4V3L: RNF38-UB-UbcH5B-Ub complex

RNF38-UB-UbcH5B-Ub complex. Determined by X-ray diffraction at 1.53 Å resolution. Released 8 Apr 2015.

Method: X-ray diffraction
Resolution: 1.53 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 3,308
Mol. weight: 43.88 kDa
Ligands: ZN
Released: 8 Apr 2015

Explore 4V3L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V3L contains 16 α-helices and 31 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: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
β-strand	21-26	6	1
β-strand	29-38	10	1
α-helix	39-40	2
β-strand	49-55	7	1
α-helix	64-65	2
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
β-strand	86	1	3
α-helix	87-89	3
α-helix	99-110	12
α-helix	121-129	9
α-helix	131-145	15

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	4
β-strand	12-17	6	4
β-strand	22	1	5
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	4
β-strand	48-49	2	4
α-helix	50-51	2
β-strand	55	1	5
α-helix	57-59	3
β-strand	66-71	6	4
β-strand	75	1	3

Chain C: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	398-400	3	6
β-strand	412-413	2	7
β-strand	418-419	2	7
β-strand	425-428	4	6
β-strand	434-436	3	6
α-helix	437-446	10
β-strand	449	1	8
β-strand	456	1	8

Chain D: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	9
β-strand	12-17	6	9
β-strand	22	1	10
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	9
β-strand	48-49	2	9
α-helix	50-51	2
β-strand	55	1	10
α-helix	57-59	3
β-strand	66-70	5	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D2	A	protein	146	HOMO SAPIENS	P62837 (AlphaFold model)
Polyubiquitin-C	B, D	protein	81	HOMO SAPIENS	P0CG48 (AlphaFold model)
E3 ubiquitin-protein ligase RNF38	C	protein	79	HOMO SAPIENS	Q9H0F5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4V3L_1 UBIQUITIN-CONJUGATING ENZYME E2 D2 (chains A)
ALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYP
FKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVP
EIARIYKTDREKYNRIAREWTQKYAM

Sequence of entity 2 (B, D), FASTA

>4V3L_2 POLYUBIQUITIN-C (chains B, D)
GSGGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRT
LSDYNIQKESTLHLVLRLRGG

Sequence of entity 3 (C), FASTA

>4V3L_3 E3 UBIQUITIN-PROTEIN LIGASE RNF38 (chains C)
GSTKADIEQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKA
NRTCPICRADASEVHRDSE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

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

Primary citation

Activation of a Primed Ring E3-E2-Ubiquitin Complex by Non-Covalent Ubiquitin. Buetow, L., Gabrielsen, M., Anthony, N.G. et al. Mol Cell (2015) 58:297. DOI 10.1016/J.MOLCEL.2015.02.017 · 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
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
8GBQ 1.74 Å, Structure of RNF125 in complex with UbcH5b

Browse structure collections

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