+Open data
-Basic information
Entry | Database: PDB / ID: 8gho | ||||||
---|---|---|---|---|---|---|---|
Title | GUCY2C-peptide bound to anti-GUCY2C-scFv antibody | ||||||
Components |
| ||||||
Keywords | PROTEIN BINDING / bi-specific antibody GUCY2C antigen | ||||||
Function / homology | Function and homology information Intestinal infectious diseases / Digestion / receptor guanylyl cyclase signaling pathway / peptide receptor activity / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / adenylate cyclase activity / toxic substance binding / response to toxic substance ...Intestinal infectious diseases / Digestion / receptor guanylyl cyclase signaling pathway / peptide receptor activity / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / adenylate cyclase activity / toxic substance binding / response to toxic substance / regulation of cell population proliferation / protein kinase activity / intracellular signal transduction / endoplasmic reticulum membrane / GTP binding / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Mosyak, L. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Sci Rep / Year: 2023 Title: Molecular insights into recognition of GUCY2C by T-cell engaging bispecific antibody anti-GUCY2CxCD3. Authors: Rampuria, P. / Mosyak, L. / Root, A.R. / Svenson, K. / Agostino, M.J. / LaVallie, E.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8gho.cif.gz | 217.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8gho.ent.gz | 173.6 KB | Display | PDB format |
PDBx/mmJSON format | 8gho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/8gho ftp://data.pdbj.org/pub/pdb/validation_reports/gh/8gho | HTTPS FTP |
---|
-Related structure data
Related structure data | 8ghpC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 13637.258 Da / Num. of mol.: 2 / Fragment: VH domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #2: Antibody | Mass: 13127.521 Da / Num. of mol.: 2 / Fragment: VL domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #3: Protein/peptide | Mass: 1956.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P25092, guanylate cyclase #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.28 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 200 mM Lithium Sulfate, bis-tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→60 Å / Num. obs: 49431 / % possible obs: 92.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.6→1.77 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.9 / Num. unique obs: 2472 / % possible all: 61.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→31.96 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.122 / SU Rfree Cruickshank DPI: 0.116
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.66 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.26 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.6→31.96 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|