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- PDB-4jzp: Crystal structure of BAP31 vDED at acidic pH -

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Basic information

Entry
Database: PDB / ID: 4jzp
TitleCrystal structure of BAP31 vDED at acidic 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 / protein localization to endoplasmic reticulum exit site / Apoptotic execution phase / positive regulation of ERAD pathway / perinuclear endoplasmic reticulum / mitochondria-associated endoplasmic reticulum membrane contact site / positive regulation of ubiquitin-dependent protein catabolic process / clathrin-coated vesicle / Golgi cisterna membrane / : ...positive regulation of retrograde protein transport, ER to cytosol / protein localization to endoplasmic reticulum exit site / Apoptotic execution phase / positive regulation of ERAD pathway / perinuclear endoplasmic reticulum / mitochondria-associated endoplasmic reticulum membrane contact site / positive regulation of ubiquitin-dependent protein catabolic process / clathrin-coated vesicle / Golgi cisterna membrane / : / Apoptotic cleavage of cellular proteins / RSV-host interactions / MHC class I protein binding / RHOA GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of intrinsic apoptotic signaling pathway / lipid droplet / endoplasmic reticulum-Golgi intermediate compartment membrane / response to endoplasmic reticulum stress / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / lumenal side of endoplasmic reticulum membrane / spermatogenesis / Golgi membrane / apoptotic process / endoplasmic reticulum membrane / protein-containing complex binding / endoplasmic reticulum / 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 / SAD / Resolution: 2.1 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 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3265
Polymers15,8412
Non-polymers4853
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-20 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.610, 70.610, 80.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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: 7920.697 Da / Num. of mol.: 2 / Fragment: vDED domain: unp residues 168-233
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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.64 Å3/Da / Density % sol: 66.21 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2011
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.543
11-h,-k,l20.457
ReflectionResolution: 2.1→28.57 Å / Num. all: 13291 / Num. obs: 13291 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rsym value: 0.046 / Net I/σ(I): 24.28
Reflection shellResolution: 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
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.1802 563 4.1 %RANDOM
Rwork0.16239 ---
obs0.16313 13261 99.42 %-
all-13291 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.589 Å2
Baniso -1Baniso -2Baniso -3
1-7.62 Å20 Å20 Å2
2--7.62 Å20 Å2
3----15.23 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms801 0 31 74 906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.019827
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9592.0471087
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6265100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19127.94939
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73915182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.838154
X-RAY DIFFRACTIONr_chiral_restr0.0580.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02560
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 39 -
Rwork0.156 960 -
obs--99.3 %

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