SAXSdb — 1h8u

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

EOSINOPHIL GRANULE MAJOR BASIC PROTEIN 1

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 106–222	Not recorded	SO4 SULFATE ION × 5 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；100MM MALONIC ACID PH6, 140MM POTTASIUM DIHYDROGEN PHOSPHATE., pH 6.00	Resolution 1.80 Å R-free 0.264
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 106–222	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；100MM MALONIC ACID PH6, 140MM POTTASIUM DIHYDROGEN PHOSPHATE., pH 6.00	Resolution 1.80 Å R-free 0.264

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 1H8U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2BRS EMBP Heparin complex Deposited 2005-05-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 106–222（117 aa）	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.291
2BRS EMBP Heparin complex Deposited 2005-05-11	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 106–222（117 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.291
4QXX Structure of the amyloid forming peptide GNLVS (residues 26-30) from the eosinophil major basic protein (EMBP) Deposited 2014-07-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain Z 131–135（5 aa） Fragment：GNLVS peptide (UNP residues 131-135)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；291 K；2 M ammonium sulfate, 0.1 M phosphate/citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.45 Å R-free 0.192
7Y5N Structure of 1:1 PAPP-A.ProMBP complex(half map) Deposited 2022-06-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–222（222 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ZN ZINC ION × 1 CA CALCIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å
8HGG Structure of 2:2 PAPP-A.ProMBP complex Deposited 2022-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–222（222 aa） Chain B 1–222（222 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.64 Å
9DKZ In situ microED structure of the Eosinophil major basic protein-1 Deposited 2024-09-10	Different construct 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 107–222（116 aa）	Not recorded	No recorded non-water small molecule	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7；secretory granule matrix cryo-EM vitrification conditions Cryogen ETHANE；Blot time of 6~8 sec, single-side back blotting	Resolution 3.20 Å R-free 0.311
9PPV In situ MicroED structure of human eosinophil major basic protein-1 Deposited 2025-07-22	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 106–222（117 aa）	Not recorded	CL CHLORIDE ION × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å R-free 0.313
9PPV In situ MicroED structure of human eosinophil major basic protein-1 Deposited 2025-07-22	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 106–222（117 aa）	Not recorded	CL CHLORIDE ION × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å R-free 0.313
9PSE In situ MicroED structure of IL-5 activated human eosinophil major basic protein-1 Deposited 2025-07-25	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 107–222（116 aa）	Not recorded	CL CHLORIDE ION × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7.4；Harvested from human donor peripheral blood and rested in 1640 RPMI medium supplemented with 0.1% human serum albumin (HSA) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å R-free 0.320
9PSE In situ MicroED structure of IL-5 activated human eosinophil major basic protein-1 Deposited 2025-07-25	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–222（116 aa）	Not recorded	CL CHLORIDE ION × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7.4；Harvested from human donor peripheral blood and rested in 1640 RPMI medium supplemented with 0.1% human serum albumin (HSA) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å R-free 0.320
9PSK In situ MicroED structure of IL-33 activated human eosinophil major basic protein-1 Deposited 2025-07-25	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 106–222（117 aa）	Not recorded	No recorded non-water small molecule	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7.4；Harvested eosinophiles resting in 1640 RPMI medium (Sigma-Aldrich) supplemented with 0.1% human serum albumin (HSA) (Sigma-Aldrich) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å R-free 0.340
9PSK In situ MicroED structure of IL-33 activated human eosinophil major basic protein-1 Deposited 2025-07-25	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 106–222（117 aa）	Not recorded	CL CHLORIDE ION × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7.4；Harvested eosinophiles resting in 1640 RPMI medium (Sigma-Aldrich) supplemented with 0.1% human serum albumin (HSA) (Sigma-Aldrich) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å R-free 0.340

8 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EMBP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–117； UniProt 106–222 Author chain B； PDBConstruct 1–117； UniProt 106–222

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	1h8u
Deposition date deposition_date	2001-02-15
Structure title title	Crystal Structure of the Eosinophil Major Basic Protein at 1.8A: An Atypical Lectin with a Paradigm Shift in Specificity
Keywords keywords	LECTIN, EOSINOPHIL GRANULE PROTEIN, EMBP; LECTIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	22.93 Å
Radius of gyration Rg (electron density) rg_electron	22.86 Å
Forward intensity I(0) i0	16114800.00
Molecular weight molecular_weight	28105.0 kDa
Excluded volume excluded_volume	34187 Å³
Envelope volume envelope_volume	43510 Å³
Hydration-shell volume shell_volume	17018 Å³
Envelope diameter envelope_diameter	75.6 Å
Shell Rg shell_rg	28.07 Å
Envelope Rg envelope_rg	22.67 Å
Shape Rg shape_rg	22.87 Å
Total Rg total_rg	23.51 Å
Total atoms total_atoms	1966
Residues n_residues	231
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	77.6 Å
Rg (real space) rg_real	23.10 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	1.6110e+07
I(0) uncertainty (real space) i0_real_error	2.3620e+05
Rg (reciprocal space) rg_reciprocal	23.06 Å
I(0) (reciprocal space) i0_reciprocal	16110000.0000
Solution quality estimate total_estimate	0.8211
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.5 Å
Skewness Skewness skewness	0.470
Kurtosis Kurtosis kurtosis	-0.512
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7349000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.633; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.781; Smooth: 0.993

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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	EOSINOPHIL GRANULE MAJOR BASIC PROTEIN 1
Molecular weight formula_weight	13820.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2124

TCRYLLVRSLQTFSQAWFTCRRCYRGNLVSIHNFNINYRIQCSVSALNQGQVWIGGRITGSGRCRRFQWVDGSRWNFAYWAAHQPWSRGGHCVALCTRGGYWRRAHCLRRLPFICSY

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	158

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1h8ua_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d1h8ub_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

CATH v4.4 (2 domains)

Domain ID domain_id	1h8uA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	1h8uB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

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8. Citations (1)

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Unit-cell length a length_a	74.328 Å
Unit-cell length b length_b	57.487 Å
Unit-cell length c length_c	60.961 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	36.180 Å
R factor r_factor	0.2340
R_work r_work	0.2340
R_free r_free	0.2640

fit	/app/data/saxs_computation/h8/1h8u/1h8u.fit
pddf	/app/data/pr_computation/h8/1h8u/1h8u.pr.out
profile	/app/data/saxs_computation/h8/1h8u/1h8u.dat

Crystal Structure of the Eosinophil Major Basic Protein at 1.8A: An Atypical Lectin with a Paradigm Shift in Specificity

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

EOSINOPHIL GRANULE MAJOR BASIC PROTEIN 1

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

Refinement Refinement

Diffraction experiment Diffraction