5XJR: Gemin2-binding domain of SMN, Gemin2dN39
Crystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39 in Complex with SmD1(1-82)/D2/F/E/G from Human. Determined by X-ray diffraction at 3.12 Å resolution. Released 4 Jul 2018.
- Method
- X-ray diffraction
- Resolution
- 3.12 Å
- Organism
- Homo sapiens
- Chains
- 7
- Atoms
- 4,890
- Mol. weight
- 83.28 kDa
- Released
- 4 Jul 2018
Explore 5XJR in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5XJR contains 27 α-helices and 28 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 2: 15 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-46 | 2 | |
| α-helix | 49-61 | 13 | |
| β-strand | 67-68 | 2 | 1 |
| β-strand | 83-84 | 2 | 2 |
| α-helix | 89-93 | 5 | |
| α-helix | 98-99 | 2 | |
| α-helix | 100-119 | 20 | |
| α-helix | 122-125 | 4 | |
| α-helix | 141-149 | 9 | |
| α-helix | 180-183 | 4 | |
| α-helix | 188-203 | 16 | |
| α-helix | 209-221 | 13 | |
| α-helix | 226-227 | 2 | |
| α-helix | 228-245 | 18 | |
| α-helix | 255-264 | 10 | |
| α-helix | 265-269 | 5 | |
| α-helix | 273-275 | 3 | |
Chain A: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-7 | 4 | |
| β-strand | 14-19 | 6 | 1 |
| β-strand | 24-32 | 9 | 1 |
| β-strand | 38-46 | 9 | 1 |
| β-strand | 53-60 | 8 | 1 |
| α-helix | 62-64 | 3 | |
| β-strand | 65-69 | 5 | 1 |
| α-helix | 76-79 | 4 | |
Chain B: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-25 | 8 | |
| α-helix | 30-38 | 9 | |
| β-strand | 41-46 | 6 | 1 |
| β-strand | 51-59 | 9 | 1 |
| β-strand | 65-76 | 12 | 1 |
| α-helix | 89 | 1 | |
| β-strand | 90-101 | 12 | 1 |
| α-helix | 103-105 | 3 | |
| β-strand | 106-110 | 5 | 1 |
| β-strand | 115-116 | 2 | 2 |
Chain E: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-26 | 10 | |
| β-strand | 30-35 | 6 | 1 |
| β-strand | 41-50 | 10 | 1 |
| β-strand | 56-65 | 10 | 1 |
| β-strand | 71-79 | 9 | 1 |
| α-helix | 81-83 | 3 | |
| β-strand | 84-89 | 6 | 1 |
Chain F: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-14 | 8 | |
| β-strand | 18-23 | 6 | 1 |
| β-strand | 27-36 | 10 | 1 |
| β-strand | 42-51 | 10 | 1 |
| β-strand | 54-64 | 11 | 1 |
| α-helix | 66-68 | 3 | |
| β-strand | 69-74 | 6 | 1 |
Chain G: 0 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 16-21 | 6 | 1 |
| β-strand | 25-34 | 10 | 1 |
| β-strand | 40-48 | 9 | 1 |
| β-strand | 54-62 | 9 | 1 |
| β-strand | 69-71 | 3 | 1 |
Chain M: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Gem-associated protein 2 | 2 | protein | 241 | Homo sapiens | O14893 (AlphaFold model) |
| Small nuclear ribonucleoprotein Sm D1 | A | protein | 82 | Homo sapiens | P62314 (AlphaFold model) |
| Small nuclear ribonucleoprotein Sm D2 | B | protein | 118 | Homo sapiens | P62316 (AlphaFold model) |
| Small nuclear ribonucleoprotein E | E | protein | 92 | Homo sapiens | P62304 (AlphaFold model) |
| Small nuclear ribonucleoprotein F | F | protein | 86 | Homo sapiens | P62306 |
| Small nuclear ribonucleoprotein G | G | protein | 76 | Homo sapiens | P62308 |
| Survival motor neuron protein | M | protein | 37 | Homo sapiens | Q16637 |
Sequence of entity 1 (2), FASTA
>5XJR_1 Gem-associated protein 2 (chains 2)
FDPSVPPRTPQEYLRRVQIEAAQCPDVVVAQIDPKKLKRKQSVNISLSGCQPAPEGYSPT
LQWQQQQVAQFSTVRQNVNKHRSHWKSQQLDSNVTMPKSEDEEGWKKFCLGEKLCADGAV
GPATNESPGIDYVQIGFPPLLSIVSRMNQATVTSVLEYLSNWFGERDFTPELGRWLYALL
ACLEKPLLPEAHSLIRQLARRCSEVRLLVDSKDDERVPALNLLICLVSRYFDQRDLADEP
S
Sequence of entity 2 (A), FASTA
>5XJR_2 Small nuclear ribonucleoprotein Sm D1 (chains A)
MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSI
RGNNIRYFILPDSLPLDTLLVD
Sequence of entity 3 (B), FASTA
>5XJR_3 Small nuclear ribonucleoprotein Sm D2 (chains B)
MSLLNKPKSEMTPEELQKREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFD
RHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNPLIAGK
Sequence of entity 4 (E), FASTA
>5XJR_4 Small nuclear ribonucleoprotein E (chains E)
MAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDD
AEEIHSKTKSRKQLGRIMLKGDNITLLQSVSN
Sequence of entity 5 (F), FASTA
>5XJR_5 Small nuclear ribonucleoprotein F (chains F)
MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLG
EVLIRCNNVLYIRGVEEEEEDGEMRE
Sequence of entity 6 (G), FASTA
>5XJR_6 Small nuclear ribonucleoprotein G (chains G)
MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMV
VIRGNSIIMLEALERV
Sequence of entity 7 (M), FASTA
>5XJR_7 Survival motor neuron protein (chains M)
GQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICET
Primary citation
Negative cooperativity between Gemin2 and RNA provides insights into RNA selection and the SMN complex's release in snRNP assembly. Yi, H., Mu, L., Shen, C. et al. Nucleic Acids Res (2019). DOI 10.1093/nar/gkz1135 · PubMed
Other PDB entries of the same protein (UniProt O14893 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5XJL 2.5 Å, Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with…
- 5XJU 2.58 Å, Crystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39 in Complex with…
- 5XJT 2.92 Å, Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with…
- 5XJQ 3.28 Å, Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with…
- 5XJS 3.38 Å, Crystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39 in Complex with…
- 2LEH Solution structure of the core SMN-Gemin2 complex
Browse structure collections
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