5m5u

Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 1)

Method: X-RAY DIFFRACTION D_max: 110.2 Å Quality: GOOD

▼

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

Clathrin heavy chain 1

Bos taurus

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–363	Not recorded	Large delta antigen × 2 （P0C6L6） GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；400 nL protein:peptide mix (14 mg/mL NTD and 3.4 mM) plus 200 nL reservoir equilibrated against a 80 uL reservoir of 1.21 M sodium malonate pH 7.0	Resolution 2.15 Å R-free 0.207
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–363	Not recorded	Large delta antigen × 2 （P0C6L6）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；400 nL protein:peptide mix (14 mg/mL NTD and 3.4 mM) plus 200 nL reservoir equilibrated against a 80 uL reservoir of 1.21 M sodium malonate pH 7.0	Resolution 2.15 Å R-free 0.207

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 5M5U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B89 CLATHRIN HEAVY CHAIN PROXIMAL LEG SEGMENT (BOVINE) Deposited 1999-05-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1074–1522（449 aa） Fragment：PROXIMAL LEG	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；250 MM SODIUM FORMATE, 100 MM TRIS-HCL, PH 8, pH 8.0	Resolution 2.60 Å R-free 0.279
1UTC Clathrin terminal domain complexed with TLPWDLWTT Deposited 2003-12-08	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–363（363 aa） Fragment：TERMINAL DOMAIN, RESIDUES 1-363	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；VAPOUR DIFFUSION OVER A RESERVOIR CONTAINING 20% PEG8000, 200 MM MGCL2, 4 MM DTT,100 MM CAPS PH 9, DRIED UP DROP	Resolution 2.30 Å R-free 0.253
1UTC Clathrin terminal domain complexed with TLPWDLWTT Deposited 2003-12-08	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–363（363 aa） Fragment：TERMINAL DOMAIN, RESIDUES 1-363	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；VAPOUR DIFFUSION OVER A RESERVOIR CONTAINING 20% PEG8000, 200 MM MGCL2, 4 MM DTT,100 MM CAPS PH 9, DRIED UP DROP	Resolution 2.30 Å R-free 0.253
1XI4 Clathrin D6 Coat Deposited 2004-09-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 216 PDB declaration: 216-MERIC	Chain A 1–1630（1630 aa） Fragment：residues 1-1630 Chain B 1–1630（1630 aa） Fragment：residues 1-1630 Chain C 1–1630（1630 aa） Fragment：residues 1-1630 Chain D 1–1630（1630 aa） Fragment：residues 1-1630 Chain E 1–1630（1630 aa） Fragment：residues 1-1630 Chain F 1–1630（1630 aa） Fragment：residues 1-1630 Chain G 1–1630（1630 aa） Fragment：residues 1-1630 Chain H 1–1630（1630 aa） Fragment：residues 1-1630 Chain I 1–1630（1630 aa） Fragment：residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25mM MES；pH 6.5；25mM MES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 7.90 Å
1XI4 Clathrin D6 Coat Deposited 2004-09-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 1–1630（1630 aa） Fragment：residues 1-1630 Chain B 1–1630（1630 aa） Fragment：residues 1-1630 Chain C 1–1630（1630 aa） Fragment：residues 1-1630 Chain D 1–1630（1630 aa） Fragment：residues 1-1630 Chain E 1–1630（1630 aa） Fragment：residues 1-1630 Chain F 1–1630（1630 aa） Fragment：residues 1-1630 Chain G 1–1630（1630 aa） Fragment：residues 1-1630 Chain H 1–1630（1630 aa） Fragment：residues 1-1630 Chain I 1–1630（1630 aa） Fragment：residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25mM MES；pH 6.5；25mM MES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 7.90 Å
1XI4 Clathrin D6 Coat Deposited 2004-09-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 1–1630（1630 aa） Fragment：residues 1-1630 Chain B 1–1630（1630 aa） Fragment：residues 1-1630 Chain C 1–1630（1630 aa） Fragment：residues 1-1630 Chain D 1–1630（1630 aa） Fragment：residues 1-1630 Chain E 1–1630（1630 aa） Fragment：residues 1-1630 Chain F 1–1630（1630 aa） Fragment：residues 1-1630 Chain G 1–1630（1630 aa） Fragment：residues 1-1630 Chain H 1–1630（1630 aa） Fragment：residues 1-1630 Chain I 1–1630（1630 aa） Fragment：residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25mM MES；pH 6.5；25mM MES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 7.90 Å
1XI5 Clathrin D6 coat with auxilin J-domain Deposited 2004-09-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 216 PDB declaration: 216-MERIC	Chain A 1–1630（1630 aa） Fragment：residues 1-1630 Chain B 1–1630（1630 aa） Fragment：residues 1-1630 Chain C 1–1630（1630 aa） Fragment：residues 1-1630 Chain D 1–1630（1630 aa） Fragment：residues 1-1630 Chain E 1–1630（1630 aa） Fragment：residues 1-1630 Chain F 1–1630（1630 aa） Fragment：residues 1-1630 Chain G 1–1630（1630 aa） Fragment：residues 1-1630 Chain H 1–1630（1630 aa） Fragment：residues 1-1630 Chain I 1–1630（1630 aa） Fragment：residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20MM HEPES；pH 7；20MM HEPES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 12.00 Å
1XI5 Clathrin D6 coat with auxilin J-domain Deposited 2004-09-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 1–1630（1630 aa） Fragment：residues 1-1630 Chain B 1–1630（1630 aa） Fragment：residues 1-1630 Chain C 1–1630（1630 aa） Fragment：residues 1-1630 Chain D 1–1630（1630 aa） Fragment：residues 1-1630 Chain E 1–1630（1630 aa） Fragment：residues 1-1630 Chain F 1–1630（1630 aa） Fragment：residues 1-1630 Chain G 1–1630（1630 aa） Fragment：residues 1-1630 Chain H 1–1630（1630 aa） Fragment：residues 1-1630 Chain I 1–1630（1630 aa） Fragment：residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20MM HEPES；pH 7；20MM HEPES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 12.00 Å
1XI5 Clathrin D6 coat with auxilin J-domain Deposited 2004-09-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 1–1630（1630 aa） Fragment：residues 1-1630 Chain B 1–1630（1630 aa） Fragment：residues 1-1630 Chain C 1–1630（1630 aa） Fragment：residues 1-1630 Chain D 1–1630（1630 aa） Fragment：residues 1-1630 Chain E 1–1630（1630 aa） Fragment：residues 1-1630 Chain F 1–1630（1630 aa） Fragment：residues 1-1630 Chain G 1–1630（1630 aa） Fragment：residues 1-1630 Chain H 1–1630（1630 aa） Fragment：residues 1-1630 Chain I 1–1630（1630 aa） Fragment：residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20MM HEPES；pH 7；20MM HEPES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 12.00 Å
3GC3 Crystal Structure of Arrestin2S and Clathrin Deposited 2009-02-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–363（363 aa） Fragment：WD domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM bis_tris propane 4 -4.5 M ammonium acetate 4.5% ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.251
3GD1 Structure of an Arrestin/Clathrin complex reveals a novel clathrin binding domain that modulates receptor trafficking Deposited 2009-02-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 1–363（363 aa） Fragment：WD domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；293 K；100mM Bicine, 7% O-(2-aminopropyl)-O'-(2-methoxyethyl)polypropylene glycol 500, 6% polyethylene glycol 8000, 4% acetone, 1% ethylene glycol and 10 mM strontium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.50 Å R-free 0.254
3IYV Clathrin D6 coat as full-length Triskelions Deposited 2010-06-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 216 PDB declaration: 216-meric	Chain A 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain B 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain C 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain D 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain E 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain F 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain G 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain H 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain I 1–1630（1630 aa） Fragment：UNP residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25MM MES；pH 6.5；25MM MES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 7.90 Å
3IYV Clathrin D6 coat as full-length Triskelions Deposited 2010-06-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain B 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain C 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain D 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain E 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain F 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain G 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain H 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain I 1–1630（1630 aa） Fragment：UNP residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25MM MES；pH 6.5；25MM MES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 7.90 Å
3IYV Clathrin D6 coat as full-length Triskelions Deposited 2010-06-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain B 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain C 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain D 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain E 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain F 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain G 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain H 1–1630（1630 aa） Fragment：UNP residues 1-1630 Chain I 1–1630（1630 aa） Fragment：UNP residues 1-1630	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25MM MES；pH 6.5；25MM MES cryo-EM vitrification conditions Cryogen ETHANE；VITRIFIED	Resolution 7.90 Å
