4XXB: Human MDM2-RPL11

Crystal structure of human MDM2-RPL11. Determined by X-ray diffraction at 2.4 Å resolution. Released 12 Aug 2015.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,628
Mol. weight: 37.42 kDa
Ligands: ZN
Released: 12 Aug 2015

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

Secondary structure: helices and β-sheets

4XXB contains 13 α-helices and 14 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: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	16-25	10	1
α-helix	31-44	14
β-strand	49-52	4	1
β-strand	57	1	2
α-helix	58-60	3
β-strand	62	1	2
β-strand	67-74	8	1
α-helix	76-89	14
β-strand	93-95	3	3
α-helix	96-98	3
β-strand	99	1	1
β-strand	105-109	5	1
α-helix	112-115	4
α-helix	117-119	3
β-strand	128-135	8	1
α-helix	155-158	4
α-helix	159-169	11
β-strand	173-175	3	3
α-helix	176-177	2

Chain B: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	299-301	3
β-strand	303-304	2	4
β-strand	311-312	2	4
β-strand	318	1	5
α-helix	324	1
β-strand	325	1	5
α-helix	326	1
α-helix	331-333	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
60S ribosomal protein L11	A	protein	178	Homo sapiens	P62913 (AlphaFold model)
E3 ubiquitin-protein ligase Mdm2	B	protein	148	Homo sapiens	Q00987 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4XXB_1 60S ribosomal protein L11 (chains A)
MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSF
GIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYD
PSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK

Sequence of entity 2 (B), FASTA

>4XXB_2 E3 ubiquitin-protein ligase Mdm2 (chains B)
SFEEDPEISLADYWKCTSCNEMNPPLPSHCNRCWALRENWLPEDKGKDKGEISEKAKLEN
STQAEEGFDVPDCKKTIVNDSRESCVEENDDKITQASQSQESEDYSQPSTSSSIIYSSQE
DVKEFEREETQDKEESVESSLPLNAIEP

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (IMD, BME) are not listed.

Primary citation

Structure of human MDM2 complexed with RPL11 reveals the molecular basis of p53 activation. Zheng, J., Lang, Y., Zhang, Q. et al. Genes Dev (2015) 29:1524-1534. DOI 10.1101/gad.261792.115 · PubMed

Other PDB entries of the same protein (UniProt P62913 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8A3D 1.67 Å, Human mature large subunit of the ribosome with eIF6 and homoharringtonine bound
8GLP 1.67 Å, mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus…
29IW 1.77 Å, Human monosomes with bound toxin NT-2, focus on 60S subunit. Cells treated with NT-2.
8QYX 1.78 Å, Human 60S ribosomal subunit
8QOI 1.9 Å, Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical…
9O3W 1.9 Å, Human 80S ribosome bound to IDB-001 stalled on MYC nascent chain
8YOO 2.0 Å, Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline
9C3H 2.0 Å, Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.
29IZ 2.08 Å, Dormant 80S:eEF2:SERBP1:tRNA complex from human cells treated with toxin NT-2
9TV2 2.1 Å, 80S ribosomes from primary B-cells infected with delta v-snoRNA1 EBV
9I2D 2.19 Å, NMT1-NAC bound human RNC with 10 amino acid ARF1-linker
9PBE 2.19 Å, In situ human 80S ribosome (composite map)

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