SAXSdb — 6e4l

▼

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

Clathrin heavy chain 1

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 1–364	Not recorded	DMS DIMETHYL SULFOXIDE × 2 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 2 ACT ACETATE ION × 3 HRS 5-bromo-N-(4-nitrophenyl)thiophene-2-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；20% PEG 3350, 150 MM POTASSIUM ACETATE, 0.1 M TRIS, pH 8.0	Resolution 1.60 Å R-free 0.214

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 6E4L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2XZG Clathrin Terminal Domain Complexed with Pitstop 1 Deposited 2010-11-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–364（364 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-364	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2 GOL GLYCEROL × 1 ACT ACETATE ION × 1 VH1 2-(4-AMINOBENZYL)-1,3-DIOXO-2,3-DIHYDRO-1H-BENZO[DE]ISOQUINOLINE-5-SULFONATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；20% PEG 3350, 150 MM POTASSIUM ACETATE, 0.1 M TRIS, PH 8.0.	Resolution 1.70 Å R-free 0.200
4G55 Clathrin terminal domain complexed with pitstop 2 Deposited 2012-07-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–364（364 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	DMS DIMETHYL SULFOXIDE × 4 ACT ACETATE ION × 5 EDO 1,2-ETHANEDIOL × 6 PEG DI(HYDROXYETHYL)ETHER × 2 VH2 N-[5-[(4-BROMOPHENYL)METHYL]-4-HYDROXY-1,3-THIAZOL-2-YL]NAPHTHALENE-1-SULFONAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；20% PEG 3350, 150 MM POTASSIUM ACETATE, 0.1 M TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.69 Å R-free 0.215
6QNN CLATHRIN HEAVY CHAIN N-TERMINAL DOMAIN BOUND TO GTSE1 LIDL MOTIF Deposited 2019-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–364（364 aa） Fragment：;LIDL motifs A-E, REFSEQ RESIDUES 661-726, N-TERMINAL 'GPLG' ARE NON-NATURAL ;	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；20% PEG 6000, 0.1M TRIS pH 8.0	Resolution 2.03 Å R-free 0.284
6QNP CLATHRIN HEAVY CHAIN N-TERMINAL DOMAIN BOUND TO GTSE1 LIDL MOTIF Deposited 2019-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–364（364 aa） Fragment：;LIDL motifs A-D, REFSEQ RESIDUES 653-719, N-TERMINAL 'GPLGS' ARE NON-NATURAL ;	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；12% PEG 4000, 0.1M SODIUM ACETATE, 0.1M HEPES pH 7.0	Resolution 2.70 Å R-free 0.291
6QNP CLATHRIN HEAVY CHAIN N-TERMINAL DOMAIN BOUND TO GTSE1 LIDL MOTIF Deposited 2019-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–364（364 aa） Fragment：;LIDL motifs A-D, REFSEQ RESIDUES 653-719, N-TERMINAL 'GPLGS' ARE NON-NATURAL ;	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；12% PEG 4000, 0.1M SODIUM ACETATE, 0.1M HEPES pH 7.0	Resolution 2.70 Å R-free 0.291
6QNP CLATHRIN HEAVY CHAIN N-TERMINAL DOMAIN BOUND TO GTSE1 LIDL MOTIF Deposited 2019-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–364（364 aa） Fragment：;LIDL motifs A-D, REFSEQ RESIDUES 653-719, N-TERMINAL 'GPLGS' ARE NON-NATURAL ;	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；12% PEG 4000, 0.1M SODIUM ACETATE, 0.1M HEPES pH 7.0	Resolution 2.70 Å R-free 0.291
6QNP CLATHRIN HEAVY CHAIN N-TERMINAL DOMAIN BOUND TO GTSE1 LIDL MOTIF Deposited 2019-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–364（364 aa） Fragment：;LIDL motifs A-D, REFSEQ RESIDUES 653-719, N-TERMINAL 'GPLGS' ARE NON-NATURAL ;	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；12% PEG 4000, 0.1M SODIUM ACETATE, 0.1M HEPES pH 7.0	Resolution 2.70 Å R-free 0.291
7BN1 Clathrin heavy chain N-terminal domain complexed with peptide from Protein mu-NS of Reovirus type 1 Deposited 2021-01-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–364（364 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；30% PEG 550 MME; PEG 20K, 0.12M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose; D-Xylose; N-Acetyl-D-Glucosamine) and 0.1M Sodium HEPES; MOPS (acid) pH-7.5	Resolution 1.97 Å R-free 0.215
7BN1 Clathrin heavy chain N-terminal domain complexed with peptide from Protein mu-NS of Reovirus type 1 Deposited 2021-01-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–364（364 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；30% PEG 550 MME; PEG 20K, 0.12M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose; D-Xylose; N-Acetyl-D-Glucosamine) and 0.1M Sodium HEPES; MOPS (acid) pH-7.5	Resolution 1.97 Å R-free 0.215
7BN2 Clathrin heavy chain N-terminal domain bound to Non structured protein 3 from Eastern Equine Encephalitis Virus Deposited 2021-01-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain AAA 1–364（364 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30% PEG 550 MME; PEG 20K and 0.1M NPS buffer system NaN03; Na2HPO4; (NH4)2SO4, pH-6.5	Resolution 1.97 Å R-free 0.219
7BN2 Clathrin heavy chain N-terminal domain bound to Non structured protein 3 from Eastern Equine Encephalitis Virus Deposited 2021-01-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain BBB 1–364（364 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30% PEG 550 MME; PEG 20K and 0.1M NPS buffer system NaN03; Na2HPO4; (NH4)2SO4, pH-6.5	Resolution 1.97 Å R-free 0.219
7ZX4 Clathrin N-terminal domain in complex with a HURP phospho-peptide Deposited 2022-05-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–364（364 aa）	Not recorded	GOL GLYCEROL × 2 CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；50 mM Tris pH 7.5, 30 % PEG 6000	Resolution 2.08 Å R-free 0.249
7ZX4 Clathrin N-terminal domain in complex with a HURP phospho-peptide Deposited 2022-05-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–364（364 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；50 mM Tris pH 7.5, 30 % PEG 6000	Resolution 2.08 Å R-free 0.249
9C0Y Clathrin terminal domain complexed with Pitstop 2c Deposited 2024-05-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–364（364 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 2 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 3 ACT ACETATE ION × 2 A1ATR N-{(5Z)-4-oxo-5-[(2-phenoxyphenyl)methylidene]-4,5-dihydro-1,3-thiazol-2-yl}naphthalene-2-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350, 150 MM POTASSIUM ACETATE, 0.1 M TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature	Resolution 1.40 Å R-free 0.206
9C0Z Clathrin terminal domain complexed with pitstop 2d Deposited 2024-05-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–364（363 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1 A1ATQ ~{N}-[4-oxidanylidene-5-[(2-phenoxyphenyl)methylidene]-1,3-thiazol-2-yl]naphthalene-1-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350, 150 MM POTASSIUM ACETATE, 0.1 M TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.51 Å R-free 0.186

