5M5U: Clathrin heavy chain N-terminal domain

Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 1). Determined by X-ray diffraction at 2.15 Å resolution. Released 23 Nov 2016.

Method: X-ray diffraction
Resolution: 2.15 Å
Organisms: Bos taurus, Hepatitis delta virus (ISOLATE ITALIAN)
Chains: 6
Atoms: 6,277
Mol. weight: 85.03 kDa
Released: 23 Nov 2016

Explore 5M5U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M5U contains 19 α-helices and 61 β-strands across 5 chains. 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: 9 helices, 29 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	62-65	4	2
β-strand	66	1	3
β-strand	70-73	4	4
β-strand	79-84	6	4
β-strand	87-92	6	4
β-strand	97-103	7	4
β-strand	108-113	6	5
β-strand	118-123	6	5
β-strand	126-131	6	5
α-helix	136-138	3
β-strand	139-143	5	5
α-helix	144-145	2
α-helix	146-148	3
α-helix	151	1
β-strand	152-158	7	6
β-strand	164-173	10	6
β-strand	176-185	10	6
β-strand	190-194	5	6
β-strand	198-204	7	7
β-strand	213-222	10	7
β-strand	225-232	8	7
α-helix	240-245	6
β-strand	246-250	5	7
β-strand	261-267	7	8
β-strand	272-277	6	8
β-strand	281-286	6	8
β-strand	292-297	6	8
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

Chain B: 10 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	9
α-helix	15-18	4
α-helix	22-24	3
β-strand	30-34	5	10
β-strand	37-44	8	10
β-strand	47-54	8	10
β-strand	62-65	4	10
β-strand	66	1	11
β-strand	70-73	4	12
β-strand	79-84	6	12
β-strand	87-92	6	12
β-strand	97-103	7	12
β-strand	108-113	6	13
β-strand	118-123	6	13
β-strand	126-131	6	13
α-helix	136-138	3
β-strand	139-143	5	13
α-helix	144-145	2
α-helix	146-148	3
α-helix	151	1
β-strand	152-158	7	14
β-strand	164-173	10	14
β-strand	176-185	10	14
β-strand	190-195	6	14
β-strand	198-204	7	15
β-strand	213-222	10	15
β-strand	225-232	8	15
α-helix	235-237	3
α-helix	240-245	6
β-strand	246-250	5	15
β-strand	261-267	7	16
β-strand	272-277	6	16
β-strand	281-286	6	16
β-strand	292-297	6	16
β-strand	303-309	7	9
β-strand	314-319	6	9
β-strand	323-329	7	9
α-helix	334-340	7
α-helix	345-354	10

Chains E and F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	3

Chain H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Clathrin heavy chain 1	A, B	protein	365	Bos taurus	P49951 (AlphaFold model)
Large delta antigen	E, F, G, H	protein	9	Hepatitis delta virus (ISOLATE ITALIAN)	P0C6L6

Sequence of entity 1 (A, B), FASTA

>5M5U_1 Clathrin heavy chain 1 (chains A, B)
GSMAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDP
SNPIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWISLNT
VALVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVV
GAMQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPT
GNQPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRI
SGETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNLA
GAEEL

Sequence of entity 2 (E, F, G, H), FASTA

>5M5U_2 Large delta antigen (chains E, F, G, H)
SDILFPADS

Primary citation

Cellular and viral peptides bind multiple sites on the N-terminal domain of clathrin. Muenzner, J., Traub, L.M., Kelly, B.T. et al. Traffic (2017) 18:44-57. DOI 10.1111/tra.12457 · PubMed

Other PDB entries of the same protein (UniProt P49951 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5M5T 1.7 Å, Clathrin heavy chain N-terminal domain bound to a non-natural clathrin-box motif peptide…
9F8T 1.71 Å, Clathrin terminal domain complexed with C-terminus of AAK1L
5M5R 1.76 Å, Clathrin heavy chain N-terminal domain bound to beta2 adaptin clathrin box motif
5M61 1.84 Å, Clathrin heavy chain N-terminal domain bound to an extended amphiphysin clathrin-box motif
5M5S 1.88 Å, Clathrin heavy chain N-terminal domain bound to amphiphysin clathrin-box motif
5M5V 1.96 Å, Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D…
3GC3 2.2 Å, Crystal Structure of Arrestin2S and Clathrin
1UTC 2.3 Å, Clathrin terminal domain complexed with TLPWDLWTT
1B89 2.6 Å, Clathrin heavy chain proximal leg segment (BOVINE)
3GD1 3.5 Å, Structure of an Arrestin/Clathrin complex reveals a novel clathrin binding domain that…
3QIL 3.92 Å, Crystal structure analysis of the clathrin trimerization domain
6WCJ 6.3 Å, Asymmetric vertex of the clathrin minicoat cage

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