7VGE: PDZ deleted variant of HtrA2 protease
Structure of the PDZ deleted variant of HtrA2 protease (S306A). Determined by X-ray diffraction at 4.0 Å resolution. Released 1 Jun 2022.
- Method
- X-ray diffraction
- Resolution
- 4.0 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 8,149
- Mol. weight
- 129.52 kDa
- Released
- 1 Jun 2022
Explore 7VGE in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7VGE contains 46 α-helices and 84 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: 7 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 143-146 | 4 | |
| α-helix | 149-157 | 9 | |
| α-helix | 158-160 | 3 | |
| β-strand | 161-165 | 5 | 1 |
| β-strand | 182-188 | 7 | 1 |
| β-strand | 192-196 | 5 | 1 |
| α-helix | 197-200 | 4 | |
| β-strand | 206-209 | 4 | 1 |
| β-strand | 215-224 | 10 | 1 |
| β-strand | 229-234 | 6 | 1 |
| β-strand | 245 | 1 | 2 |
| α-helix | 251-252 | 2 | |
| β-strand | 257-259 | 3 | 2 |
| β-strand | 271-273 | 3 | 2 |
| β-strand | 275 | 1 | 2 |
| β-strand | 295-297 | 3 | 2 |
| α-helix | 308 | 1 | |
| β-strand | 309-312 | 4 | 2 |
| β-strand | 317-324 | 8 | 2 |
| β-strand | 330-334 | 5 | 2 |
| α-helix | 335-339 | 5 | |
Chain B: 7 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 143-147 | 5 | |
| α-helix | 149-157 | 9 | |
| α-helix | 158-160 | 3 | |
| β-strand | 161-165 | 5 | 3 |
| β-strand | 181-188 | 8 | 3 |
| β-strand | 192-195 | 4 | 3 |
| α-helix | 197-200 | 4 | |
| β-strand | 205-209 | 5 | 3 |
| β-strand | 215-224 | 10 | 3 |
| β-strand | 229-234 | 6 | 3 |
| α-helix | 239-241 | 3 | |
| β-strand | 245 | 1 | 4 |
| α-helix | 248-250 | 3 | |
| β-strand | 256-259 | 4 | 4 |
| β-strand | 272-277 | 6 | 4 |
| β-strand | 295-297 | 3 | 4 |
| β-strand | 309-312 | 4 | 4 |
| β-strand | 317-322 | 6 | 4 |
| β-strand | 330-334 | 5 | 4 |
| α-helix | 335-337 | 3 | |
Chain C: 9 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 143-147 | 5 | |
| α-helix | 149-157 | 9 | |
| α-helix | 158-160 | 3 | |
| β-strand | 161-165 | 5 | 5 |
| β-strand | 181-186 | 6 | 5 |
| β-strand | 192-196 | 5 | 5 |
| α-helix | 197-200 | 4 | |
| β-strand | 207-210 | 4 | 5 |
| β-strand | 215-217 | 3 | 5 |
| β-strand | 219-224 | 6 | 5 |
| β-strand | 229-233 | 5 | 5 |
| α-helix | 239-241 | 3 | |
| α-helix | 243-244 | 2 | |
| β-strand | 245 | 1 | 6 |
| α-helix | 251-252 | 2 | |
| β-strand | 256-259 | 4 | 6 |
| β-strand | 271-275 | 5 | 6 |
| β-strand | 295-297 | 3 | 6 |
| α-helix | 308 | 1 | |
| β-strand | 309-312 | 4 | 6 |
| β-strand | 317-323 | 7 | 6 |
| β-strand | 330-334 | 5 | 6 |
| α-helix | 335-341 | 7 | |
Chain D: 8 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 143-147 | 5 | |
| α-helix | 149-157 | 9 | |
| β-strand | 161-165 | 5 | 7 |
| β-strand | 182-188 | 7 | 7 |
| β-strand | 192-196 | 5 | 7 |
| α-helix | 197-200 | 4 | |
| β-strand | 205-209 | 5 | 7 |
| β-strand | 215-224 | 10 | 7 |
| β-strand | 229-233 | 5 | 7 |
| α-helix | 239-241 | 3 | |
| α-helix | 243-244 | 2 | |
| β-strand | 245 | 1 | 8 |
| α-helix | 251-252 | 2 | |
| β-strand | 257-259 | 3 | 8 |
| β-strand | 271-273 | 3 | 8 |
| β-strand | 275-277 | 3 | 8 |
| β-strand | 295-297 | 3 | 8 |
| α-helix | 303-305 | 3 | |
| β-strand | 309-312 | 4 | 8 |
| β-strand | 317-321 | 5 | 8 |
| β-strand | 330-334 | 5 | 8 |
| α-helix | 335-339 | 5 | |
Chain E: 7 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 144-147 | 4 | |
| α-helix | 149-157 | 9 | |
| α-helix | 158-160 | 3 | |
| β-strand | 161-166 | 6 | 9 |
| β-strand | 181-186 | 6 | 9 |
| β-strand | 192-196 | 5 | 9 |
| α-helix | 197-200 | 4 | |
