6wcj

Asymmetric vertex of the clathrin minicoat cage

Method: ELECTRON MICROSCOPY D_max: 274.7 Å Quality: GOOD

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

Clathrin heavy chain 1

OrganismNot specified

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 × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count	Chain A； UniProt 1–1675 Chain C； UniProt 1–1675 Chain D； UniProt 1–1675 Chain G； UniProt 1–1675 Chain H； UniProt 1–1675 Chain I； UniProt 1–1675 Chain K； UniProt 1–1675 Chain L； UniProt 1–1675 Chain M； UniProt 1–1675	Not recorded	Clathrin light chain B × 6 （P04975）	ELECTRON MICROSCOPY cryo-EM buffer：pH 6.7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 6.30 Å

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 6WCJ	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 method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 mutation/modification 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 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 mutation/modification Different oligomeric state Different experimental method 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 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 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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 × 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 construct Different mutation/modification Different oligomeric state Different experimental method 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
5M5U Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 1) Deposited 2016-10-22	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 1–363（363 aa）	Not recorded	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
5M5U Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 1) Deposited 2016-10-22	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 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；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
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 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 × 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 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 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 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 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
9F8T Clathrin terminal domain complexed with C-terminus of AAK1L Deposited 2024-05-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 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 36 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 1–1675； UniProt 1–1675 Author chain C； PDBConstruct 1–1675； UniProt 1–1675 Author chain D； PDBConstruct 1–1675； UniProt 1–1675 Author chain G； PDBConstruct 1–1675； UniProt 1–1675 Author chain H； PDBConstruct 1–1675； UniProt 1–1675 Author chain I； PDBConstruct 1–1675； UniProt 1–1675 Author chain K； PDBConstruct 1–1675； UniProt 1–1675 Author chain L； PDBConstruct 1–1675； UniProt 1–1675 Author chain M； PDBConstruct 1–1675； UniProt 1–1675

Clathrin light chain B

OrganismNot specified

UniProt P04975

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 × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count	Chain B； UniProt 1–228 Chain E； UniProt 1–228 Chain F； UniProt 1–228 Chain J； UniProt 1–228 Chain N； UniProt 1–228 Chain O； UniProt 1–228	Not recorded	Clathrin heavy chain 1 × 9 （P49951）	ELECTRON MICROSCOPY cryo-EM buffer：pH 6.7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 6.30 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6WCJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 89–169（81 aa） Chain E 89–169（81 aa） Chain F 89–169（81 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–169（169 aa） Chain E 1–169（169 aa） Chain F 1–169（169 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 9.00 Å R-free 0.487

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CLCB_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–228； UniProt 1–228 Author chain E； PDBConstruct 1–228； UniProt 1–228 Author chain F； PDBConstruct 1–228； UniProt 1–228 Author chain J； PDBConstruct 1–228； UniProt 1–228 Author chain N； PDBConstruct 1–228； UniProt 1–228 Author chain O； PDBConstruct 1–228； UniProt 1–228

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6wcj
Deposition date deposition_date	2020-03-30
Structure title title	Asymmetric vertex of the clathrin minicoat cage
Keywords keywords	Clathrin coated vesicle, clathrin heavy chain, clathrin light chain, clathrin cage, ENDOCYTOSIS; ENDOCYTOSIS
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	82.08 Å
Radius of gyration Rg (electron density) rg_electron	82.74 Å
Forward intensity I(0) i0	4725800000.00
Molecular weight molecular_weight	584770.0 kDa
Excluded volume excluded_volume	733760 Å³
Envelope volume envelope_volume	1212800 Å³
Hydration-shell volume shell_volume	138860 Å³
Envelope diameter envelope_diameter	274.0 Å
Shell Rg shell_rg	63.74 Å
Envelope Rg envelope_rg	80.94 Å
Shape Rg shape_rg	82.74 Å
Total Rg total_rg	82.38 Å
Total atoms total_atoms	41184
Residues n_residues	5007
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	274.7 Å
Rg (real space) rg_real	86.15 Å
Rg uncertainty (real space) rg_real_error	1.49 Å
I(0) (real space) i0_real	4.7280e+09
I(0) uncertainty (real space) i0_real_error	9.9970e+07
Rg (reciprocal space) rg_reciprocal	80.58 Å
I(0) (reciprocal space) i0_reciprocal	4705000000.0000
Solution quality estimate total_estimate	0.8590
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	57.8 Å
Skewness Skewness skewness	0.388
Kurtosis Kurtosis kurtosis	-0.595
Angular range angular_range	— – 0.0950 Å⁻¹
Current regularization parameter α current_alpha	1.6820
Highest regularization parameter α highest_alpha	507800000.0000
Real-space data points n_real_points	20
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 0.872; Sysdev: 1.000; Positv: 1.000; Valcen: 0.934; Smooth: 0.017

