- PDB-4jzp: Crystal structure of BAP31 vDED at acidic pH -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4jzp
Title
Crystal structure of BAP31 vDED at acidic pH
Components
B-cell receptor-associated protein 31
Keywords
APOPTOSIS / TRANSPORT PROTEIN
Function / homology
Function and homology information
positive regulation of retrograde protein transport, ER to cytosol / positive regulation of mitochondrial calcium ion concentration / protein localization to endoplasmic reticulum exit site / mitochondria-associated endoplasmic reticulum membrane contact site / Apoptotic execution phase / positive regulation of ERAD pathway / perinuclear endoplasmic reticulum / negative regulation of endoplasmic reticulum calcium ion concentration / positive regulation of ubiquitin-dependent protein catabolic process / protein targeting to mitochondrion ...positive regulation of retrograde protein transport, ER to cytosol / positive regulation of mitochondrial calcium ion concentration / protein localization to endoplasmic reticulum exit site / mitochondria-associated endoplasmic reticulum membrane contact site / Apoptotic execution phase / positive regulation of ERAD pathway / perinuclear endoplasmic reticulum / negative regulation of endoplasmic reticulum calcium ion concentration / positive regulation of ubiquitin-dependent protein catabolic process / protein targeting to mitochondrion / clathrin-coated vesicle / Golgi cisterna membrane / RSV-host interactions / Apoptotic cleavage of cellular proteins / MHC class I protein binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / : / RHOA GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of intrinsic apoptotic signaling pathway / response to endoplasmic reticulum stress / endoplasmic reticulum-Golgi intermediate compartment membrane / lipid droplet / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / positive regulation of cytosolic calcium ion concentration / spermatogenesis / Golgi membrane / apoptotic process / protein-containing complex binding / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / membrane / plasma membrane / cytosol Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.64 Å3/Da / Density % sol: 66.21 %
Crystal grow
Temperature: 292 K / Method: vapor diffusion / pH: 4.2 Details: 100 mM Na citrate, 33% PEG400 and 200 mM LiSO4, VAPOR DIFFUSION, temperature 292K, pH 4.2
Resolution: 2.1→2.21 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.99 / Rsym value: 0.424 / % possible all: 99.7
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Processing
Software
Name
Version
Classification
XDS
datascaling
PHASER
phasing
REFMAC
5.7.0029
refinement
XDS
datareduction
XSCALE
datascaling
Refinement
Method to determine structure: SAD / Resolution: 2.1→28.57 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.19 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1802
563
4.1 %
RANDOM
Rwork
0.16239
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obs
0.16313
13261
99.42 %
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all
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13291
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK