SAXSdb — 1c9l

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

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 3–359 Chain B； UniProt 3–359	Fragment：N-TERMINAL DOMAIN	B-ADAPTIN 3 × 2	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

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 1C9L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BPO CLATHRIN HEAVY-CHAIN TERMINAL DOMAIN AND LINKER Deposited 1998-08-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER Chain B 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER Chain C 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.60 Å R-free 0.292
1BPO CLATHRIN HEAVY-CHAIN TERMINAL DOMAIN AND LINKER Deposited 1998-08-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER Chain B 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER Chain C 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.60 Å R-free 0.292
1BPO CLATHRIN HEAVY-CHAIN TERMINAL DOMAIN AND LINKER Deposited 1998-08-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER Chain C 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.60 Å R-free 0.292
1BPO CLATHRIN HEAVY-CHAIN TERMINAL DOMAIN AND LINKER Deposited 1998-08-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.60 Å R-free 0.292
1C9I PEPTIDE-IN-GROOVE INTERACTIONS LINK TARGET PROTEINS TO THE B-PROPELLER OF CLATHRIN Deposited 1999-08-02	Different construct 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
9R9B Crystal structure of clathrin heavy chain in complex with a peptidomimetic inhibitor of the TACC3 interaction Deposited 2025-05-19	Different construct Different mutation/modification 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 6 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 1–357； UniProt 3–359 Author chain B； PDBConstruct 1–357； UniProt 3–359

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	1c9l
Deposition date deposition_date	1999-08-02
Structure title title	PEPTIDE-IN-GROOVE INTERACTIONS LINK TARGET PROTEINS TO THE B-PROPELLER OF CLATHRIN
Keywords keywords	BETA-PROPELLER, HELICAL HAIRPIN, ENDOCYTOSIS-EXOCYTOSIS COMPLEX; ENDOCYTOSIS/EXOCYTOSIS
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	31.60 Å
Radius of gyration Rg (electron density) rg_electron	31.06 Å
Forward intensity I(0) i0	103588000.00
Molecular weight molecular_weight	81370.0 kDa
Excluded volume excluded_volume	102210 Å³
Envelope volume envelope_volume	126340 Å³
Hydration-shell volume shell_volume	35171 Å³
Envelope diameter envelope_diameter	113.2 Å
Shell Rg shell_rg	36.64 Å
Envelope Rg envelope_rg	31.01 Å
Shape Rg shape_rg	31.04 Å
Total Rg total_rg	31.62 Å
Total atoms total_atoms	5716
Residues n_residues	730
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	107.1 Å
Rg (real space) rg_real	31.76 Å
Rg uncertainty (real space) rg_real_error	0.94 Å
I(0) (real space) i0_real	1.0360e+08
I(0) uncertainty (real space) i0_real_error	1.6170e+06
Rg (reciprocal space) rg_reciprocal	31.70 Å
I(0) (reciprocal space) i0_reciprocal	103600000.0000
Solution quality estimate total_estimate	0.8636
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.1 Å
Skewness Skewness skewness	0.462
Kurtosis Kurtosis kurtosis	-0.397
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19390000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.940

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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	CLATHRIN
Molecular weight formula_weight	39751.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5716

QILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSNPIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWISLNTVALVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVVGAMQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGNQPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRISGETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNLAG

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

Entity 2 Entity 2 polymer

Description description	B-ADAPTIN 3
Molecular weight formula_weight	980.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

DTNLIEFE

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1c9la1
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	d1c9la2
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	d1c9lb1
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	d1c9lb2
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 (2 domains)

Domain ID domain_id	1c9lA00
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	1c9lB00
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

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8. Citations (1)

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Unit-cell length a length_a	137.620 Å
Unit-cell length b length_b	130.787 Å
Unit-cell length c length_c	78.468 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.47 °
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	2.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2210
R_work r_work	0.2210
R_free r_free	0.2630

fit	/app/data/saxs_computation/c9/1c9l/1c9l.fit
pddf	/app/data/pr_computation/c9/1c9l/1c9l.pr.out
profile	/app/data/saxs_computation/c9/1c9l/1c9l.dat

PEPTIDE-IN-GROOVE INTERACTIONS LINK TARGET PROTEINS TO THE B-PROPELLER OF CLATHRIN

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

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)