6SC6: DAb3/HOIP-RBR apo structure

Name: PDB 6SC6: dAb3/HOIP-RBR apo structure
Published: 2019-11-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

dAb3/HOIP-RBR apo structure. Determined by X-ray diffraction at 2.25 Å resolution. Released 27 Nov 2019.

Method: X-ray diffraction
Resolution: 2.25 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 4,928
Mol. weight: 70.47 kDa
Ligands: ZN
Released: 27 Nov 2019

Explore 6SC6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6SC6 contains 24 α-helices and 41 β-strands across 3 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, 16 β-strands

Element	Residues	Length	Sheet
α-helix	708-710	3
β-strand	712-713	2	1
β-strand	720-721	2	1
α-helix	723-736	14
α-helix	739-741	3
α-helix	758-772	15
α-helix	775-785	11
α-helix	786-790	5
β-strand	796-798	3	2
β-strand	805-807	3	2
β-strand	814-816	3	3
β-strand	823-825	3	3
α-helix	830	1
β-strand	831	1	3
α-helix	832	1
α-helix	834-836	3
α-helix	841-849	9
α-helix	853-857	5
α-helix	860-866	7
β-strand	869-870	2	4
β-strand	877-878	2	4
β-strand	887-889	3	5
β-strand	896-898	3	5
β-strand	904	1	5
β-strand	905-906	2	6
β-strand	923-924	2	6
α-helix	931-934	4
α-helix	939-947	9
β-strand	972-977	6	7
β-strand	980-985	6	7
α-helix	999-1012	14
α-helix	1017-1020	4
α-helix	1023-1029	7
α-helix	1030-1034	5
α-helix	1046-1060	15

Chain B: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	11-12	2	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	46-51	6	10
β-strand	58-60	3	10
β-strand	65	1	8
β-strand	68-73	6	8
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-99	8	10
β-strand	107-110	4	10
β-strand	114-116	3	10
β-strand	117-118	2	9

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	11-12	2	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	45-51	7	10
β-strand	58-60	3	10
α-helix	62-64	3
β-strand	68-73	6	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-99	8	10
β-strand	107-110	4	10
β-strand	114-116	3	10
β-strand	117-118	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RNF31	A	protein	376	Homo sapiens	Q96EP0 (AlphaFold model)
Single domain antibody	B, C	protein	120	synthetic construct

Sequence of entity 1 (A), FASTA

>6SC6_1 E3 ubiquitin-protein ligase RNF31 (chains A)
QECAVCGWALPHNRMQALTSCECTICPDCFRQHFTIALKEKHITDMVCPACGRPDLTDDT
QLLSYFSTLDIQLRESLEPDAYALFHKKLTEGVLMRDPKFLWCAQCSFGFIYEREQLEAT
CPQCHQTFCVRCKRQWEEQHRGRSCEDFQNWKRMNDPEYQAQGLAMYLQENGIDCPKCKF
SYALARGGCMHFHCTQCRHQFCSGCYNAFYAKNKCPEPNCRVKKSLHGHHPRDCLFYLRD
WTALRLQKLLQDNNVMFNTEPPAGARAVPGGGCRVIEQKEVPNGLRDEACGKETPAGYAG
LCQAHYKEYLVSLINAHSLDPATLYEVEELETATERYLHVRPQPLAGEDPPAYQARLLQK
LTEEVPLGQSIPRRRK

Sequence of entity 2 (B, C), FASTA

>6SC6_2 Single domain antibody (chains B, C)
EVQLLESGGGLVQPGGSLRLSCAASGFTFRGYSMAWVRQAPGKGLEWVSTISPIGTYTYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKGSYSRGTPFDYWGQGTLVTVSS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Water and common crystallization additives (CL, SO4) are not listed.

Primary citation

Single-Domain Antibodies as Crystallization Chaperones to Enable Structure-Based Inhibitor Development for RBR E3 Ubiquitin Ligases. Tsai, Y.I., Johansson, H., Dixon, D. et al. Cell Chem Biol (2020) 27:83. DOI 10.1016/j.chembiol.2019.11.007 · PubMed

Other PDB entries of the same protein (UniProt Q96EP0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KC5 1.54 Å, HOIP-HOIPIN1 complex
4LJO 1.56 Å, Structure of an active ligase (HOIP)/ubiquitin transfer complex
7V8F 1.66 Å, Crystal structure of UBE2L3 bound to HOIP RING1 domain.
4P09 1.7 Å, Crystal structure of HOIP PUB domain
9B0B 1.7 Å, Structure of Optineurin bound to HOIP NZF1 domain
9B12 1.81 Å, Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal…
4OWF 2.0 Å, Crystal structure of the NEMO CoZi in complex with HOIP NZF1 domain
4OYK 2.0 Å, Structure of HOIP PUB domain bound to OTULIN PIM
6SC5 2.1 Å, dAb3/HOIP-RBR-Ligand2
6SC8 2.11 Å, dAb3/HOIP-RBR-Ligand4
6KC6 2.12 Å, HOIP-HOIPIN8 complex
4LJP 2.15 Å, Structure of an active ligase (HOIP-H889A)/ubiquitin transfer complex

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