5DQU: Cas-DNA-10 complex
Crystal Structure of Cas-DNA-10 complex. Determined by X-ray diffraction at 4.5 Å resolution. Released 11 Nov 2015.
- Method
- X-ray diffraction
- Resolution
- 4.5 Å
- Organisms
- Escherichia coli K12, Escherichia coli
- Chains
- 10
- Atoms
- 10,672
- Mol. weight
- 170.43 kDa
- Released
- 11 Nov 2015
Explore 5DQU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5DQU contains 60 α-helices and 46 β-strands across 6 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: 14 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 17-20 | 4 | 1 |
| β-strand | 23-28 | 6 | 2 |
| β-strand | 31-36 | 6 | 2 |
| β-strand | 39-44 | 6 | 2 |
| β-strand | 51-54 | 4 | 1 |
| α-helix | 55 | 1 | |
| β-strand | 58-61 | 4 | 2 |
| α-helix | 62-70 | 9 | |
| α-helix | 73 | 1 | |
| β-strand | 74-78 | 5 | 1 |
| α-helix | 80-82 | 3 | |
| β-strand | 85-89 | 5 | 1 |
| α-helix | 96-107 | 12 | |
| α-helix | 109-124 | 16 | |
| α-helix | 127-129 | 3 | |
| α-helix | 134-156 | 23 | |
| α-helix | 175-198 | 24 | |
| α-helix | 214-223 | 10 | |
| α-helix | 224-228 | 5 | |
| α-helix | 229-238 | 10 | |
| α-helix | 243-257 | 15 | |
| α-helix | 260-273 | 14 | |
Chain B: 14 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-13 | 3 | |
| β-strand | 15-20 | 6 | 1 |
| β-strand | 23-28 | 6 | 2 |
| β-strand | 31-35 | 5 | 2 |
| β-strand | 41-43 | 3 | 2 |
| α-helix | 46-48 | 3 | |
| β-strand | 49-54 | 6 | 1 |
| α-helix | 55 | 1 | |
| β-strand | 58-61 | 4 | 2 |
| α-helix | 62-70 | 9 | |
| α-helix | 73 | 1 | |
| β-strand | 74-78 | 5 | 1 |
| β-strand | 84-89 | 6 | 1 |
| α-helix | 96-107 | 12 | |
| α-helix | 109-124 | 16 | |
| α-helix | 127-129 | 3 | |
| α-helix | 134-156 | 23 | |
| α-helix | 175-197 | 23 | |
| α-helix | 214-227 | 14 | |
| α-helix | 229-237 | 9 | |
| α-helix | 244-257 | 14 | |
| α-helix | 260-273 | 14 | |
Chain C: 15 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-13 | 3 | |
| β-strand | 15-20 | 6 | 5 |
| β-strand | 23-28 | 6 | 4 |
| β-strand | 31-35 | 5 | 4 |
| β-strand | 41-43 | 3 | 4 |
| α-helix | 46-48 | 3 | |
| β-strand | 49-54 | 6 | 5 |
| α-helix | 55 | 1 | |
| β-strand | 58-61 | 4 | 4 |
| α-helix | 62-70 | 9 | |
| α-helix | 73 | 1 | |
| β-strand | 74-78 | 5 | 5 |
| β-strand | 84-89 | 6 | 5 |
| α-helix | 96-107 | 12 | |
| α-helix | 109-124 | 16 | |
| α-helix | 127-129 | 3 | |
| α-helix | 134-156 | 23 | |
| α-helix | 175-197 | 23 | |
| α-helix | 214-227 | 14 | |
| α-helix | 229-237 | 9 | |
| α-helix | 244-257 | 14 | |
| α-helix | 260-273 | 14 | |
| α-helix | 278-281 | 4 | |
Chain D: 13 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 17-20 | 4 | 5 |
| β-strand | 23-28 | 6 | 4 |
| β-strand | 31-36 | 6 | 4 |
| β-strand | 39-44 | 6 | 4 |
| β-strand | 51-54 | 4 | 5 |
| α-helix | 55 | 1 | |
| β-strand | 58-61 | 4 | 4 |
| α-helix | 62-70 | 9 | |
| α-helix | 73 | 1 | |
| β-strand | 74-78 | 5 | 5 |
| α-helix | 80-82 | 3 | |
| β-strand | 85-89 | 5 | 5 |
| α-helix | 96-107 | 12 | |
| α-helix | 109-122 | 14 | |
| α-helix | 135-156 | 22 | |
| α-helix | 175-197 | 23 | |
| α-helix | 214-223 | 10 | |
| α-helix | 224-228 | 5 | |
| α-helix | 229-238 | 10 | |
| α-helix | 243-257 | 15 | |
| α-helix | 260-273 | 14 | |