3LVG Crystal structure of a clathrin heavy chain and clathrin light chain complex Deposited 2010-02-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1074–1675（602 aa） Chain B 1074–1675（602 aa） Chain C 1074–1675（602 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；200mM citrate, 16-22% glycerol, 2% trifluoroethanol, vapor diffusion, hanging drop, temperature 298K	Resolution 7.94 Å R-free 0.425
3LVH Crystal structure of a clathrin heavy chain and clathrin light chain complex Deposited 2010-02-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1074–1675（602 aa） Fragment：Hub Chain B 1074–1675（602 aa） Fragment：Hub Chain C 1074–1675（602 aa） Fragment：Hub	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；200mM citrate, 16-22% glycerol, 2% trifluoroethanol, vapor diffusion, hanging drop, temperature 298K	Resolution 9.00 Å R-free 0.487
3QIL Crystal structure analysis of the clathrin trimerization domain Deposited 2011-01-27	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 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain B 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain C 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN	Mutation：C1528A, T1585L Mutation：C1528A, T1585L Mutation：C1528A, T1585L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；NaCl, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.92 Å R-free 0.386
3QIL Crystal structure analysis of the clathrin trimerization domain Deposited 2011-01-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain E 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain F 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN	Mutation：C1528A, T1585L Mutation：C1528A, T1585L Mutation：C1528A, T1585L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；NaCl, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.92 Å R-free 0.386
3QIL Crystal structure analysis of the clathrin trimerization domain Deposited 2011-01-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain G 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain H 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain I 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN	Mutation：C1528A, T1585L Mutation：C1528A, T1585L Mutation：C1528A, T1585L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；NaCl, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.92 Å R-free 0.386
3QIL Crystal structure analysis of the clathrin trimerization domain Deposited 2011-01-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain J 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain K 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain L 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN	Mutation：C1528A, T1585L Mutation：C1528A, T1585L Mutation：C1528A, T1585L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；NaCl, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.92 Å R-free 0.386
3QIL Crystal structure analysis of the clathrin trimerization domain Deposited 2011-01-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain M 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain N 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain O 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN	Mutation：C1528A, T1585L Mutation：C1528A, T1585L Mutation：C1528A, T1585L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；NaCl, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.92 Å R-free 0.386
3QIL Crystal structure analysis of the clathrin trimerization domain Deposited 2011-01-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain P 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain Q 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain R 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN	Mutation：C1528A, T1585L Mutation：C1528A, T1585L Mutation：C1528A, T1585L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；NaCl, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.92 Å R-free 0.386
3QIL Crystal structure analysis of the clathrin trimerization domain Deposited 2011-01-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 7 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain S 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain T 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain U 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN	Mutation：C1528A, T1585L Mutation：C1528A, T1585L Mutation：C1528A, T1585L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；NaCl, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.92 Å R-free 0.386
3QIL Crystal structure analysis of the clathrin trimerization domain Deposited 2011-01-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 8 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain V 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain W 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN Chain X 1521–1624（104 aa） Fragment：CLATHRIN TRIMERIZATION DOMAIN	Mutation：C1528A, T1585L Mutation：C1528A, T1585L Mutation：C1528A, T1585L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；NaCl, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.92 Å R-free 0.386
