5UDH: HHARI/ARIH1-UBCH7~Ubiquitin

HHARI/ARIH1-UBCH7~Ubiquitin. Determined by X-ray diffraction at 3.24 Å resolution. Released 14 Jun 2017.

Method: X-ray diffraction
Resolution: 3.24 Å
Organism: Homo sapiens
Chains: 5
Atoms: 9,178
Mol. weight: 157.62 kDa
Ligands: ZN
Released: 14 Jun 2017

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

Secondary structure: helices and β-sheets

5UDH contains 50 α-helices and 56 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: 19 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	101-105	5	1
α-helix	106-124	19
α-helix	128-137	10
α-helix	142-149	8
α-helix	154-161	8
α-helix	195-197	3
β-strand	198-200	3	2
β-strand	206-208	3	2
α-helix	209-219	11
β-strand	229-230	2	3
β-strand	239-240	2	3
α-helix	241	1
α-helix	242-248	7
α-helix	252-268	17
β-strand	273-275	3	1
β-strand	283-287	5	1
β-strand	294-296	3	4
β-strand	302-304	3	4
β-strand	310	1	4
α-helix	311	1
α-helix	317-325	9
β-strand	341-343	3	5
β-strand	350-352	3	5
β-strand	359-361	3	6
β-strand	370-372	3	6
β-strand	378	1	6
α-helix	411-432	22
α-helix	434-444	11
α-helix	452-480	29
α-helix	482	1
β-strand	483	1	7
α-helix	484	1
α-helix	486-507	22
α-helix	508-512	5
α-helix	521-548	28
β-strand	553	1	7

Chain B: 18 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	101-105	5	10
α-helix	106-124	19
α-helix	128-137	10
α-helix	142-149	8
α-helix	195-197	3
β-strand	198-200	3	11
β-strand	206-208	3	11
α-helix	209-219	11
β-strand	230	1	12
α-helix	238	1
β-strand	239	1	12
α-helix	240-241	2
α-helix	242-246	5
α-helix	252-261	10
α-helix	264-268	5
β-strand	275	1	10
β-strand	283-287	5	10
β-strand	294-296	3	13
β-strand	302-304	3	13
β-strand	310	1	13
α-helix	317-326	10
β-strand	341-343	3	14
β-strand	350-352	3	14
β-strand	359-361	3	15
β-strand	370-372	3	15
β-strand	378	1	15
α-helix	410-432	23
α-helix	435-438	4
α-helix	458-480	23
α-helix	482-484	3
α-helix	487-507	21
α-helix	508-512	5
α-helix	520-549	30

Chain C: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	1-17	17
β-strand	22-27	6	8
β-strand	35-39	5	8
β-strand	51-54	4	8
β-strand	69-70	2	8
β-strand	76	1	9
β-strand	79	1	9
β-strand	84	1	8
β-strand	85	1	9
α-helix	88-90	3
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-147	15

Chain D: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	0-17	18
β-strand	22-23	2	16
β-strand	34-39	6	16
α-helix	46-48	3
β-strand	50	1	17
β-strand	51-56	6	16
β-strand	67-70	4	16
β-strand	79	1	18
β-strand	84	1	16
β-strand	85	1	18
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-147	15
β-strand	149	1	17
α-helix	150-152	3

Chain E: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	19
β-strand	13-16	4	19
β-strand	22	1	20
α-helix	23-34	12
β-strand	43-45	3	19
β-strand	48-49	2	19
α-helix	50-51	2
β-strand	55	1	20
β-strand	66-69	4	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase ARIH1	A, B	protein	470	Homo sapiens	Q9Y4X5 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 L3	C, D	protein	156	Homo sapiens	P68036 (AlphaFold model)
Ubiquitin C variant	E	protein	82	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5UDH_1 E3 ubiquitin-protein ligase ARIH1 (chains A, B)
GSGPGHEQEEDYRYEVLTAEQILQHMVECIREVNEVIQNPATITRILLSHFNWDKEKLME
RYFDGNLEKLFAECHVINPSKKSRTRQMNTRSSAQDMPCQICYLNYPNSYFTGLECGHKF
CMQCWSEYLTTKIMEEGMGQTISCPAHGCDILVDDNTVMRLITDSKVKLKYQHLITNSFV
ECNRLLKWCPAPDCHHVVKVQYPDAKPVRCKCGRQFCFNCGENWHDPVKCKWLKKWIKKC
DDDSETSNWIAANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGSAWY
NCNRYNEDDAKAARDAQERSRAALQRYLFYCNRYMNHMQSLRFEHKLYAQVKQKMEEMQQ
HNMSWIEVQFLKKAVDVLCQCRATLMYTYVFAFYLKKNNQSIIFENNQADLENATEVLSG
YLERDISQDSLQDIKQKVQDKYRYCESRRRVLLQHVHEGYEKDLWEYIED

Sequence of entity 2 (C, D), FASTA

>5UDH_2 Ubiquitin-conjugating enzyme E2 L3 (chains C, D)
GSMAASRRLMKELEEIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFP
AEYPFKPPKITFKTKIYHPNIDEKGQVKLPVISAENWKPATKTDQVIQSLIALVNDPQPE
HPLRADLAEEYSKDRKKFCKNAEEFTKKYGEKRPVD

Sequence of entity 3 (E), FASTA

>5UDH_3 Ubiquitin C variant (chains E)
HHHHHHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGR
TLSDYNIQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	12

Primary citation

Structural Studies of HHARI/UbcH7Ub Reveal Unique E2Ub Conformational Restriction by RBR RING1. Dove, K.K., Olszewski, J.L., Martino, L. et al. Structure (2017) 25:890-900.e5. DOI 10.1016/j.str.2017.04.013 · PubMed

Other PDB entries of the same protein (UniProt Q9Y4X5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4KBL 3.3 Å, Structure of HHARI, a RING-IBR-RING ubiquitin ligase: autoinhibition of an…
5TTE 3.5 Å, Crystal Structure of an RBR E3 ubiquitin ligase in complex with an E2-Ub thioester…
7B5N 3.6 Å, Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly:…
7B5S 3.6 Å, Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly:…
4KC9 3.6 Å, Structure of HHARI, a RING-IBR-RING ubiquitin ligase: autoinhibition of an…
7B5L 3.8 Å, Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly:…
7B5M 3.91 Å, Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly:…
1WD2 Solution Structure of the C-terminal RING from a RING-IBR-RING (TRIAD) motif
2M9Y Solution Structure of the Catalytic Domain of HHARI

Browse structure collections

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