1D3B: D3B subcomplex of the human core snrnp domain
Crystal structure of the D3B subcomplex of the human core snrnp domain at 2.0A resolution. Determined by X-ray diffraction at 2.0 Å resolution. Released 22 Dec 1999.
- Method
- X-ray diffraction
- Resolution
- 2.0 Å
- Organism
- Homo sapiens
- Chains
- 12
- Atoms
- 8,248
- Mol. weight
- 115.64 kDa
- Ligands
- CIT
- Released
- 22 Dec 1999
Explore 1D3B in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
1D3B contains 31 α-helices and 62 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.
Chains A, C and K: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-12 | 7 | |
| β-strand | 17-22 | 6 | 1 |
| β-strand | 27-35 | 9 | 1 |
| β-strand | 41-49 | 9 | 1 |
| β-strand | 55-63 | 9 | 1 |
| α-helix | 65-67 | 3 | |
| β-strand | 68-73 | 6 | 1 |
Chain B: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-12 | 3 | |
| β-strand | 16-21 | 6 | 1 |
| β-strand | 26-33 | 8 | 1 |
| β-strand | 40-51 | 12 | 1 |
| α-helix | 59-60 | 2 | |
| β-strand | 61-72 | 12 | 1 |
| α-helix | 74-76 | 3 | |
| β-strand | 77-84 | 8 | 1 |
Chain D: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-9 | 4 | |
| α-helix | 10-12 | 3 | |
| β-strand | 16-21 | 6 | 2 |
| β-strand | 26-34 | 9 | 2 |
| β-strand | 40-51 | 12 | 2 |
| α-helix | 59-60 | 2 | |
| β-strand | 61-72 | 12 | 2 |
| α-helix | 74-76 | 3 | |
| β-strand | 77-84 | 8 | 2 |
Chains E and I: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-13 | 8 | |
| β-strand | 17-22 | 6 | 3 |
| β-strand | 27-35 | 9 | 3 |
| β-strand | 41-49 | 9 | 3 |
| β-strand | 55-63 | 9 | 3 |
| α-helix | 65-67 | 3 | |
| β-strand | 68-73 | 6 | 3 |
Chain F: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-12 | 3 | |
| β-strand | 16-21 | 6 | 3 |
| β-strand | 26-34 | 9 | 3 |
| β-strand | 40-51 | 12 | 3 |
| β-strand | 61-72 | 12 | 3 |
| α-helix | 74-76 | 3 | |
| β-strand | 77-84 | 8 | 3 |
Chain G: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-11 | 6 | |
| β-strand | 17-22 | 6 | 4 |
| β-strand | 27-35 | 9 | 4 |
| β-strand | 41-49 | 9 | 4 |
| β-strand | 55-63 | 9 | 4 |
| α-helix | 65-67 | 3 | |
| β-strand | 68-73 | 6 | 4 |
Chain H: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-12 | 4 | |
| β-strand | 16-21 | 6 | 4 |
| β-strand | 26-34 | 9 | 4 |
| β-strand | 40-51 | 12 | 4 |
| α-helix | 59-60 | 2 | |
| β-strand | 61-72 | 12 | 4 |
| α-helix | 74-76 | 3 | |
| β-strand | 77-84 | 8 | 4 |
| α-helix | 86-87 | 2 | |
Chain J: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-10 | 5 | |
| β-strand | 16-21 | 6 | 3 |
| β-strand | 26-34 | 9 | 3 |
| β-strand | 40-51 | 12 | 3 |
| β-strand | 61-72 | 12 | 3 |
| α-helix | 74-76 | 3 | |
| β-strand | 77-84 | 8 | 3 |
1 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 |
|---|
| Protein (small nuclear ribonucleoprotein sm D3) | A, C, E, G, I, K | protein | 75 | Homo sapiens | P62318 (AlphaFold model) |
| Protein (small nuclear ribonucleoprotein associated protein B) | B, D, F, H, J, L | protein | 91 | Homo sapiens | P14678 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G, I, K), FASTA
>1D3B_1 PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3) (chains A, C, E, G, I, K)
MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ
VYIRGCKIRFLILPD
Sequence of entity 2 (B, D, F, H, J, L), FASTA
>1D3B_2 PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B) (chains B, D, F, H, J, L)
MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAE
REEKRVLGLVLLRGENLVSMTVEGPPPKDTG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CIT | Citric acid | C6 H8 O7 | 3 |
Water and common crystallization additives (GOL) are not listed.
Primary citation
Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs. Kambach, C., Walke, S., Young, R. et al. Cell (1999) 96:375-387. DOI 10.1016/S0092-8674(00)80550-4 · PubMed
Other PDB entries of the same protein (UniProt P62318 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3VRI 1.6 Å, HLA-B*57:01-RVAQLENVYI in complex with abacavir
- 9S2E 2.4 Å, Human intron-lariat spliceosome-Aquarius (ILSaqr)
- 7EVO 2.5 Å, The cryo-EM structure of the human 17S U2 snRNP
- 8H6L 2.6 Å, Cryo-EM structure of human exon-defined spliceosome in the early B state.
- 8H6K 2.7 Å, Cryo-EM structure of human exon-defined spliceosome in the mature B state.
- 8HK1 2.7 Å, The cryo-EM structure of human pre-17S U2 snRNP
- 8C6J 2.8 Å, Human spliceosomal PM5 C* complex
- 9NH5 2.82 Å, CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA…
- 9NH6 2.82 Å, cryo-EM structure of human U7 snrnp with methylated noncleavable H2A* substrate pre-mRNA…
- 6ID1 2.86 Å, Cryo-EM structure of a human intron lariat spliceosome after Prp43 loaded (ILS2 complex)…
- 7DVQ 2.89 Å, Cryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex)
- 6ID0 2.9 Å, Cryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded (ILS1…
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