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- PDB-4jzl: Crystal structure of BAP31 vDED at alkaline pH -

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Basic information

Entry
Database: PDB / ID: 4jzl
TitleCrystal structure of BAP31 vDED at alkaline pH
ComponentsB-cell receptor-associated protein 31
KeywordsAPOPTOSIS / 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 / perinuclear endoplasmic reticulum / negative regulation of endoplasmic reticulum calcium ion concentration / protein targeting to mitochondrion / clathrin-coated vesicle ...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 / perinuclear endoplasmic reticulum / negative regulation of endoplasmic reticulum calcium ion concentration / protein targeting to mitochondrion / clathrin-coated vesicle / Golgi cisterna membrane / Apoptotic cleavage of cellular proteins / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / : / RHOA GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class I protein binding / positive regulation of intrinsic apoptotic signaling pathway / endoplasmic reticulum-Golgi intermediate compartment membrane / response to endoplasmic reticulum stress / lipid droplet / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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
B-cell receptor-associated protein 29/31 / BAP29/BAP31, transmembrane domain / Bap31/Bap29 cytoplasmic coiled-coil domain / Bap31/Bap29 transmembrane region / Bap31/Bap29 cytoplasmic coiled-coil domain
Similarity search - Domain/homology
B-cell receptor-associated protein 31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsQuistgaard, E.M. / Low, C. / Moberg, P. / Guettou, F. / Maddi, K. / Nordlund, P.
CitationJournal: Plos One / Year: 2013
Title: Structural and Biophysical Characterization of the Cytoplasmic Domains of Human BAP29 and BAP31.
Authors: Quistgaard, E.M. / Low, C. / Moberg, P. / Guettou, F. / Maddi, K. / Nordlund, P.
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B-cell receptor-associated protein 31
B: B-cell receptor-associated protein 31
C: B-cell receptor-associated protein 31
D: B-cell receptor-associated protein 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4005
Polymers31,3084
Non-polymers921
Water2,054114
1
A: B-cell receptor-associated protein 31
D: B-cell receptor-associated protein 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7463
Polymers15,6542
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-35 kcal/mol
Surface area9710 Å2
MethodPISA
2
B: B-cell receptor-associated protein 31
C: B-cell receptor-associated protein 31


Theoretical massNumber of molelcules
Total (without water)15,6542
Polymers15,6542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-34 kcal/mol
Surface area9620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.690, 42.900, 62.670
Angle α, β, γ (deg.)90.00, 115.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
B-cell receptor-associated protein 31 / BCR-associated protein 31 / Bap31 / 6C6-AG tumor-associated antigen / Protein CDM / p28


Mass: 7826.907 Da / Num. of mol.: 4 / Fragment: vDED domain: unp residues 168-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAP31, BAP31, DXS1357E / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta 2 / References: UniProt: P51572
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8
Details: 100 mM Tris-HCl, 34% PEG2000 monomethyl ether (mme) and 150 mM KBr, pH 8.0, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→28.3 Å / Num. all: 13838 / Num. obs: 13838 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rsym value: 0.067 / Net I/σ(I): 15.8
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.575 / % possible all: 98.3

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JZP

4jzp


Resolution: 2.2→28.3 Å / SU ML: 0.23 / σ(F): 2.01 / Phase error: 28.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2458 555 4.03 %Random
Rwork0.2204 ---
obs0.2214 13771 98.37 %-
all-13771 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 6 114 2124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042013
X-RAY DIFFRACTIONf_angle_d0.682671
X-RAY DIFFRACTIONf_dihedral_angle_d15.404842
X-RAY DIFFRACTIONf_chiral_restr0.048302
X-RAY DIFFRACTIONf_plane_restr0.002348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1999-2.42110.29871490.25763243X-RAY DIFFRACTION98
2.4211-2.77120.28671550.24043253X-RAY DIFFRACTION99
2.7712-3.49050.23731330.22243344X-RAY DIFFRACTION99
3.4905-28.34290.21991180.2043376X-RAY DIFFRACTION98
Refinement TLS params.

S33: -0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2856-0.0743-0.03830.33560.288-0.04460.01960.17920.0803-0.04420.0159-0.0142-0.0072-0.38160.13950.0072-0.02710.25890.03420.160935.71969.87923.2161
20.19820.14150.07820.0019-0.20080.13930.0433-0.05780.01190.02530.01260.0278-0.03680.20990.1950.00360.00160.14550.00550.19348.788110.229926.7316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' or chain 'D')
2X-RAY DIFFRACTION2(chain 'B' or chain 'C')

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