| β-strand | 206-209 | 4 | 9 |
| β-strand | 215-224 | 10 | 9 |
| β-strand | 229-234 | 6 | 9 |
| β-strand | 245 | 1 | 10 |
| α-helix | 251-252 | 2 | |
| β-strand | 256-259 | 4 | 10 |
| β-strand | 271-275 | 5 | 10 |
| α-helix | 293-294 | 2 | |
| β-strand | 295-297 | 3 | 10 |
| β-strand | 309-312 | 4 | 10 |
| β-strand | 317-321 | 5 | 10 |
| β-strand | 330-334 | 5 | 10 |
| α-helix | 335-339 | 5 | |
Chain F: 8 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 143-146 | 4 | |
| α-helix | 149-157 | 9 | |
| β-strand | 161-166 | 6 | 11 |
| β-strand | 180 | 1 | 11 |
| β-strand | 183-186 | 4 | 11 |
| β-strand | 192-196 | 5 | 11 |
| α-helix | 197-200 | 4 | |
| β-strand | 206-209 | 4 | 11 |
| β-strand | 215-217 | 3 | 11 |
| β-strand | 219-224 | 6 | 11 |
| β-strand | 229-233 | 5 | 11 |
| α-helix | 239-241 | 3 | |
| α-helix | 243-244 | 2 | |
| β-strand | 245 | 1 | 12 |
| α-helix | 248-250 | 3 | |
| β-strand | 257-259 | 3 | 12 |
| β-strand | 272-273 | 2 | 12 |
| β-strand | 275-277 | 3 | 12 |
| β-strand | 295-297 | 3 | 12 |
| α-helix | 303-305 | 3 | |
| β-strand | 309-312 | 4 | 12 |
| β-strand | 317-321 | 5 | 12 |
| β-strand | 330-334 | 5 | 12 |
| α-helix | 335-340 | 6 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Serine protease HTRA2, mitochondrial | A, B, C | protein | 203 | Homo sapiens | O43464 (AlphaFold model) |
| Serine protease HTRA2, mitochondrial | D, F | protein | 202 | Homo sapiens | O43464 (AlphaFold model) |
| Serine protease HTRA2, mitochondrial | E | protein | 201 | Homo sapiens | O43464 (AlphaFold model) |
Sequence of entity 1 (A, B, C), FASTA
>7VGE_1 Serine protease HTRA2, mitochondrial (chains A, B, C)
PASPRSQYNFIADVVEKTAPAVVYIEILDRHPFLGREVPISNGSGFVVAADGLIVTNAHV
VADRRRVRVRLLSGDTYEAVVTAVDPVADIATLRIQTKEPLPTLPLGRSADVRQGEFVVA
MGSPFALQNTITSGIVSSAQRPARDLGLPQTNVEYIQTDAAIDFGNAGGPLVNLDGEVIG
VNTMKVTAGISFAIPSDRLREFL
Sequence of entity 2 (D, F), FASTA
>7VGE_2 Serine protease HTRA2, mitochondrial (chains D, F)
PASPRSQYNFIADVVEKTAPAVVYIEILDRHPFLGREVPISNGSGFVVAADGLIVTNAHV
VADRRRVRVRLLSGDTYEAVVTAVDPVADIATLRIQTKEPLPTLPLGRSADVRQGEFVVA
MGSPFALQNTITSGIVSSAQRPARDLGLPQTNVEYIQTDAAIDFGNAGGPLVNLDGEVIG
VNTMKVTAGISFAIPSDRLREF
Sequence of entity 3 (E), FASTA
>7VGE_3 Serine protease HTRA2, mitochondrial (chains E)
PASPRSQYNFIADVVEKTAPAVVYIEILDRHPFLGREVPISNGSGFVVAADGLIVTNAHV
VADRRRVRVRLLSGDTYEAVVTAVDPVADIATLRIQTKEPLPTLPLGRSADVRQGEFVVA
MGSPFALQNTITSGIVSSAQRPARDLGLPQTNVEYIQTDAAIDFGNAGGPLVNLDGEVIG
VNTMKVTAGISFAIPSDRLRE
Primary citation
Inter-subunit crosstalk via PDZ synergistically governs allosteric activation of proapoptotic HtrA2. Parui, A.L., Mishra, V., Dutta, S. et al. Structure (2022) 30:1307-1320.e5. DOI 10.1016/j.str.2022.06.001 · PubMed
Other PDB entries of the same protein (UniProt O43464 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5M3N 1.65 Å, HTRA2 wild-type structure
- 5TO1 1.69 Å, HtrA2 exposed (L266R, F303A) mutant
- 5M3O 1.7 Å, HTRA2 A141S mutant structure
- 5TNY 1.7 Å, HTRA2 G399S mutant
- 5TNZ 1.75 Å, HtrA2 S142D mutant
- 5TO0 1.9 Å, HTRA2 S276C mutant
- 5FHT 1.95 Å, HtrA2 protease mutant V226K
- 1LCY 2.0 Å, Crystal Structure of the Mitochondrial Serine Protease HtrA2
- 5WYN 2.05 Å, HtrA2 Pathogenic Mutant
- 2PZD 2.75 Å, Crystal Structure of the HtrA2/Omi PDZ Domain Bound to a Phage-Derived Ligand (WTMFWV)
- 8E2K 3.21 Å, Cryo-EM structure of BIRC6/HtrA2-S306A
- 8AUK 6.2 Å, Cryo-EM structure of human BIRC6 in complex with HTRA2.
Browse structure collections
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