6W9D: RNF12 RING domain

RNF12 RING domain in complex with a Ube2d2~Ub conjugate. Determined by X-ray diffraction at 3.19 Å resolution. Released 20 May 2020.

Method: X-ray diffraction
Resolution: 3.19 Å
Organism: Homo sapiens
Chains: 9
Atoms: 6,872
Mol. weight: 113.89 kDa
Ligands: ZN
Released: 20 May 2020

Explore 6W9D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W9D contains 34 α-helices and 64 β-strands across 9 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.

Chains A and D: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
β-strand	21-25	5	1
β-strand	32-38	7	1
α-helix	39-40	2
β-strand	49-55	7	1
β-strand	66-69	4	1
β-strand	78	1	2
β-strand	83	1	1
β-strand	84	1	2
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Chain B: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	551-554	4
β-strand	557-559	3	3
β-strand	570	1	4
β-strand	575	1	4
β-strand	583-585	3	3
β-strand	591-593	3	3
α-helix	594-601	8
β-strand	606	1	5
β-strand	613	1	5

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	6
β-strand	12-16	5	6
β-strand	22	1	7
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	6
β-strand	48-49	2	6
α-helix	50-51	2
β-strand	55	1	7
α-helix	57-59	3
β-strand	66-70	5	6

Chain E: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	551-554	4
β-strand	557-560	4	10
β-strand	569-570	2	11
β-strand	575-576	2	11
β-strand	582-585	4	10
β-strand	591-593	3	10
α-helix	594-601	8

Chain F: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	12
β-strand	12-16	5	12
β-strand	22	1	13
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	12
β-strand	48-49	2	12
β-strand	52	1	14
β-strand	54	1	14
β-strand	55	1	13
α-helix	56-59	4
β-strand	66-69	4	12

Chain G: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
β-strand	21-25	5	15
β-strand	32-38	7	15
α-helix	39-40	2
β-strand	49-55	7	15
α-helix	56-57	2
β-strand	66-69	4	15
β-strand	75	1	16
β-strand	78	1	16
β-strand	83	1	15
β-strand	84	1	16
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Chain H: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	550-554	5
β-strand	557-560	4	17
β-strand	569-570	2	18
β-strand	575-576	2	18
β-strand	582-585	4	17
β-strand	591-593	3	17
α-helix	594-601	8
β-strand	606	1	19
β-strand	613	1	19

Chain I: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	20
β-strand	12-16	5	20
β-strand	22	1	21
α-helix	23-33	11
α-helix	38-40	3
β-strand	41-45	5	20
β-strand	48-49	2	20
β-strand	55	1	21
β-strand	66-71	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D2	A, D, G	protein	155	Homo sapiens	P62837 (AlphaFold model)
E3 ubiquitin-protein ligase RLIM	B, E, H	protein	98	Homo sapiens	Q9NVW2 (AlphaFold model)
Ubiquitin	C, F, I	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, D, G), FASTA

>6W9D_1 Ubiquitin-conjugating enzyme E2 D2 (chains A, D, G)
MALKRIHKELNDLARDPPAQSRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDY
PFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSISSLLSDPNPDDPLV
PEIARIYKTDREKYNRIAREWTQKYAMLEHHHHHH

Sequence of entity 2 (B, E, H), FASTA

>6W9D_2 E3 ubiquitin-protein ligase RLIM (chains B, E, H)
GPLGSLAQFFLLNEDDDDQPRGLTKEQIDNLAMRSFGENDALKTCSVCITEYTEGNKLRK
LPCSHEYHVHCIDRWLSENSTCPICRRAVLASGNRESV

Sequence of entity 3 (C, F, I), FASTA

>6W9D_3 Ubiquitin (chains C, F, I)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Water and common crystallization additives (IOD) are not listed.

Primary citation

The RING Domain of RING Finger 12 Efficiently Builds Degradative Ubiquitin Chains. Middleton, A.J., Zhu, J., Day, C.L. J Mol Biol (2020) 432:3790-3801. DOI 10.1016/j.jmb.2020.05.001 · PubMed

Other PDB entries of the same protein (UniProt P62837 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GLS 1.25 Å, Crystal Structure of Human UBCH5B C85E
2ESK 1.36 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type
6SQO 1.41 Å, Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub
2ESQ 1.44 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ser94Gly
2ESO 1.5 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ile37Ala
2ESP 1.52 Å, Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala
4V3L 1.53 Å, RNF38-UB-UbcH5B-Ub complex
7AI0 1.56 Å, Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal…
5D1M 1.58 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A)
3L1Y 1.6 Å, Crystal structure of human UBC4 E2 conjugating enzyme
5D1L 1.62 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (Y165A)
6HPR 1.7 Å, Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub

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