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- PDB-4eew: Crystal structure of the Ubl domain of BAG6 -

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Basic information

Entry
Database: PDB / ID: 4eew
TitleCrystal structure of the Ubl domain of BAG6
ComponentsLarge proline-rich protein BAG6
KeywordsCHAPERONE / ubiquitin-like fold / gp78-binding
Function / homology
Function and homology information


BAT3 complex / immune response-activating cell surface receptor signaling pathway / NK T cell activation / maintenance of unfolded protein / tail-anchored membrane protein insertion into ER membrane / positive regulation of ERAD pathway / synaptonemal complex assembly / post-translational protein targeting to endoplasmic reticulum membrane / internal peptidyl-lysine acetylation / misfolded protein binding ...BAT3 complex / immune response-activating cell surface receptor signaling pathway / NK T cell activation / maintenance of unfolded protein / tail-anchored membrane protein insertion into ER membrane / positive regulation of ERAD pathway / synaptonemal complex assembly / post-translational protein targeting to endoplasmic reticulum membrane / internal peptidyl-lysine acetylation / misfolded protein binding / endoplasmic reticulum stress-induced pre-emptive quality control / natural killer cell activation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / proteasome binding / ubiquitin-specific protease binding / regulation of embryonic development / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / polyubiquitin modification-dependent protein binding / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / proteasomal protein catabolic process / ERAD pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Hsp70 protein binding / molecular function activator activity / kidney development / negative regulation of proteolysis / lung development / regulation of protein stability / brain development / chromatin organization / ribosome binding / ubiquitin-dependent protein catabolic process / spermatogenesis / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / protein stabilization / receptor ligand activity / signaling receptor binding / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Large proline-rich protein BAG6 / : / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues ...Large proline-rich protein BAG6 / : / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Large proline-rich protein BAG6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKozlov, G. / LePage, K. / Vinaik, R. / Gehring, K.
CitationJournal: To be Published
Title: Crystal structure of the Ubl domain of BAG6
Authors: Kozlov, G. / LePage, K. / Vinaik, R. / Gehring, K.
History
DepositionMar 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Large proline-rich protein BAG6
B: Large proline-rich protein BAG6


Theoretical massNumber of molelcules
Total (without water)19,7682
Polymers19,7682
Non-polymers00
Water4,179232
1
A: Large proline-rich protein BAG6


Theoretical massNumber of molelcules
Total (without water)9,8841
Polymers9,8841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Large proline-rich protein BAG6


Theoretical massNumber of molelcules
Total (without water)9,8841
Polymers9,8841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.572, 43.193, 51.734
Angle α, β, γ (deg.)90.00, 104.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Large proline-rich protein BAG6 / BAG6 / BAG family molecular chaperone regulator 6 / BCL2-associated athanogene 6 / BAG-6 / HLA-B- ...BAG6 / BAG family molecular chaperone regulator 6 / BCL2-associated athanogene 6 / BAG-6 / HLA-B-associated transcript 3 / Protein G3 / Protein Scythe


Mass: 9884.153 Da / Num. of mol.: 2 / Fragment: Ubiquitin-like domain (UNP residues 1-87)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAG6, BAT3, G3 / Plasmid: pET42a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P46379
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 1.67 Å3/Da / Density % sol: 26.53 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M trimethylamine N-oxide, 0.1 M Tris, pH 8.5, 20% w/v PEG2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9767 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 18, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9767 Å / Relative weight: 1
ReflectionResolution: 1.3→32.72 Å / Num. all: 30472 / Num. obs: 28619 / % possible obs: 93.92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Rsym value: 0.039 / Net I/σ(I): 25.9
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 3 / Num. unique all: 1318 / Rsym value: 0.2 / % possible all: 58.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UBQ

1ubq


Resolution: 1.3→32.72 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.767 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.063 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19975 1520 5 %RANDOM
Rwork0.18447 ---
all0.186 30472 --
obs0.18527 28619 93.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.862 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å2-0.77 Å2
2---1.01 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.3→32.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1187 0 0 232 1419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221246
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9781686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3675161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96225.51758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7115255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.824157
X-RAY DIFFRACTIONr_chiral_restr0.0860.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02903
X-RAY DIFFRACTIONr_nbd_refined0.1960.2576
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2843
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2148
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.250
X-RAY DIFFRACTIONr_mcbond_it0.711.5794
X-RAY DIFFRACTIONr_mcangle_it1.09521244
X-RAY DIFFRACTIONr_scbond_it1.843503
X-RAY DIFFRACTIONr_scangle_it2.9184.5435
LS refinement shellResolution: 1.3→1.336 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 72 -
Rwork0.218 1318 -
obs--58.6 %
Refinement TLS params.

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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.27910.02980.50810.78250.00060.9444-0.064-0.02950.068-0.0434-0.0175-0.007-0.0206-0.02040.08150.0148-0.0054-0.00550.03680.010.046-7.3719-6.3934-21.6095
20.7750.0464-0.39561.34370.17241.1978-0.03-0.04890.02370.1078-0.02240.00450.0615-0.03750.05240.01680.00240.00780.0432-0.00710.0294-11.8216-11.6899-15.7816
31.14540.98940.89222.69052.95523.29460.15240.0044-0.04890.0210.0484-0.25810.18070.066-0.20080.04450.0181-0.00360.02710.00330.0466-0.7173-17.1301-17.8584
42.0490.8177-0.22380.4646-0.06042.3715-0.07260.04410.0098-0.10160.02670.01270.15760.05430.04590.03120.02620.01350.00950.0040.0291-5.8385-13.1264-22.3886
50.4371-0.8672-0.76021.74061.40741.83290.04950.02420.05760.0004-0.0288-0.09960.0539-0.0728-0.02070.01670.00640.01520.0350.00450.04880.0738-36.6466-1.9907
61.5487-0.697-0.93190.90910.492.6098-0.06990.01180.0053-0.1083-0.00590.06110.1011-0.1910.0759-0.0036-0.0049-0.02470.0558-0.00240.0423-8.6453-32.9389-7.8514
72.53421.65610.61741.32340.88721.12080.001-0.047-0.1027-0.16-0.0136-0.0426-0.0609-0.00570.01260.01890.0036-0.01130.03340.00230.05070.3071-24.2798-5.1044
85.6861-1.74533.26853.4733-1.22135.9047-0.02680.2179-0.0701-0.1495-0.0587-0.2083-0.22830.23230.08550.0167-0.00860.00090.02890.00070.0351.8292-29.6104-14.0338
91.406-0.69270.03461.04830.91261.2232-0.10750.06620.02030.0878-0.0126-0.0167-0.16140.06880.1201-0.0049-0.0094-0.00010.04180.01940.05090.3638-28.5861-3.2681
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 41
2X-RAY DIFFRACTION2A42 - 61
3X-RAY DIFFRACTION3A62 - 71
4X-RAY DIFFRACTION4A72 - 87
5X-RAY DIFFRACTION5B13 - 36
6X-RAY DIFFRACTION6B37 - 56
7X-RAY DIFFRACTION7B57 - 66
8X-RAY DIFFRACTION8B67 - 73
9X-RAY DIFFRACTION9B74 - 87

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