6QNP: Clathrin heavy chain N-terminal domain

Clathrin heavy chain N-terminal domain bound to GTSE1 lidl motif. Determined by X-ray diffraction at 2.7 Å resolution. Released 28 Aug 2019.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 8
Atoms: 12,084
Mol. weight: 190.34 kDa
Released: 28 Aug 2019

Explore 6QNP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6QNP contains 38 α-helices and 124 β-strands across 8 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: 10 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	1
α-helix	15-18	4
β-strand	30-31	2	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	110-113	4	5
β-strand	118-122	5	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
β-strand	152-158	7	6
β-strand	164-172	9	6
β-strand	177-185	9	6
β-strand	190-195	6	6
β-strand	198-205	8	7
α-helix	206	1
β-strand	212-221	10	7
β-strand	226-232	7	7
α-helix	235-237	3
α-helix	241-245	5
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	334-336	3
α-helix	337-341	5
α-helix	345-354	10

Chain B: 9 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	9
α-helix	15-18	4
β-strand	30-31	2	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	110-113	4	13
β-strand	118-122	5	13
β-strand	126-131	6	13
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	164-172	9	14
β-strand	177-185	9	14
β-strand	190-195	6	14
β-strand	198-204	7	15
α-helix	205-206	2
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	345-355	11

Chain C: 10 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	17
α-helix	15-17	3
α-helix	22-24	3
β-strand	30-31	2	18
β-strand	37-44	8	18
β-strand	47-54	8	18
β-strand	62-65	4	18
β-strand	66	1	19
β-strand	70-73	4	20
β-strand	79-84	6	20
β-strand	87-92	6	20
β-strand	97-103	7	20
β-strand	110-113	4	21
β-strand	118-122	5	21
β-strand	126-131	6	21
β-strand	138-143	6	21
α-helix	144-145	2
α-helix	146-148	3
α-helix	151	1
β-strand	152-158	7	22
β-strand	164-173	10	22
β-strand	176-185	10	22
β-strand	190-194	5	22
β-strand	198-204	7	23
α-helix	205-206	2
β-strand	213-220	8	23
β-strand	226-232	7	23
α-helix	241-245	5
β-strand	246-250	5	23
β-strand	261-267	7	24
β-strand	272-277	6	24
β-strand	281-286	6	24
β-strand	292-297	6	24
β-strand	303-309	7	17
β-strand	314-319	6	17
β-strand	323-329	7	17
α-helix	334-336	3
α-helix	337-341	5
α-helix	345-354	10

Chain D: 9 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	25
α-helix	15-17	3
β-strand	30-31	2	26
β-strand	37-44	8	26
β-strand	47-54	8	26
β-strand	62-65	4	26
β-strand	66	1	27
β-strand	70-73	4	28
β-strand	79-84	6	28
β-strand	87-92	6	28
β-strand	97-103	7	28
β-strand	110-113	4	29
β-strand	118-122	5	29
β-strand	126-131	6	29
α-helix	138	1
β-strand	139-143	5	29
α-helix	144-145	2
α-helix	146-148	3
β-strand	152-158	7	30
β-strand	164-171	8	30
β-strand	178-185	8	30
β-strand	190-194	5	30
β-strand	198-204	7	31
β-strand	213-220	8	31
β-strand	226-232	7	31
α-helix	236-237	2
α-helix	241-245	5
β-strand	246-250	5	31
β-strand	261-267	7	32
β-strand	272-277	6	32
β-strand	281-286	6	32
β-strand	292-297	6	32
β-strand	303-309	7	25
β-strand	314-319	6	25
β-strand	323-329	7	25
α-helix	334-337	4
α-helix	338-342	5
α-helix	345-354	10

Chains H and I: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	690	1	3
β-strand	710	1	6

Chains J and K: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	670	1	19
β-strand	710	1	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Clathrin heavy chain 1	A, B, C, D	protein	364	Homo sapiens	Q00610 (AlphaFold model)
G2 and S phase-expressed protein 1	H, I, J, K	protein	67	Homo sapiens	Q9NYZ3 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6QNP_1 Clathrin heavy chain 1 (chains A, B, C, D)
MAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSN
PIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWISLNTVA
LVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVVGA
MQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGN
QPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRISG
ETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNLAGA
EELF

Sequence of entity 2 (H, I, J, K), FASTA

>6QNP_2 G2 and S phase-expressed protein 1 (chains H, I, J, K)
LAVTPDAASQPLIDLPLIDFCDTPEAHVAVGSESRPLIDLMTNTPDMNKNVAKPSPVVGQ
LIDLSSP

Primary citation

Clathrin's adaptor interaction sites are repurposed to stabilize microtubules during mitosis. Rondelet, A., Lin, Y.C., Singh, D. et al. J Cell Biol (2020) 219. DOI 10.1083/jcb.201907083 · PubMed

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

9C0Y 1.4 Å, Clathrin terminal domain complexed with Pitstop 2c
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

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