5M5R Clathrin heavy chain N-terminal domain bound to beta2 adaptin clathrin box motif Deposited 2016-10-22	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–363（363 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；293 K；1 uL protein plus peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 2 uL reservoir equilibrated against a 200 uL reservoir of 0.94 M sodium malonate pH 6.7	Resolution 1.76 Å R-free 0.205
5M5S Clathrin heavy chain N-terminal domain bound to amphiphysin clathrin-box motif Deposited 2016-10-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–363（363 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1 uL protein:peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 2 uL reservoir equilibrated against a 200 uL reservoir of 0.85 M sodium malonate pH 7.5	Resolution 1.88 Å R-free 0.234
5M5S Clathrin heavy chain N-terminal domain bound to amphiphysin clathrin-box motif Deposited 2016-10-22	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–363（363 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1 uL protein:peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 2 uL reservoir equilibrated against a 200 uL reservoir of 0.85 M sodium malonate pH 7.5	Resolution 1.88 Å R-free 0.234
5M5T Clathrin heavy chain N-terminal domain bound to a non-natural clathrin-box motif peptide (Amph4T1) Deposited 2016-10-22	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–363（363 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1 uL protein:peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 1 uL reservoir equilibrated against a 200 uL reservoir of 1.1 M sodium malonate pH 8.0	Resolution 1.70 Å R-free 0.185
5M5T Clathrin heavy chain N-terminal domain bound to a non-natural clathrin-box motif peptide (Amph4T1) Deposited 2016-10-22	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–363（363 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1 uL protein:peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 1 uL reservoir equilibrated against a 200 uL reservoir of 1.1 M sodium malonate pH 8.0	Resolution 1.70 Å R-free 0.185
5M5V Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 2) Deposited 2016-10-22	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–363（363 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；200 nL protein:peptide (20 mg/mL NTD and 3.6 mM peptide) plus 400 nL reservoir equilibrated against a 80 uL reservoir of 1.75 M sodium malonate pH 7.0	Resolution 1.96 Å R-free 0.193
5M5V Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 2) Deposited 2016-10-22	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–363（363 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；200 nL protein:peptide (20 mg/mL NTD and 3.6 mM peptide) plus 400 nL reservoir equilibrated against a 80 uL reservoir of 1.75 M sodium malonate pH 7.0	Resolution 1.96 Å R-free 0.193
5M61 Clathrin heavy chain N-terminal domain bound to an extended amphiphysin clathrin-box motif Deposited 2016-10-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–363（363 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；293 K；1 uL protein:peptide mix (14 mg/mL protein, 3.4 mM peptide) plus 2 uL of 1.04 M sodium malonate pH 7.1, 0.2 M sodium perchlorate equilibrated against a 200 uL reservoir of 1.15 M sodium malonate pH 7.1	Resolution 1.84 Å R-free 0.182
5M61 Clathrin heavy chain N-terminal domain bound to an extended amphiphysin clathrin-box motif Deposited 2016-10-23	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–363（363 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；293 K；1 uL protein:peptide mix (14 mg/mL protein, 3.4 mM peptide) plus 2 uL of 1.04 M sodium malonate pH 7.1, 0.2 M sodium perchlorate equilibrated against a 200 uL reservoir of 1.15 M sodium malonate pH 7.1	Resolution 1.84 Å R-free 0.182
6WCJ Asymmetric vertex of the clathrin minicoat cage Deposited 2020-03-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 1–1675（1675 aa） Chain C 1–1675（1675 aa） Chain D 1–1675（1675 aa） Chain G 1–1675（1675 aa） Chain H 1–1675（1675 aa） Chain I 1–1675（1675 aa） Chain K 1–1675（1675 aa） Chain L 1–1675（1675 aa） Chain M 1–1675（1675 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.30 Å
9F8T Clathrin terminal domain complexed with C-terminus of AAK1L Deposited 2024-05-07	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–363（363 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；20% PEG 3,350; 100 mM Bis-Tris propane, pH 6.0; 200 mM sodium citrate; 10 mM DTT	Resolution 1.71 Å R-free 0.209

