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- PDB-4x86: Crystal structure of BAG6-Ubl4a complex -

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Basic information

Entry
Database: PDB / ID: 4x86
TitleCrystal structure of BAG6-Ubl4a complex
Components
  • Large proline-rich protein BAG6
  • Ubiquitin-like protein 4A
KeywordsPROTEIN BINDING / tail-anchored transmembrane protein biogenesis / quality control of proteins
Function / homology
Function and homology information


BAT3 complex / immune response-activating cell surface receptor signaling pathway / maintenance of unfolded protein / ubiquitin-like protein transferase activity / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / 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 / maintenance of unfolded protein / ubiquitin-like protein transferase activity / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / synaptonemal complex assembly / 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 / ERAD pathway / regulation of embryonic development / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / Hsp70 protein binding / proteasomal protein catabolic process / kidney development / molecular function activator activity / negative regulation of proteolysis / lung development / brain development / protein modification process / regulation of protein stability / ribosome binding / chromatin organization / protein-folding chaperone binding / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / molecular adaptor activity / cell differentiation / protein stabilization / signaling receptor binding / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubl4, C-terminal TUGS domain / UBL4A-like, ubiquitin-like domain / Tethering Ubl4a to BAGS domain / Large proline-rich protein BAG6 / : / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain ...Ubl4, C-terminal TUGS domain / UBL4A-like, ubiquitin-like domain / Tethering Ubl4a to BAGS domain / Large proline-rich protein BAG6 / : / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-like protein 4A / Large proline-rich protein BAG6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsKuwabara, N. / Kato, R.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structure of a BAG6 (Bcl-2-associated Athanogene 6)-Ubl4a (Ubiquitin-like Protein 4a) Complex Reveals a Novel Binding Interface That Functions in Tail-anchored Protein Biogenesis
Authors: Kuwabara, N. / Minami, R. / Yokota, N. / Matsumoto, H. / Senda, T. / Kawahara, H. / Kato, R.
History
DepositionDec 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Oct 4, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_detector ...citation / diffrn_detector / diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 23, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.5Mar 20, 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: Ubiquitin-like protein 4A
B: Large proline-rich protein BAG6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4685
Polymers15,6612
Non-polymers8073
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-69 kcal/mol
Surface area7050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.987, 72.987, 48.481
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Detailsbiological unit is the same as asym.

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Components

#1: Protein Ubiquitin-like protein 4A / Ubiquitin-like protein GDX


Mass: 6657.555 Da / Num. of mol.: 1 / Fragment: UNP residues 95-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBL4A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11441
#2: Protein Large proline-rich protein BAG6 / BAG family molecular chaperone regulator 6 / BCL2-associated athanogene 6 / BAG6 / HLA-B-associated ...BAG family molecular chaperone regulator 6 / BCL2-associated athanogene 6 / BAG6 / HLA-B-associated transcript 3 / Protein G3 / Protein Scythe


Mass: 9003.036 Da / Num. of mol.: 1 / Fragment: UNP residues 1048-1123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAG6 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P46379
#3: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS / CHAPS detergent


Mass: 614.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.6
Details: CAPS-NaOH, AmSO4, LiSO4, 2,2,2-trifluoroethanol, CHAPS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.85→48.48 Å / Num. obs: 12717 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 46.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.011 / Net I/σ(I): 31.6 / Num. measured all: 249572 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.85-1.8919.83.4911.1156457890.530.802100
9.06-48.4817.90.027109.9214512010.00698.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
Aimless0.1.27data reduction
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→38.469 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2371 1263 9.95 %
Rwork0.2042 --
obs0.2075 12693 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→38.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms828 0 52 21 901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007890
X-RAY DIFFRACTIONf_angle_d1.151209
X-RAY DIFFRACTIONf_dihedral_angle_d15.672354
X-RAY DIFFRACTIONf_chiral_restr0.049142
X-RAY DIFFRACTIONf_plane_restr0.005149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-1.92410.35611410.32321272X-RAY DIFFRACTION100
1.9241-2.01170.32221400.27931255X-RAY DIFFRACTION100
2.0117-2.11780.25211350.21931262X-RAY DIFFRACTION100
2.1178-2.25040.23661410.20761256X-RAY DIFFRACTION100
2.2504-2.42420.26671390.19971273X-RAY DIFFRACTION100
2.4242-2.66810.24011410.2091250X-RAY DIFFRACTION100
2.6681-3.0540.28861450.22011275X-RAY DIFFRACTION100
3.054-3.84710.22591370.19481285X-RAY DIFFRACTION100
3.8471-38.4770.21441440.19561302X-RAY DIFFRACTION100
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)
15.05441.09542.86452.08312.28152.85-0.1113-0.227-0.03490.0928-0.0421-0.0313-0.13730.44670.20450.3471-0.0016-0.00720.3169-0.01540.3961-77.2316165.93829.0552
28.70283.60852.94848.48336.66068.3037-0.19760.4142-0.8760.43780.4611-0.41781.13171.2046-0.20320.56120.07450.02980.40410.01640.4869-71.3769155.19946.9386
39.8092-4.0297-0.27983.3297-0.08187.75721.04730.5814-2.2358-1.7235-0.18590.03451.6389-1.3207-0.92291.2531-0.1659-0.00570.6312-0.23940.9206-87.1387143.0609-3.6862
44.2392.7024.43265.81223.30215.89070.5602-0.3943-0.4741.1723-0.51430.17422.4476-0.8358-0.20790.8234-0.05630.06390.44210.01440.5139-79.948151.514910.4981
53.6661-0.0328-2.6991.8904-0.03643.014-0.5326-1.062-0.08971.57580.8257-0.14470.9262-0.2382-0.80960.6364-0.0488-0.02050.44520.00930.4069-76.7109160.998921.894
63.2874-3.17692.43317.37830.29721.99930.211-0.6251-0.40570.7906-0.34680.7070.5224-3.4694-0.54950.6413-0.18830.00890.62330.07730.5576-86.1906162.282115.3656
79.7789-6.0411-3.43189.64174.48769.04630.34350.7931-0.2829-0.7236-0.2253-0.40010.16130.3312-0.11320.5257-0.13650.00310.5844-0.03040.4799-82.2622155.9141-4.4459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 93 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 143 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1058 through 1075 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1076 through 1082 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1083 through 1092 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1093 through 1113 )

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