9 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CLH1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–369； UniProt 1–364

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6e4l
Deposition date deposition_date	2018-07-17
Structure title title	The structure of the N-terminal domain of human clathrin heavy chain 1 (nTD) in complex with ES9
Keywords keywords	Clathrin-mediated endocytosis (CME), Clathrin N-terminal domain (nTD), chemical inhibition, ENDOCYTOSIS; ENDOCYTOSIS
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	21.95 Å
Radius of gyration Rg (electron density) rg_electron	20.71 Å
Forward intensity I(0) i0	28260000.00
Molecular weight molecular_weight	40825.0 kDa
Excluded volume excluded_volume	51169 Å³
Envelope volume envelope_volume	60319 Å³
Hydration-shell volume shell_volume	23891 Å³
Envelope diameter envelope_diameter	69.2 Å
Shell Rg shell_rg	27.73 Å
Envelope Rg envelope_rg	20.92 Å
Shape Rg shape_rg	20.69 Å
Total Rg total_rg	21.67 Å
Total atoms total_atoms	5719
Residues n_residues	358
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

▼

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

Maximum dimension Dmax dmax	68.1 Å
Rg (real space) rg_real	21.80 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	2.8260e+07
I(0) uncertainty (real space) i0_real_error	3.4030e+05
Rg (reciprocal space) rg_reciprocal	21.83 Å
I(0) (reciprocal space) i0_reciprocal	28260000.0000
Solution quality estimate total_estimate	0.9014
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.4 Å
Skewness Skewness skewness	0.143
Kurtosis Kurtosis kurtosis	-0.452
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8222000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.967

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Clathrin heavy chain 1
Molecular weight formula_weight	41061.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5969

GSPEFMAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSNPIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWISLNTVALVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVVGAMQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGNQPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRISGETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNLAGAEELF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	2

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	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	5-bromo-N-(4-nitrophenyl)thiophene-2-sulfonamide
Molecular weight formula_weight	363.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	180

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d6e4la1
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	d6e4la2
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.118.1.0 — automated matches

Domain ID domain_id	d6e4la3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	6e4lA00
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	71.210 Å
Unit-cell length b length_b	74.340 Å
Unit-cell length c length_c	84.230 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	51.424 Å
R factor r_factor	0.1888
R_work r_work	0.1879
R_free r_free	0.2143

fit	/app/data/saxs_computation/e4/6e4l/6e4l.fit
pddf	/app/data/pr_computation/e4/6e4l/6e4l.pr.out
profile	/app/data/saxs_computation/e4/6e4l/6e4l.dat

The structure of the N-terminal domain of human clathrin heavy chain 1 (nTD) in complex with ES9