17 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CLH1_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–365； UniProt 1–363 Author chain B； PDBConstruct 3–365； UniProt 1–363

Large delta antigen

OrganismNot specified

UniProt P0C6L6

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 196–204 Chain G； UniProt 196–204	Fragment：Clathrin-box motif, UNP Residues 197-203	Clathrin heavy chain 1 × 1 （P49951） GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；400 nL protein:peptide mix (14 mg/mL NTD and 3.4 mM) plus 200 nL reservoir equilibrated against a 80 uL reservoir of 1.21 M sodium malonate pH 7.0	Resolution 2.15 Å R-free 0.207
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 196–204 Chain H； UniProt 196–204	Fragment：Clathrin-box motif, UNP Residues 197-203	Clathrin heavy chain 1 × 1 （P49951）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；400 nL protein:peptide mix (14 mg/mL NTD and 3.4 mM) plus 200 nL reservoir equilibrated against a 80 uL reservoir of 1.21 M sodium malonate pH 7.0	Resolution 2.15 Å R-free 0.207

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	LHDAG_HDVIT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–9； UniProt 196–204 Author chain F； PDBConstruct 1–9； UniProt 196–204 Author chain G； PDBConstruct 1–9； UniProt 196–204 Author chain H； PDBConstruct 1–9； UniProt 196–204

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5m5u
Deposition date deposition_date	2016-10-22
Structure title title	Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 1)
Keywords keywords	endocytosis, hepatitis delta virus, HDAg-L; ENDOCYTOSIS
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	31.34 Å
Radius of gyration Rg (electron density) rg_electron	30.82 Å
Forward intensity I(0) i0	105775000.00
Molecular weight molecular_weight	82934.0 kDa
Excluded volume excluded_volume	104410 Å³
Envelope volume envelope_volume	127910 Å³
Hydration-shell volume shell_volume	35739 Å³
Envelope diameter envelope_diameter	113.9 Å
Shell Rg shell_rg	36.69 Å
Envelope Rg envelope_rg	30.84 Å
Shape Rg shape_rg	30.79 Å
Total Rg total_rg	31.40 Å
Total atoms total_atoms	5828
Residues n_residues	746
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	110.2 Å
Rg (real space) rg_real	31.49 Å
Rg uncertainty (real space) rg_real_error	0.96 Å
I(0) (real space) i0_real	1.0580e+08
I(0) uncertainty (real space) i0_real_error	1.6240e+06
Rg (reciprocal space) rg_reciprocal	31.43 Å
I(0) (reciprocal space) i0_reciprocal	105800000.0000
Solution quality estimate total_estimate	0.8420
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	32.4 Å
Skewness Skewness skewness	0.465
Kurtosis Kurtosis kurtosis	-0.378
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21700000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.709; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.823; Smooth: 0.992

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Clathrin heavy chain 1
Molecular weight formula_weight	40540.5 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	6277

GSMAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSNPIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWISLNTVALVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVVGAMQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGNQPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRISGETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNLAGAEEL

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	Bovine
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Large delta antigen
Molecular weight formula_weight	964.0 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

SDILFPADS

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	437

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5m5uA00
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	5m5uB00
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	136.230 Å
Unit-cell length b length_b	131.190 Å
Unit-cell length c length_c	77.870 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.61 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	48.370 Å
R factor r_factor	0.1770
R_work r_work	0.1754
R_free r_free	0.2070

fit	/app/data/saxs_computation/m5/5m5u/5m5u.fit
pddf	/app/data/pr_computation/m5/5m5u/5m5u.pr.out
profile	/app/data/saxs_computation/m5/5m5u/5m5u.dat

Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 1)

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

Clathrin heavy chain 1

State in the Current Structure

Other States of the Same Protein in the Database

Large delta antigen

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)