09-27	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–172（172 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.20 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CD79A_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 9–177； UniProt 1–169

B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein

Mus musculus

UniProt P21578

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–194	Not recorded	Isoform 2 of Immunoglobulin heavy constant mu × 2 （P01872） B-cell antigen receptor complex-associated protein beta chain × 1 （P15530） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8E4C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8EMA mouse full length B cell receptor Deposited 2022-09-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–194（194 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.20 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LUXY_ALIFS
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 185–378； UniProt 1–194

B-cell antigen receptor complex-associated protein beta chain

Mus musculus

UniProt P15530

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 1–228	Not recorded	Isoform 2 of Immunoglobulin heavy constant mu × 2 （P01872） B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein × 1 （P11911,P21578） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8E4C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3KHO Crystal structure of murine Ig-beta (CD79b) homodimer Deposited 2009-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–159（133 aa） Chain B 27–159（133 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；0.7-1.0 M Ammonium Sulfate, 100mM Tris, pH 8.0, VAPOR DIFFUSION, temperature 298K	Resolution 3.11 Å R-free 0.258
3KHQ Crystal structure of murine Ig-beta (CD79b) in the monomeric form Deposited 2009-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–159（133 aa） Fragment：extracellular domain	Not recorded	MG MAGNESIUM ION × 1 FLC CITRATE ANION × 1 GSH Glutathione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5；298 K；20% Peg 750 MME, 0.2M MgCl2, 100mM Na Citrate, pH 5.0, VAPOR DIFFUSION, temperature 298K	Resolution 1.70 Å R-free 0.197
8EMA mouse full length B cell receptor Deposited 2022-09-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–228（228 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.20 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CD79B_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–228； UniProt 1–228

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	8e4c
Deposition date deposition_date	2022-08-18
Structure title title	IgM BCR fab truncated form
Keywords keywords	complex, membrane protein, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	37.72 Å
Radius of gyration Rg (electron density) rg_electron	38.33 Å
Forward intensity I(0) i0	124074000.00
Molecular weight molecular_weight	90702.0 kDa
Excluded volume excluded_volume	114280 Å³
Envelope volume envelope_volume	172740 Å³
Hydration-shell volume shell_volume	41336 Å³
Envelope diameter envelope_diameter	147.1 Å
Shell Rg shell_rg	39.43 Å
Envelope Rg envelope_rg	39.11 Å
Shape Rg shape_rg	38.33 Å
Total Rg total_rg	38.43 Å
Total atoms total_atoms	6398
Residues n_residues	805
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	139.4 Å
Rg (real space) rg_real	38.11 Å
Rg uncertainty (real space) rg_real_error	1.72 Å
I(0) (real space) i0_real	1.2410e+08
I(0) uncertainty (real space) i0_real_error	2.3520e+06
Rg (reciprocal space) rg_reciprocal	37.87 Å
I(0) (reciprocal space) i0_reciprocal	124000000.0000
Solution quality estimate total_estimate	0.8244
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.2 Å
Skewness Skewness skewness	0.598
Kurtosis Kurtosis kurtosis	0.077
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12150000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.670; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.862; Smooth: 0.840

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Isoform 2 of Immunoglobulin heavy constant mu
Molecular weight formula_weight	45753.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	6398

MGWSCIILFLVATATGVHSGGWSHPQFEKAEAAAKEAAAKEAAAKAAVAEMNPNVNVFVPPRDGFSGPAPRKSKLICEATNFTPKPITVSWLKDGKLVESGFTTDPVTIENKGSTPQTYKVISTLTISEIDWLNLNVYTCRVDHRGLTFLKNVSSTCAASPSTDILTFTIPPSFADIFLSKSANLTCLVSNLATYETLNISWASQSGEPLETKIKIMESHPNGTFSAKGVASVCVEDWNNRKEFVCTVTHRDLPSPQKKFISKPNEVHKHPPAVYLLPPAREQLNLRESATVTCLVKGFSPADISVQWLQRGQLLPQEKYVTSAPMPEPGAPGFYFTHSILTVTEEEWNSGETYTCVVGHEALPHLVTERTVDKSTEGEVNAEEEGFENLWTTASTFIVLFLLSLFYSTTVTLFKVK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Mus musculus

Entity 2 Entity 2 polymer

Description description	B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein
Molecular weight formula_weight	42837.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

DYKDDDDKMPGGLEALRALPLLLFLSYACLGPGCQALRVEGGPPSLTVNLGEEARLTCENNGRNPNITWWFSLQSNITWPPVPLGPGQGTTGQLFFPEVNKNHRGLYWCQVIENNILKRSCGTYLRVRNPVPRPFLDMGEGTKNRIITAEGIILLFCAVVPGTLLLFRKRWQNEKFGRSIATRSMFKGIVEGIGIIEKIDIYTDLDKYAIRFPENMLNGIKKESSIMFNGCFLTVTSVNSNIVWFDIFEKEARKLDTFREYKVGDRVNLGTFPKFGAASGGHILSARISCVASIIEIIENEDYQQMWIQIPENFTEFLIDKDYIAVDGISLTIDTIKNNQFFISLPLKIAQNTNMKWRKKGDKVNVELSNKINANQCW

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Mus musculus

Entity 3 Entity 3 polymer

Description description	B-cell antigen receptor complex-associated protein beta chain
Molecular weight formula_weight	25752.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MATLVLSSMPCHWLLFLLLLFSGEPVPAMTSSDLPLNFQGSPCSQIWQHPRFAAKKRSSMVKFHCYTNHSGALTWFRKRGSQQPQELVSEEGRIVQTQNGSVYTLTIQNIQYEDNGIYFCKQKCDSANHNVTDSCGTELLVLGFSTLDQLKRRNTLKDGIILIQTLLIILFIIVPIFLLLDKDDGKAGMEEDHTYEGLNIDQTATYEDIVTLRTGEVKWSVGEHPGQE

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Mus musculus

Entity 4 Entity 4 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	5

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8. Citations (1)

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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	4.00 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	282429

fit	/app/data/saxs_computation/e4/8e4c/8e4c.fit
pddf	/app/data/pr_computation/e4/8e4c/8e4c.pr.out
profile	/app/data/saxs_computation/e4/8e4c/8e4c.dat

IgM BCR fab truncated form

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

Isoform 2 of Immunoglobulin heavy constant mu

State in the Current Structure

Other States of the Same Protein in the Database

B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein

State in the Current Structure

Other States of the Same Protein in the Database

B-cell antigen receptor complex-associated protein alpha chain,Yellow fluorescent protein

State in the Current Structure

Other States of the Same Protein in the Database

B-cell antigen receptor complex-associated protein beta chain

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)