SAXSdb — 1erh

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

CD59

Homo sapiens

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 26–95	Not recorded	No other associated polymer	SOLUTION NMR mmCIF provides none of the parsed experimental conditions	Resolution not provided

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 1ERH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CDQ STRUCTURE OF A SOLUBLE, GLYCOSYLATED FORM OF THE HUMAN COMPLEMENT REGULATORY PROTEIN CD59 Deposited 1994-06-01	Different construct	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–102（77 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1CDR STRUCTURE OF A SOLUBLE, GLYCOSYLATED FORM OF THE HUMAN COMPLEMENT REGULATORY PROTEIN CD59 Deposited 1994-06-01	Different construct Different oligomeric state	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–102（77 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1CDS STRUCTURE OF A SOLUBLE, GLYCOSYLATED FORM OF THE HUMAN COMPLEMENT REGULATORY PROTEIN CD59 Deposited 1994-06-01	Different construct Different oligomeric state	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–102（77 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1ERG THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE EXTRACELLULAR REGION OF THE COMPLEMENT REGULATORY PROTEIN, CD59, A NEW CELL SURFACE PROTEIN DOMAIN RELATED TO NEUROTOXINS Deposited 1993-12-13	Parsed fields agree	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–95（70 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2J8B High resolution structure of human CD59 Deposited 2006-10-24	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–103（78 aa） Fragment：MATURE POLYPEPTIDE, RESIDUES 26-103	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 28 % PEG 4000 0.25M AMMONIUM SULPHATE	Resolution 1.15 Å R-free 0.197
2OFS Crystal structure of human CD59 Deposited 2007-01-04	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–99（74 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；294 K；0.1 M sodium citrate, 16 % polyethylene glycol 6000, 5% isopropanol, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.12 Å R-free 0.254
2UWR High resolution structure of human CD59 Deposited 2007-03-23	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–102（77 aa） Fragment：RESIDUES 26-102	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 23% PEG8000, 20% ETHANOL, 0.03M POTASSIUM PHOSPHATE	Resolution 1.34 Å R-free 0.227
2UX2 High resolution structure of human CD59 Deposited 2007-03-26	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–102（77 aa） Fragment：RESIDUES 26-102	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 25% PEG8000, 0.03M POTASSIUM PHOSPHATE	Resolution 1.80 Å R-free 0.223
2UX2 High resolution structure of human CD59 Deposited 2007-03-26	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 26–102（77 aa） Fragment：RESIDUES 26-102	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 25% PEG8000, 0.03M POTASSIUM PHOSPHATE	Resolution 1.80 Å R-free 0.223
2UX2 High resolution structure of human CD59 Deposited 2007-03-26	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 26–102（77 aa） Fragment：RESIDUES 26-102	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 25% PEG8000, 0.03M POTASSIUM PHOSPHATE	Resolution 1.80 Å R-free 0.223
4BIK Structure of a disulfide locked mutant of Intermedilysin with human CD59 Deposited 2013-04-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 26–102（77 aa） Fragment：MATURE POLYPEPTIDE, RESIDUES 26-102	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；20% PEG6000, 0.1 M HEPES PH 7, 0.2 M LICL	Resolution 3.49 Å R-free 0.266
4BIK Structure of a disulfide locked mutant of Intermedilysin with human CD59 Deposited 2013-04-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 26–102（77 aa） Fragment：MATURE POLYPEPTIDE, RESIDUES 26-102	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；20% PEG6000, 0.1 M HEPES PH 7, 0.2 M LICL	Resolution 3.49 Å R-free 0.266
5IMT Toxin receptor complex Deposited 2016-03-06	Different construct 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 D 26–102（77 aa）	Not recorded	PGE TRIETHYLENE GLYCOL × 2 SO4 SULFATE ION × 6 ZN ZINC ION × 14 CU COPPER (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 8000, zinc acetate, MES pH 6.0, copper sulfate	Resolution 2.70 Å R-free 0.257
5IMT Toxin receptor complex Deposited 2016-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 26–102（77 aa）	Not recorded	PGE TRIETHYLENE GLYCOL × 1 SO4 SULFATE ION × 3 ZN ZINC ION × 7 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 8000, zinc acetate, MES pH 6.0, copper sulfate	Resolution 2.70 Å R-free 0.257
5IMY Trapped Toxin Deposited 2016-03-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 26–102（77 aa） Chain D 26–102（77 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Ammonium acetate, PEG 10000, Bis-Tris, Magnesium chloride	Resolution 2.40 Å R-free 0.276
6ZD0 Disulfide-locked early prepore intermedilysin-CD59 Deposited 2020-06-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 26–102（77 aa） Chain D 26–102（77 aa） Chain F 26–102（77 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Wait time of 60 s, blot time 2.5 s, blot force 3	Resolution 4.60 Å
8B0F CryoEM structure of C5b8-CD59 Deposited 2022-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain G 1–120（120 aa）	Not recorded	CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8B0G 2C9, C5b9-CD59 structure Deposited 2022-09-07	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain G 26–102（77 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20 mM HEPES pH 7.4, 120 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8B0H 2C9, C5b9-CD59 cryoEM structure Deposited 2022-09-07	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain G 1–128（128 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20 mM HEPES pH 7.4, 120 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8CN6 CD59 in complex with CP-06 peptide Deposited 2023-02-22	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 × 3 PDB declaration: trimeric	Chain A 26–101（76 aa） Chain C 26–101（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.01 M ZnCl2, 0.1 M HEPES pH 7.0, 20% w/v PEG 6000	Resolution 2.43 Å R-free 0.298
8CN6 CD59 in complex with CP-06 peptide Deposited 2023-02-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 26–101（76 aa） Chain E 26–101（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.01 M ZnCl2, 0.1 M HEPES pH 7.0, 20% w/v PEG 6000	Resolution 2.43 Å R-free 0.298
8CN6 CD59 in complex with CP-06 peptide Deposited 2023-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 26–101（76 aa） Chain F 26–101（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.01 M ZnCl2, 0.1 M HEPES pH 7.0, 20% w/v PEG 6000	Resolution 2.43 Å R-free 0.298