Chain E: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-9 | 8 | 3 |
| α-helix | 13-22 | 10 | |
| β-strand | 24-27 | 4 | 3 |
| β-strand | 30-35 | 6 | 3 |
| α-helix | 37-50 | 14 | |
| β-strand | 55-61 | 7 | 3 |
| β-strand | 68-73 | 6 | 3 |
| β-strand | 78-83 | 6 | 4 |
| β-strand | 86-91 | 6 | 4 |
Chain F: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 6 |
| α-helix | 13-22 | 10 | |
| β-strand | 24-27 | 4 | 6 |
| β-strand | 30-34 | 5 | 6 |
| α-helix | 37-50 | 14 | |
| β-strand | 55-61 | 7 | 6 |
| β-strand | 68-73 | 6 | 6 |
| β-strand | 78-83 | 6 | 2 |
| β-strand | 86-91 | 6 | 2 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| CRISPR-associated endonuclease Cas1 | A, B, C, D | protein | 305 | Escherichia coli K12 | Q46896 (AlphaFold model) |
| CRISPR-associated endoribonuclease Cas2 | E, F | protein | 94 | Escherichia coli K12 | P45956 (AlphaFold model) |
| DNA (5'-d(*gp*ap*gp*tp*cp*gp*ap*tp*gp*cp*tp*tp*tp*tp*t)-3') | H, I | DNA | 15 | Escherichia coli | |
| DNA (5'-d(p*tp*tp*gp*cp*ap*tp*cp*gp*ap*cp*tp*c)-3') | G, J | DNA | 12 | Escherichia coli | |
Sequence of entity 1 (A, B, C, D), FASTA
>5DQU_1 CRISPR-associated endonuclease Cas1 (chains A, B, C, D)
MTWLPLNPIPLKDRVSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPGTRV
SHAAVRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLKVVRKMF
ELRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTINQCI
SAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIARRNP
GEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPAPPEDAQPVAIPLPVSLGDA
GHRSS
Sequence of entity 2 (E, F), FASTA
>5DQU_2 CRISPR-associated endoribonuclease Cas2 (chains E, F)
MSMLVVVTENVPPRLRGRLAIWLLEVRAGVYVGDVSAKIREMIWEQIAGLAEEGNVVMAW
ATNTETGFEFQTFGLNRRTPVDLDGLRLVSFLPV
Sequence of entity 3 (H, I), FASTA
>5DQU_3 DNA (5'-D(*GP*AP*GP*TP*CP*GP*AP*TP*GP*CP*TP*TP*TP*TP*T)-3') (chains H, I)
GAGTCGATGCTTTTT
Sequence of entity 4 (G, J), FASTA
>5DQU_4 DNA (5'-D(P*TP*TP*GP*CP*AP*TP*CP*GP*AP*CP*TP*C)-3') (chains G, J)
TTGCATCGACTC
Primary citation
Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems. Wang, J., Li, J., Zhao, H. et al. Cell (2015) 163:840-853. DOI 10.1016/j.cell.2015.10.008 · PubMed
Other PDB entries of the same protein (UniProt Q46896 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3NKE 1.4 Å, High resolution structure of the C-terminal domain CRISP-associated protein Cas1 from…
- 3NKD 1.95 Å, Structure of CRISP-associated protein Cas1 from Escherichia coli str. K-12
- 4P6I 2.3 Å, Crystal structure of the Cas1-Cas2 complex from Escherichia coli
- 5DLJ 2.6 Å, Crystal Structure of Cas-DNA-N1 complex
- 4QDL 2.7 Å, Crystal structure of E.coli Cas1-Cas2 complex
- 5DQZ 2.7 Å, Crystal Structure of Cas-DNA-PAM complex
- 5VVK 2.9 Å, Cas1-Cas2 bound to full-site mimic
- 5DS5 2.95 Å, Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA and Mg
- 5DQT 3.1 Å, Crystal Structure of Cas-DNA-22 complex
- 5DS4 3.2 Å, Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA
- 5VVL 3.31 Å, Cas1-Cas2 bound to full-site mimic with Ni
- 5DS6 3.35 Å, Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA with…
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