+Open data
-Basic information
Entry | Database: PDB / ID: 7lgc | ||||||
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Title | MOAP1 CA-like C-terminal domain | ||||||
Components | Modulator of apoptosis 1 | ||||||
Keywords | APOPTOSIS / domesticated Gag | ||||||
Function / homology | Function and homology information : / positive regulation of release of cytochrome c from mitochondria / extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway in absence of ligand / apoptotic signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / ubiquitin protein ligase binding ...: / positive regulation of release of cytochrome c from mitochondria / extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway in absence of ligand / apoptotic signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / ubiquitin protein ligase binding / mitochondrion / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Zurowska, K. / Pornillos, O. / Ganser-Pornillos, B.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proteins / Year: 2022 Title: Structural evidence that MOAP1 and PEG10 are derived from retrovirus/retrotransposon Gag proteins. Authors: Zurowska, K. / Alam, A. / Ganser-Pornillos, B.K. / Pornillos, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lgc.cif.gz | 109.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lgc.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 7lgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lgc_validation.pdf.gz | 425.9 KB | Display | wwPDB validaton report |
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Full document | 7lgc_full_validation.pdf.gz | 426.5 KB | Display | |
Data in XML | 7lgc_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 7lgc_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/7lgc ftp://data.pdbj.org/pub/pdb/validation_reports/lg/7lgc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (0.0850261478233, -0.996375649977, 0.0024735238471), (-0.99637026138, -0.0850149345878, 0.00433164337043), (-0.00410565751062, -0.0028328485516, -0.999987559195)Vector: ...NCS oper: (Code: given Matrix: (0.0850261478233, -0.996375649977, 0.0024735238471), Vector: |
-Components
#1: Protein | Mass: 12427.097 Da / Num. of mol.: 2 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MOAP1, PNMA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96BY2 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Tris 20% PEG 3350 3% hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 20575 / % possible obs: 94.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 18.77 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.039 / Rrim(I) all: 0.093 / Net I/σ(I): 18.35 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 713 / Rpim(I) all: 0.604 / Rrim(I) all: 1 / % possible all: 65.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Low resolution experimental model Resolution: 1.85→30.16 Å / SU ML: 0.2408 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.6924 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→30.16 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.806472204472 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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