6SQR: Cat MDM2-S429E RING domain

Crystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub. Determined by X-ray diffraction at 2.18 Å resolution. Released 6 May 2020.

Method: X-ray diffraction
Resolution: 2.18 Å
Organisms: Felis catus, Homo sapiens
Chains: 12
Atoms: 9,560
Mol. weight: 132.41 kDa
Ligands: ZN
Released: 6 May 2020

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

Secondary structure: helices and β-sheets

6SQR contains 51 α-helices and 85 β-strands across 12 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: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	432-435	4
β-strand	448-452	5	1
β-strand	455-460	6	1
α-helix	462-470	9
β-strand	484-489	6	1

Chain B: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
β-strand	21-25	5	2
β-strand	32-38	7	2
α-helix	39-40	2
β-strand	49-55	7	2
α-helix	64-65	2
β-strand	66-69	4	2
β-strand	75	1	3
β-strand	78	1	3
β-strand	83	1	2
β-strand	84	1	3
β-strand	86	1	4
α-helix	87-89	3
α-helix	99-110	12
α-helix	121-129	9
α-helix	131-145	15

Chain C: 3 helices, 8 β-strands

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

Chain D: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	432-435	4
β-strand	448-452	5	1
β-strand	455-460	6	1
α-helix	462-470	9
β-strand	474	1	7
β-strand	481	1	7
β-strand	484-489	6	1

Chain E: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
β-strand	21-26	6	8
β-strand	29-38	10	8
α-helix	39-40	2
β-strand	49-55	7	8
α-helix	64-65	2
β-strand	66-69	4	8
β-strand	78	1	9
β-strand	83	1	8
β-strand	84	1	9
β-strand	86	1	10
α-helix	87-89	3
α-helix	99-110	12
α-helix	121-129	9
α-helix	131-145	15

Chain F: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	11
β-strand	12-17	6	11
β-strand	22	1	12
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	11
β-strand	48-49	2	11
α-helix	50-51	2
β-strand	55	1	12
β-strand	66-71	6	11
β-strand	75	1	10

Chain G: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	432-435	4
β-strand	437	1	13
β-strand	445	1	13
β-strand	448-452	5	14
β-strand	455-457	3	14
α-helix	462-470	9
β-strand	474	1	15
β-strand	481	1	15
β-strand	484-489	6	14

Chain H: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
β-strand	21-25	5	16
β-strand	32-38	7	16
α-helix	39-40	2
β-strand	49-55	7	16
α-helix	64-65	2
β-strand	66-69	4	16
β-strand	75	1	17
β-strand	78	1	17
β-strand	83	1	16
β-strand	84	1	17
β-strand	86	1	18
α-helix	87-89	3
α-helix	99-109	11
α-helix	121-129	9
α-helix	131-145	15

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase Mdm2	A	protein	69	Felis catus	Q7YRZ8 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 D2	B, E, H, K	protein	146	Homo sapiens	P62837 (AlphaFold model)
Ubiquitin-40S ribosomal protein S27a	C, F, L	protein	77	Homo sapiens	P62979 (AlphaFold model)
E3 ubiquitin-protein ligase Mdm2	D, J	protein	64	Felis catus	Q7YRZ8 (AlphaFold model)
E3 ubiquitin-protein ligase Mdm2	G	protein	63	Felis catus	Q7YRZ8 (AlphaFold model)
Polyubiquitin-C	I	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6SQR_1 E3 ubiquitin-protein ligase Mdm2 (chains A)
EEIVEPEFPHNAIEPCVICQTRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPI
QMIVLTYFP

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

>6SQR_2 Ubiquitin-conjugating enzyme E2 D2 (chains B, E, H, K)
ALKRIHKELNDLARDPPAQCRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYP
FKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVP
EIARIYKTDREKYNRIAREWTQKYAM

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

>6SQR_3 Ubiquitin-40S ribosomal protein S27a (chains C, F, L)
SMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY
NIQKESTLHLVLRLRGG

Sequence of entity 4 (D, J), FASTA

>6SQR_4 E3 ubiquitin-protein ligase Mdm2 (chains D, J)
PEFPHNAIEPCVICQTRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVL
TYFP

Sequence of entity 5 (G), FASTA

>6SQR_5 E3 ubiquitin-protein ligase Mdm2 (chains G)
EFPHNAIEPCVICQTRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLT
YFP

Sequence of entity 6 (I), FASTA

>6SQR_6 Polyubiquitin-C (chains I)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Water and common crystallization additives (NO3, EDO) are not listed.

Primary citation

Structural basis for DNA damage-induced phosphoregulation of MDM2 RING domain. Magnussen, H.M., Ahmed, S.F., Sibbet, G.J. et al. Nat Commun (2020) 11:2094-2094. DOI 10.1038/s41467-020-15783-y · PubMed

Other PDB entries of the same protein (UniProt Q7YRZ8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6SQP 1.21 Å, Crystal structure of Cat MDM2-S429E RING domain homodimer
6SQS 1.83 Å, Crystal structure of cat phospho-Ser429 MDM2 RING domain bound to UbcH5B-Ub

Browse structure collections

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