6W9A: RNF12 RING domain

RNF12 RING domain in complex with Ube2e2. Determined by X-ray diffraction at 2.3 Å resolution. Released 20 May 2020.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,596
Mol. weight: 61.87 kDa
Ligands: ZN
Released: 20 May 2020

Explore 6W9A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W9A contains 22 α-helices and 30 β-strands across 4 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: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	52-69	18
α-helix	71-72	2
β-strand	75-79	5	1
β-strand	86-92	7	1
α-helix	93-94	2
β-strand	103-109	7	1
α-helix	118-119	2
β-strand	120-123	4	1
β-strand	129	1	2
β-strand	132	1	2
β-strand	137	1	1
β-strand	138	1	2
α-helix	141-143	3
α-helix	153-165	13
α-helix	175-183	9
α-helix	185-200	16

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	550-554	5
β-strand	559-560	2	3
α-helix	563-567	5
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	594-603	10
β-strand	606	1	5
β-strand	613	1	5

Chain C: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	50-69	20
α-helix	71-72	2
β-strand	75-79	5	6
β-strand	86-92	7	6
α-helix	93-94	2
β-strand	103-109	7	6
α-helix	118-119	2
β-strand	120-123	4	6
β-strand	129	1	7
β-strand	132	1	7
β-strand	137	1	6
β-strand	138	1	7
α-helix	141-143	3
α-helix	153-165	13
α-helix	175-183	9
α-helix	185-199	15

Chain D: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	550-554	5
β-strand	558-560	3	8
α-helix	563-567	5
β-strand	569-570	2	9
β-strand	575-576	2	9
β-strand	582-585	4	8
β-strand	591-593	3	8
α-helix	594-603	10
β-strand	606	1	10
β-strand	613	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 E2	A, C	protein	177	Homo sapiens	Q96LR5 (AlphaFold model)
E3 ubiquitin-protein ligase RLIM	B, D	protein	98	Homo sapiens	Q9NVW2 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6W9A_1 Ubiquitin-conjugating enzyme E2 E2 (chains A, C)
GPLGSEPEREQVQPKKKEGKISSKTAAKLSTSAKRIQKELAEITLDPPPNCSAGPKGDNI
YEWRSTILGPPGSVYEGGVFFLDITFSPDYPFKPPKVTFRTRIYHCNINSQGVICLDILK
DNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT

Sequence of entity 2 (B, D), FASTA

>6W9A_2 E3 ubiquitin-protein ligase RLIM (chains B, D)
GPLGSLAQFFLLNEDDDDQPRGLTKEQIDNLAMRSFGENDALKTCSVCITEYTEGNKLRK
LPCSHEYHVHCIDRWLSENSTCPICRRAVLASGNRESV

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

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 Q96LR5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1Y6L 1.85 Å, Human ubiquitin conjugating enzyme E2E2
9BJZ 2.83 Å, Structure of the human DDD-Ube2e2 complex
9LTO 2.92 Å, Cryo-EM structure of DDB1-DDA1-DET1-Ube2e2 complex
9LTR 3.03 Å, Cryo-EM structure of dimeric DDB1-DDA1-DET1-Ube2e2-COP1 complex
9LTZ 3.26 Å, protein structure of DDB1-DDA1-DET1-Ube2e2 complex
9LU1 3.62 Å, protein structure of DDB1-DDA1-DET1-Ube2e2 bound to COP1 dimer
9W90 3.7 Å, DDB1-DDA1-DET1-Ube2e2-COP1-c-Jun-STK40 complex
9M0Y 4.25 Å, Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 2)
9LUL 4.99 Å, Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 1)

Browse structure collections

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