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- PDB-6au8: 1.8 angstrom crystal structure of the human Bag6-NLS & TRC35 complex -

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Basic information

Entry
Database: PDB / ID: 6au8
Title1.8 angstrom crystal structure of the human Bag6-NLS & TRC35 complex
Components
  • Golgi to ER traffic protein 4 homolog
  • Large proline-rich protein BAG6
KeywordsCHAPERONE / TRC Pathway Complex
Function / homology
Function and homology information


BAT3 complex / immune response-activating cell surface receptor signaling pathway / maintenance of unfolded protein / TRC complex / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / cytoplasmic sequestering of protein / synaptonemal complex assembly / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane ...BAT3 complex / immune response-activating cell surface receptor signaling pathway / maintenance of unfolded protein / TRC complex / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / cytoplasmic sequestering of protein / synaptonemal complex assembly / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / internal peptidyl-lysine acetylation / misfolded protein binding / natural killer cell activation / endoplasmic reticulum stress-induced pre-emptive quality control / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / proteasome binding / ubiquitin-specific protease binding / regulation of embryonic development / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / ERAD pathway / Hsp70 protein binding / kidney development / molecular function activator activity / negative regulation of proteolysis / lung development / regulation of protein stability / brain development / ribosome binding / chromatin organization / chromosome / protein-folding chaperone binding / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / molecular adaptor activity / cell differentiation / protein stabilization / intracellular membrane-bounded organelle / signaling receptor binding / apoptotic process / ubiquitin protein ligase binding / nucleolus / negative regulation of apoptotic process / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Golgi to ER traffic protein 4 / Large proline-rich protein BAG6 / : / Golgi to ER traffic protein 4 / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin family / Ubiquitin homologues ...Golgi to ER traffic protein 4 / Large proline-rich protein BAG6 / : / Golgi to ER traffic protein 4 / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin family / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Large proline-rich protein BAG6 / Golgi to ER traffic protein 4 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsMock, J.Y. / Clemons Jr., W.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097572 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis for regulation of the nucleo-cytoplasmic distribution of Bag6 by TRC35.
Authors: Mock, J.Y. / Xu, Y. / Ye, Y. / Clemons, W.M.
History
DepositionAug 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Golgi to ER traffic protein 4 homolog
C: Large proline-rich protein BAG6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1174
Polymers36,9332
Non-polymers1842
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-19 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.660, 84.560, 102.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Golgi to ER traffic protein 4 homolog / Conserved edge-expressed protein / Transmembrane domain recognition complex 35 kDa subunit / TRC35


Mass: 32103.553 Da / Num. of mol.: 1 / Fragment: UNP residues 23-305
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GET4, C7orf20, CEE, TRC35, CGI-20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7L5D6
#2: Protein/peptide Large proline-rich protein BAG6 / BAG family molecular chaperone regulator 6 / BCL2-associated athanogene 6 / BAG-6 / HLA-B- ...BAG family molecular chaperone regulator 6 / BCL2-associated athanogene 6 / BAG-6 / HLA-B-associated transcript 3 / Protein G3 / Protein Scythe


Mass: 4829.552 Da / Num. of mol.: 1 / Fragment: UNP residues 1008-1050
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAG6, BAT3, G3 / Production host: Escherichia coli (E. coli) / References: UniProt: P46379
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG-3350, 0.2 M DL-malic acid, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9200, 0.8154
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
20.81541
ReflectionResolution: 1.8→39.09 Å / Num. obs: 34348 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.432 % / Biso Wilson estimate: 23.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.085 / Χ2: 0.992 / Net I/σ(I): 19.15 / Num. measured all: 323983 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.859.7950.7083.4624370248924880.9330.747100
1.85-1.99.6840.5624.2523677244524450.9550.593100
1.9-1.959.5190.4595.0922418235723550.9720.48699.9
1.95-2.019.2620.3666.2821543233123260.9780.38899.8
2.01-2.088.7220.2837.7419573224622440.9870.30199.9
2.08-2.159.8760.23610.1421262215421530.9930.249100
2.15-2.239.8710.20511.9720670209420940.9940.216100
2.23-2.329.7030.1714.0119716203320320.9950.179100
2.32-2.439.6780.14416.0718765193919390.9960.152100
2.43-2.559.4530.11618.7417498185518510.9970.12399.8
2.55-2.688.660.10820.9415320177517690.9980.11599.7
2.68-2.8510.0260.09425.6516944169016900.9980.099100
2.85-3.049.8830.08429.3115754159415940.9980.089100
3.04-3.299.6440.06535.2414235147614760.9990.069100
3.29-3.69.2450.05540.0712647137113680.9990.05899.8
3.6-4.038.2940.04344.1710343125212470.9990.04599.6
4.03-4.659.4590.03851.4210622112411230.9990.04199.9
4.65-5.699.1620.03950.2186589459450.9990.042100
5.69-8.058.1350.0445.4161427647550.9990.04298.8
8.05-39.098.4270.0355.2238264584540.9990.03299.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.8→39.09 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2018 1998 5.82 %
Rwork0.159 32337 -
obs0.1615 34335 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.82 Å2 / Biso mean: 34.5005 Å2 / Biso min: 16.04 Å2
Refinement stepCycle: final / Resolution: 1.8→39.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2567 0 28 150 2745
Biso mean--45.46 38.94 -
Num. residues----322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012649
X-RAY DIFFRACTIONf_angle_d1.1673586
X-RAY DIFFRACTIONf_chiral_restr0.044385
X-RAY DIFFRACTIONf_plane_restr0.006462
X-RAY DIFFRACTIONf_dihedral_angle_d14.067980
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8001-1.84510.28561390.243922502389
1.8451-1.8950.21241410.206322902431
1.895-1.95080.21671400.187822522392
1.9508-2.01370.23981430.178223062449
2.0137-2.08570.21741400.167822692409
2.0857-2.16920.20591400.151222822422
2.1692-2.26790.19031410.151222662407
2.2679-2.38750.20591410.147122982439
2.3875-2.5370.19011440.154223072451
2.537-2.73290.17181420.153523102452
2.7329-3.00780.22271440.161723312475
3.0078-3.44280.21911450.16723312476
3.4428-4.33670.18651450.139723592504
4.3367-39.09910.1891530.157324862639

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