3LDZ: Human STAM1 VHS domain
Crystal structure of human STAM1 VHS domain in complex with ubiquitin. Determined by X-ray diffraction at 2.6 Å resolution. Released 2 Mar 2010.
- Method
- X-ray diffraction
- Resolution
- 2.6 Å
- Organisms
- Bos taurus, Homo sapiens
- Chains
- 7
- Atoms
- 6,112
- Mol. weight
- 87.54 kDa
- Released
- 2 Mar 2010
Explore 3LDZ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3LDZ contains 50 α-helices and 21 β-strands across 7 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: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-7 | 3 | |
| α-helix | 10-16 | 7 | |
| α-helix | 26-36 | 11 | |
| α-helix | 42-54 | 13 | |
| α-helix | 59-75 | 17 | |
| α-helix | 78-84 | 7 | |
| α-helix | 87-99 | 13 | |
| α-helix | 102-119 | 18 | |
| α-helix | 123-125 | 3 | |
| α-helix | 127-137 | 11 | |
Chain B: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-7 | 3 | |
| α-helix | 10-15 | 6 | |
| α-helix | 26-36 | 11 | |
| α-helix | 42-54 | 13 | |
| α-helix | 59-75 | 17 | |
| α-helix | 77-84 | 8 | |
| α-helix | 87-99 | 13 | |
| α-helix | 102-119 | 18 | |
| α-helix | 123-125 | 3 | |
| α-helix | 127-137 | 11 | |
Chain C: 9 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-15 | 6 | |
| α-helix | 26-36 | 11 | |
| α-helix | 42-54 | 13 | |
| α-helix | 59-75 | 17 | |
| α-helix | 78-84 | 7 | |
| α-helix | 87-99 | 13 | |
| α-helix | 102-119 | 18 | |
| α-helix | 123-125 | 3 | |
| α-helix | 127-137 | 11 | |
Chain D: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-7 | 3 | |
| α-helix | 10-15 | 6 | |
| α-helix | 26-36 | 11 | |
| α-helix | 42-54 | 13 | |
| α-helix | 59-75 | 17 | |
| α-helix | 78-84 | 7 | |
| α-helix | 87-99 | 13 | |
| α-helix | 102-119 | 18 | |
| α-helix | 123-125 | 3 | |
| α-helix | 127-137 | 11 | |
Chains E and F: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 3 |
| β-strand | 12-16 | 5 | 3 |
| β-strand | 22 | 1 | 4 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 3 |
| β-strand | 48-49 | 2 | 3 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 4 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 3 |
Chain G: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 5 |
| β-strand | 12-16 | 5 | 5 |
| β-strand | 22 | 1 | 6 |
| α-helix | 23-34 | 12 | |
| β-strand | 42-45 | 4 | 5 |
| β-strand | 48-49 | 2 | 5 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 6 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-70 | 5 | 5 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ubiquitin | E, F, G | protein | 73 | Bos taurus | P0CG48 (AlphaFold model) |
| Signal transducing adapter molecule 1 | A, B, C, D | protein | 140 | Homo sapiens | Q92783 (AlphaFold model) |
Sequence of entity 1 (E, F, G), FASTA
>3LDZ_1 Ubiquitin (chains E, F, G)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRL
Sequence of entity 2 (A, B, C, D), FASTA
>3LDZ_2 Signal transducing adapter molecule 1 (chains A, B, C, D)
FATNPFDQDVEKATSEMNTAEDWGLILDICDKVGQSRTGPKDCLRSIMRRVNHKDPHVAM
QALTLLGACVSNCGKIFHLEVCSRDFASEVSNVLNKGHPKVCEKLKALMVEWTDEFKNDP
QLSLISAMIKNLKEQGVTFP
Primary citation
VHS domains of ESCRT-0 cooperate in high-avidity binding to polyubiquitinated cargo. Ren, X., Hurley, J.H. EMBO J (2010) 29:1045-1054. DOI 10.1038/emboj.2010.6 · PubMed
Other PDB entries of the same protein (UniProt P0CG48 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6Q00 0.85 Å, TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1
- 1OGW 1.32 Å, Synthetic Ubiquitin with fluoro-Leu at 50 and 67
- 5NL4 1.32 Å, Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35…
- 2GBJ 1.35 Å, Crystal Structure of the 9-10 8 Glycine Insertion Mutant of Ubiquitin.
- 4HK2 1.4 Å, U7Ub25.2540
- 9FJ3 1.4 Å, Structure of ubiquitin bound of coiled-coil UIM form 2
- 1XD3 1.45 Å, Crystal structure of UCHL3-UbVME complex
- 4IUM 1.45 Å, Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin
- 7UV5 1.45 Å, The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in…
- 5NLF 1.5 Å, Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100…
- 9F6G 1.5 Å, Human USP30 chimera bound to Ubiquitin-PA
- 9OVX 1.5 Å, Crystal structure of ubiquitin K27M mutant
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