6W7Z: RNF12 RING domain

RNF12 RING domain in complex with Ube2d2. Determined by X-ray diffraction at 1.8 Å resolution. Released 20 May 2020.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,960
Mol. weight: 28.55 kDa
Ligands: ZN
Released: 20 May 2020

Explore 6W7Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W7Z contains 10 α-helices and 15 β-strands across 2 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	0-15	16
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	75	1	2
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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	550-554	5
β-strand	558-560	3	3
α-helix	561-562	2
α-helix	565-567	3
β-strand	569-570	2	4
β-strand	575-576	2	4
β-strand	582-585	4	3
β-strand	591-593	3	3
α-helix	594-601	8
β-strand	606	1	5
β-strand	613	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D2	A	protein	152	Homo sapiens	P62837 (AlphaFold model)
E3 ubiquitin-protein ligase RLIM	B	protein	99	Homo sapiens	Q9NVW2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6W7Z_1 Ubiquitin-conjugating enzyme E2 D2 (chains A)
GPLGSMALKRIHKELNDLARDPPAQSRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIH
FPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSISSLLSDPNP
DDPLVPEIARIYKTDREKYNRIAREWTQKYAM

Sequence of entity 2 (B), FASTA

>6W7Z_2 E3 ubiquitin-protein ligase RLIM (chains B)
GPLGSLAQFFLLNEDDDDQPRGLTKEQIDNLAMRSFGENDALKTCSVCITEYTEGNKLRK
LPCSHEYHVHCIDRWLSENSTCPICRRAVLASGNRESVV

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (GOL) 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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