+Open data
-Basic information
Entry | Database: PDB / ID: 7lfd | ||||||
---|---|---|---|---|---|---|---|
Title | Fab 7D6 bound to ApoL1 BH3 like peptide | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / Complex | ||||||
Function / homology | Function and homology information lipoprotein metabolic process / very-low-density lipoprotein particle / high-density lipoprotein particle / lipid transport / chloride channel activity / cytolysis by host of symbiont cells / Scavenging of heme from plasma / chloride transmembrane transport / cholesterol metabolic process / Post-translational protein phosphorylation ...lipoprotein metabolic process / very-low-density lipoprotein particle / high-density lipoprotein particle / lipid transport / chloride channel activity / cytolysis by host of symbiont cells / Scavenging of heme from plasma / chloride transmembrane transport / cholesterol metabolic process / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood microparticle / endoplasmic reticulum lumen / innate immune response / lipid binding / extracellular space / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.157 Å | ||||||
Authors | Ultsch, M. / Kirchhofer, D. | ||||||
Citation | Journal: Commun Biol / Year: 2021 Title: Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif. Authors: Ultsch, M. / Holliday, M.J. / Gerhardy, S. / Moran, P. / Scales, S.J. / Gupta, N. / Oltrabella, F. / Chiu, C. / Fairbrother, W. / Eigenbrot, C. / Kirchhofer, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7lfd.cif.gz | 200.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7lfd.ent.gz | 158 KB | Display | PDB format |
PDBx/mmJSON format | 7lfd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/7lfd ftp://data.pdbj.org/pub/pdb/validation_reports/lf/7lfd | HTTPS FTP |
---|
-Related structure data
Related structure data | 7l6kC 7lf7C 7lf8C 7lfaC 7lfbSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein/peptide , 1 types, 1 molecules A
#1: Protein/peptide | Mass: 1957.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O14791 |
---|
-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 24050.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: AEP1 / Production host: Escherichia coli (E. coli) / Strain (production host): 64B4 |
---|---|
#3: Antibody | Mass: 23325.795 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: AEP1 / Production host: Escherichia coli (E. coli) / Strain (production host): 64B4 |
-Non-polymers , 5 types, 191 molecules
#4: Chemical | ChemComp-FLC / | ||||
---|---|---|---|---|---|
#5: Chemical | ChemComp-EOH / | ||||
#6: Chemical | #7: Chemical | ChemComp-NH4 / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Description: rods |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8M Ammonium Citrate pH 7.0 / PH range: 6.5 - 7.5 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.157→70.674 Å / Num. obs: 40614 / % possible obs: 89.6 % / Redundancy: 9.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.074 / Rrim(I) all: 0.167 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.163→2.273 Å / Rmerge(I) obs: 1.638 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2033 / CC1/2: 0.371 / Rpim(I) all: 0.855 / Rrim(I) all: 1.855 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7LFB Resolution: 2.157→70.674 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.7 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 178.8 Å2 / Biso mean: 46.5584 Å2 / Biso min: 22.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.157→70.674 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 115.9727 Å / Origin y: 82.7508 Å / Origin z: 6.8589 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|