SAXSdb — 1bpo

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

PROTEIN (CLATHRIN)

Rattus norvegicus

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–494 Chain B； UniProt 1–494 Chain C； UniProt 1–494	Fragment：TERMINAL DOMAIN AND LINKER	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.60 Å R-free 0.292
2	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–494 Chain B； UniProt 1–494 Chain C； UniProt 1–494	Fragment：TERMINAL DOMAIN AND LINKER	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.60 Å R-free 0.292
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–494 Chain C； UniProt 1–494	Fragment：TERMINAL DOMAIN AND LINKER	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.60 Å R-free 0.292
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–494	Fragment：TERMINAL DOMAIN AND LINKER	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.60 Å R-free 0.292

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 1BPO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C9I PEPTIDE-IN-GROOVE INTERACTIONS LINK TARGET PROTEINS TO THE B-PROPELLER OF CLATHRIN Deposited 1999-08-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–359（359 aa） Fragment：N-TERMINAL DOMAIN Chain B 1–359（359 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 4000, KOAc, DTT, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.269
1C9L PEPTIDE-IN-GROOVE INTERACTIONS LINK TARGET PROTEINS TO THE B-PROPELLER OF CLATHRIN Deposited 1999-08-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 3–359（357 aa） Fragment：N-TERMINAL DOMAIN Chain B 3–359（357 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 400, KOAc, DTT, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.263
9R9B Crystal structure of clathrin heavy chain in complex with a peptidomimetic inhibitor of the TACC3 interaction Deposited 2025-05-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–574（574 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；291 K；20% w/v polyethylene glycol 3350 200 mM tri-potassium citrate	Resolution 2.15 Å R-free 0.268

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

View Construct and Data Evidence

UniProt name	CLH_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–494； UniProt 1–494 Author chain B； PDBConstruct 1–494； UniProt 1–494 Author chain C； PDBConstruct 1–494； UniProt 1–494

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	1bpo
Deposition date deposition_date	1998-08-11
Structure title title	CLATHRIN HEAVY-CHAIN TERMINAL DOMAIN AND LINKER
Keywords keywords	CLATHRIN ENDOCYTOSIS BETA-PROPELLER COATED-PITS, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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	39.78 Å
Radius of gyration Rg (electron density) rg_electron	39.02 Å
Forward intensity I(0) i0	391125000.00
Molecular weight molecular_weight	163330.0 kDa
Excluded volume excluded_volume	205630 Å³
Envelope volume envelope_volume	283310 Å³
Hydration-shell volume shell_volume	59739 Å³
Envelope diameter envelope_diameter	123.6 Å
Shell Rg shell_rg	45.83 Å
Envelope Rg envelope_rg	37.86 Å
Shape Rg shape_rg	39.05 Å
Total Rg total_rg	39.36 Å
Total atoms total_atoms	11482
Residues n_residues	1467
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	122.2 Å
Rg (real space) rg_real	39.51 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	3.9110e+08
I(0) uncertainty (real space) i0_real_error	6.0060e+06
Rg (reciprocal space) rg_reciprocal	39.68 Å
I(0) (reciprocal space) i0_reciprocal	391200000.0000
Solution quality estimate total_estimate	0.9025
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	55.0 Å
Skewness Skewness skewness	0.065
Kurtosis Kurtosis kurtosis	-0.604
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	49170000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.882

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	PROTEIN (CLATHRIN)
Molecular weight formula_weight	55090.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	11517

MAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSNPIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWISLNTVALVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVVGAMQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGNQPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRISGETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNLAGAEELFARKFNALFAQGNYSEAAKVAANAPKGILRTPDTIRRFQSVPAQPGQTSPLLQYFGILLDQGQLNKYESLELCRPVLQQGRKQLLEKWLKEDKLECSEELGDLVKSVDPTLALSVYLRANVPNKVIQCFAE

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	35

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1bpoa1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.4 — Clathrin heavy-chain linker domain

Domain ID domain_id	d1bpoa2
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.6 — Clathrin heavy-chain terminal domain
Family Family family	b.69.6.1 — Clathrin heavy-chain terminal domain

Domain ID domain_id	d1bpob1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.4 — Clathrin heavy-chain linker domain

Domain ID domain_id	d1bpob2
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.6 — Clathrin heavy-chain terminal domain
Family Family family	b.69.6.1 — Clathrin heavy-chain terminal domain

Domain ID domain_id	d1bpoc1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.4 — Clathrin heavy-chain linker domain

Domain ID domain_id	d1bpoc2
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.6 — Clathrin heavy-chain terminal domain
Family Family family	b.69.6.1 — Clathrin heavy-chain terminal domain

CATH v4.4 (6 domains)

Domain ID domain_id	1bpoA01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	110 — Clathrin heavy-chain terminal domain

Domain ID domain_id	1bpoA02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1bpoB01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	110 — Clathrin heavy-chain terminal domain

Domain ID domain_id	1bpoB02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1bpoC01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	110 — Clathrin heavy-chain terminal domain

Domain ID domain_id	1bpoC02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	30 —

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8. Citations (1)

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Unit-cell length a length_a	205.825 Å
Unit-cell length b length_b	205.825 Å
Unit-cell length c length_c	87.630 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	18

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2260
R_work r_work	0.2260
R_free r_free	0.2920

fit	/app/data/saxs_computation/bp/1bpo/1bpo.fit
pddf	/app/data/pr_computation/bp/1bpo/1bpo.pr.out
profile	/app/data/saxs_computation/bp/1bpo/1bpo.dat

CLATHRIN HEAVY-CHAIN TERMINAL DOMAIN AND LINKER

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

PROTEIN (CLATHRIN)

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