16 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CD59_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–70； UniProt 26–95

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	1erh
Deposition date deposition_date	1993-12-13
Structure title title	THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE EXTRACELLULAR REGION OF THE COMPLEMENT REGULATORY PROTEIN, CD59, A NEW CELL SURFACE PROTEIN DOMAIN RELATED TO NEUROTOXINS
Keywords keywords	COMPLEMENT FACTOR; COMPLEMENT FACTOR
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	11.13 Å
Radius of gyration Rg (electron density) rg_electron	10.59 Å
Forward intensity I(0) i0	106493000.00
Molecular weight molecular_weight	80863.0 kDa
Excluded volume excluded_volume	96197 Å³
Envelope volume envelope_volume	7538 Å³
Hydration-shell volume shell_volume	6552 Å³
Envelope diameter envelope_diameter	33.0 Å
Shell Rg shell_rg	15.13 Å
Envelope Rg envelope_rg	10.70 Å
Shape Rg shape_rg	10.70 Å
Total Rg total_rg	10.71 Å
Total atoms total_atoms	—
Residues n_residues	—
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	33.7 Å
Rg (real space) rg_real	11.17 Å
Rg uncertainty (real space) rg_real_error	0.05 Å
I(0) (real space) i0_real	1.0480e+08
I(0) uncertainty (real space) i0_real_error	7.2140e+05
Rg (reciprocal space) rg_reciprocal	11.08 Å
I(0) (reciprocal space) i0_reciprocal	106500000.0000
Solution quality estimate total_estimate	0.7276
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	13.6 Å
Skewness Skewness skewness	0.179
Kurtosis Kurtosis kurtosis	-0.528
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	8.3990
Highest regularization parameter α highest_alpha	142200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.980; Stabil: 0.945; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.714

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1erha_
Class class	g — Small proteins
Fold Fold fold	g.7 — Snake toxin-like
Superfamily Superfamily superfamily	g.7.1 — Snake toxin-like
Family Family family	g.7.1.3 — Extracellular domain of cell surface receptors

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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	1

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

Description description	CD59
Molecular weight formula_weight	8095.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	700

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE EXTRACELLULAR REGION OF THE COMPLEMENT REGULATORY PROTEIN, CD59, A NEW CELL SURFACE PROTEIN DOMAIN RELATED TO NEUROTOXINS

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

CD59

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/er/1erh/1erh.fit
pddf	/app/data/pr_computation/er/1erh/1erh.pr.out
profile	/app/data/saxs_computation/er/1erh/1erh.dat