9C0Y: Clathrin terminal domain

Name: PDB 9C0Y: Clathrin terminal domain complexed with Pitstop 2c
Published: 2024-06-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: endocytosis

Clathrin terminal domain complexed with Pitstop 2c. Determined by X-ray diffraction at 1.4 Å resolution. Released 26 Jun 2024.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,227
Mol. weight: 42.45 kDa
Ligands: A1ATR
Released: 26 Jun 2024

Explore 9C0Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C0Y contains 11 α-helices and 28 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 11 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	1
α-helix	15-18	4
α-helix	22-24	3
β-strand	30-34	5	2
β-strand	37-44	8	2
β-strand	47-54	8	2
β-strand	62-64	3	2
β-strand	70-73	4	3
β-strand	79-84	6	3
β-strand	87-92	6	3
β-strand	97-103	7	3
β-strand	108-113	6	4
β-strand	118-123	6	4
β-strand	126-131	6	4
α-helix	136-138	3
β-strand	139-143	5	4
α-helix	144-145	2
α-helix	146-148	3
α-helix	151	1
β-strand	152-158	7	5
β-strand	164-173	10	5
β-strand	176-185	10	5
β-strand	190-194	5	5
β-strand	198-204	7	6
β-strand	213-222	10	6
β-strand	225-232	8	6
α-helix	235-237	3
α-helix	240-245	6
β-strand	246-249	4	6
α-helix	254-256	3
β-strand	261-267	7	7
β-strand	272-277	6	7
β-strand	281-286	6	7
β-strand	292-297	6	7
β-strand	303-309	7	1
β-strand	314-319	6	1
β-strand	323-329	7	1
α-helix	334-340	7
α-helix	345-354	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Clathrin heavy chain 1	A	protein	369	Homo sapiens	Q00610 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9C0Y_1 Clathrin heavy chain 1 (chains A)
GSPEFMAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDM
NDPSNPIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWIS
LNTVALVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQN
RVVGAMQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGT
PPTGNQPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYM
NRISGETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRN
NLAGAEELF

Ligands and cofactors

ID	Name	Formula	Copies
A1ATR	N-{(5Z)-4-oxo-5-[(2-phenoxyphenyl)methylidene]-4,5-dihydro-1,3-thiazol-2-yl}nap…	C26 H18 N2 O4 S2	1

Water and common crystallization additives (DMS, PEG, EDO, GOL, ACT) are not listed.

Primary citation

Next-generation small molecule inhibitors of clathrin function acutely inhibit endocytosis. Horatscheck, A., Krauss, M., Bulut, H. et al. Structure (2025) 33:878. DOI 10.1016/j.str.2025.02.011 · PubMed

Other PDB entries of the same protein (UniProt Q00610 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9C0Z 1.51 Å, Clathrin terminal domain complexed with pitstop 2d
6E4L 1.6 Å, The structure of the N-terminal domain of human clathrin heavy chain 1 (nTD) in complex…
4G55 1.69 Å, Clathrin terminal domain complexed with pitstop 2
2XZG 1.7 Å, Clathrin Terminal Domain Complexed with Pitstop 1
7BN2 1.97 Å, Clathrin heavy chain N-terminal domain bound to Non structured protein 3 from Eastern…
7BN1 1.97 Å, Clathrin heavy chain N-terminal domain complexed with peptide from Protein mu-NS of…
6QNN 2.03 Å, Clathrin heavy chain N-terminal domain bound to GTSE1 lidl motif
7ZX4 2.08 Å, Clathrin N-terminal domain in complex with a HURP phospho-peptide
6QNP 2.7 Å, Clathrin heavy chain N-terminal domain bound to GTSE1 lidl motif

Browse structure collections

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