2L0T: Complex of ubiquitin and the VHS domain of Stam2

Solution structure of the complex of ubiquitin and the VHS domain of Stam2. Determined by solution NMR. Released 15 Dec 2010.

Method: Solution NMR
Organism: Homo sapiens
Chains: 2
Atoms: 1,836
Mol. weight: 26.26 kDa
Released: 15 Dec 2010

Explore 2L0T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2L0T contains 11 α-helices and 5 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: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	11-16	6	1
α-helix	23-34	12
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	66-71	6	1

Chain B: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	15-23	9
α-helix	34-45	12
α-helix	49-61	13
α-helix	66-82	17
α-helix	85-91	7
α-helix	94-106	13
α-helix	110-126	17
α-helix	134-144	11
α-helix	156-162	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A	protein	76	Homo sapiens	P62979 (AlphaFold model)
Signal transducing adapter molecule 2	B	protein	163	Homo sapiens	O75886 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2L0T_1 Ubiquitin (chains A)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (B), FASTA

>2L0T_2 Signal transducing adapter molecule 2 (chains B)
GSSGSSGMPLFTANPFEQDVEKATNEYNTTEDWSLIMDICDKVGSTPNGAKDCLKAIMKR
VNHKVPHVALQALTLLGACVANCGKIFHLEVCSRDFATEVRAVIKNKAHPKVCEKLKSLM
VEWSEEFQKDPQFSLISATIKSMKEEGITFPPAGSQTSGPSSG

Primary citation

NMR reveals a different mode of binding of the Stam2 VHS domain to ubiquitin and diubiquitin. Lange, A., Hoeller, D., Wienk, H. et al. Biochemistry (2011) 50:48-62. DOI 10.1021/bi101594a · PubMed

Other PDB entries of the same protein (UniProt P62979 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3NHE 1.26 Å, High Resolution Structure (1.26A) of USP2a in Complex with Ubiquitin
6SQO 1.41 Å, Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub
7F0N 1.6 Å, Structure of deamidated Ubiquitin
8GLP 1.67 Å, mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus…
3NS8 1.71 Å, Crystal structure of an open conformation of Lys48-linked diubiquitin at pH 7.5
3N32 1.79 Å, The crystal structure of human Ubiquitin adduct with Zeise's salt
6SQS 1.83 Å, Crystal structure of cat phospho-Ser429 MDM2 RING domain bound to UbcH5B-Ub
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
5WVO 2.0 Å, Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated…
3PHW 2.0 Å, OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with Ubiquitin
8YOO 2.0 Å, Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline

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