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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 heavy chain 1
Molecular weight formula_weight	191800.3 kDa
Source method src_method	nat
Copy count entity_count	9

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,D,L,M,G,H,I,K
Atom count atom_count	41184

MAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSNPIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWISLNTVALVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVVGAMQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGNQPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRISGETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNLAGAEELFARKFNALFAQGNYSEAAKVAANAPKGILRTPDTIRRFQSVPAQPGQTSPLLQYFGILLDQGQLNKYESLELCRPVLQQGRKQLLEKWLKEDKLECSEELGDLVKSVDPTLALSVYLRANVPNKVIQCFAETGQVQKIVLYAKKVGYTPDWIFLLRNVMRISPDQGQQFAQMLVQDEEPLADITQIVDVFMEYNLIQQCTAFLLDALKNNRPSEGPLQTRLLEMNLMHAPQVADAILGNQMFTHYDRAHIAQLCEKAGLLQRALEHFTDLYDIKRAVVHTHLLNPEWLVNYFGSLSVEDSLECLRAMLSANIRQNLQICVQVASKYHEQLSTQSLIELFESFKSFEGLFYFLGSIVNFSQDPDVHFKYIQAACKTGQIKEVERICRESNCYDPERVKNFLKEAKLTDQLPLIIVCDRFDFVHDLVLYLYRNNLQKYIEIYVQKVNPSRLPVVIGGLLDVDCSEDVIKNLILVVRGQFSTDELVAEVEKRNRLKLLLPWLEARIHEGCEEPATHNALAKIYIDSNNNPERFLRENPYYDSRVVGKYCEKRDPHLACVAYERGQCDLELINVCNENSLFKSLSRYLVRRKDPELWGSVLLESNPYRRPLIDQVVQTALSETQDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSEHRNLQNLLILTAIKADRTRVMEYINRLDNYDAPDIANIAISNELFEEAFAIFRKFDVNTSAVQVLIEHIGNLDRAYEFAERCNEPAVWSQLAKAQLQKGMVKEAIDSYIKADDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLAELEEFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYLEFKPLLLNDLLMVLSPRLDHTRAVNYFSKVKQLPLVKPYLRSVQNHNNKSVNESLNNLFITEEDYQALRTSIDAYDNFDNISLAQRLEKHELIEFRRIAAYLFKGNNRWKQSVELCKKDSLYKDAMQYASESKDTELAEELLQWFLQEEKRECFGACLFTCYDLLRPDVVLETAWRHNIMDFAMPYFIQVMKEYLTKVDKLDASESLRKEEEQATETQPIVYGQPQLMLTAGPSVAVPPQAPFGYGYTAPAYGQPQPGFGYSM

Entity 2 Entity 2 polymer

Description description	Clathrin light chain B
Molecular weight formula_weight	25109.4 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,F,O,J,N

MADDFGFFSSSESGAPEAAEEDPAAAFLAQQESEIAGIENDEGFGAPAGSQGGLAQPGPASGASEDMGATVNGDVFQEANGPADGYAAIAQADRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFYQQPDADIIGYVASEEAFVKESKEETPGTEWEKVAQLCDFNPKSSKQCKDVSRLRSVLMSLKQTPLSR

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8. Citations (1)

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Resolution resolution	6.30 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	305413

fit	/app/data/saxs_computation/wc/6wcj/6wcj.fit
pddf	/app/data/pr_computation/wc/6wcj/6wcj.pr.out
profile	/app/data/saxs_computation/wc/6wcj/6wcj.dat

Asymmetric vertex of the clathrin minicoat cage

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

Clathrin light chain B

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)