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Open data
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Basic information
Entry | Database: PDB / ID: 7sjm | ||||||
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Title | anti-HtrA1 Fab15H6.v4 | ||||||
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![]() | IMMUNE SYSTEM / Fab | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ultsch, M.H. / Gerhardy, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Allosteric inhibition of HTRA1 activity by a conformational lock mechanism to treat age-related macular degeneration. Authors: Stefan Gerhardy / Mark Ultsch / Wanjian Tang / Evan Green / Jeffrey K Holden / Wei Li / Alberto Estevez / Chris Arthur / Irene Tom / Alexis Rohou / Daniel Kirchhofer / ![]() Abstract: The trimeric serine protease HTRA1 is a genetic risk factor associated with geographic atrophy (GA), a currently untreatable form of age-related macular degeneration. Here, we describe the allosteric ...The trimeric serine protease HTRA1 is a genetic risk factor associated with geographic atrophy (GA), a currently untreatable form of age-related macular degeneration. Here, we describe the allosteric inhibition mechanism of HTRA1 by a clinical Fab fragment, currently being evaluated for GA treatment. Using cryo-EM, X-ray crystallography and biochemical assays we identify the exposed LoopA of HTRA1 as the sole Fab epitope, which is approximately 30 Å away from the active site. The cryo-EM structure of the HTRA1:Fab complex in combination with molecular dynamics simulations revealed that Fab binding to LoopA locks HTRA1 in a non-competent conformational state, incapable of supporting catalysis. Moreover, grafting the HTRA1-LoopA epitope onto HTRA2 and HTRA3 transferred the allosteric inhibition mechanism. This suggests a conserved conformational lock mechanism across the HTRA family and a critical role of LoopA for catalysis, which was supported by the reduced activity of HTRA1-3 upon LoopA deletion or perturbation. This study reveals the long-range inhibition mechanism of the clinical Fab and identifies an essential function of the exposed LoopA for activity of HTRA family proteases. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.8 KB | Display | ![]() |
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PDB format | ![]() | 147.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.3 KB | Display | ![]() |
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Full document | ![]() | 449.4 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 34 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sjnC ![]() 7sjoC ![]() 7sjpC ![]() 1fvdS S: Starting model for refinement C: citing same article ( |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Antibody | Mass: 24232.924 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Antibody | Mass: 23181.654 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.68 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.1 Details: 2.1M ammonium sulfate, 0.1M Tri-sodium citrate pH 5.1 PH range: 5.0-6.0 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 10, 2018 / Details: Liquid nitrogen-cooled double crystal Si(111) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→39.47 Å / Num. obs: 44014 / % possible obs: 97.27 % / Redundancy: 2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.07 / Rrim(I) all: 0.101 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.4061 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 4284 / CC1/2: 0.674 / Rpim(I) all: 0.639 / Rrim(I) all: 0.919 / % possible all: 95.37 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1FVD Resolution: 1.8→39.47 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.9425 / SU R Cruickshank DPI: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.12 / SU Rfree Blow DPI: 0.111 / SU Rfree Cruickshank DPI: 0.108
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Displacement parameters | Biso max: 113.44 Å2 / Biso mean: 27.38 Å2 / Biso min: 10.15 Å2
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Refine analyze | Luzzati coordinate error obs: 0.196 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→39.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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