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- PDB-4z4m: Crystal structure of GFP-TAX1BP1 UBZ2 domain fusion protein -

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Basic information

Entry
Database: PDB / ID: 4z4m
TitleCrystal structure of GFP-TAX1BP1 UBZ2 domain fusion protein
ComponentsGreen fluorescent protein,Tax1-binding protein 1
KeywordsFlurorescent Protein / Metal Binding Protein / GFP / TAX1BP1 / UBZ / Zinc-finger
Function / homology
Function and homology information


protein localization to phagocytic vesicle / negative regulation of interleukin-1-mediated signaling pathway / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / phagophore assembly site / negative regulation of tumor necrosis factor-mediated signaling pathway / signaling adaptor activity / negative regulation of canonical NF-kappaB signal transduction / autophagosome / bioluminescence ...protein localization to phagocytic vesicle / negative regulation of interleukin-1-mediated signaling pathway / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / phagophore assembly site / negative regulation of tumor necrosis factor-mediated signaling pathway / signaling adaptor activity / negative regulation of canonical NF-kappaB signal transduction / autophagosome / bioluminescence / generation of precursor metabolites and energy / Negative regulators of DDX58/IFIH1 signaling / Regulation of TNFR1 signaling / autophagy / kinase binding / cytoplasmic vesicle / protein-macromolecule adaptor activity / innate immune response / apoptotic process / negative regulation of apoptotic process / mitochondrion / extracellular exosome / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Calcium binding and coiled-coil domain-like / Calcium binding and coiled-coil domain (CALCOCO1) like / Autophagy receptor zinc finger-C2H2 domain / SKICH domain / : / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / Green Fluorescent Protein / Green fluorescent protein ...Calcium binding and coiled-coil domain-like / Calcium binding and coiled-coil domain (CALCOCO1) like / Autophagy receptor zinc finger-C2H2 domain / SKICH domain / : / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein / Tax1-binding protein 1
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsRohaim, A. / Kawasaki, M. / Wakatsuki, S.
CitationJournal: Febs J. / Year: 2016
Title: A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1.
Authors: Suzuki, N. / Rohaim, A. / Kato, R. / Dikic, I. / Wakatsuki, S. / Kawasaki, M.
History
DepositionApr 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein,Tax1-binding protein 1
B: Green fluorescent protein,Tax1-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3094
Polymers59,1782
Non-polymers1312
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.731, 88.773, 91.949
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein,Tax1-binding protein 1 / TRAF6-binding protein


Mass: 29589.242 Da / Num. of mol.: 2 / Fragment: UBZ2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human)
Gene: GFP, TAX1BP1, T6BP, PRO0105 / Production host: Escherichia coli (E. coli) / References: UniProt: P42212, UniProt: Q86VP1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.4
Details: 0.2 M Ammonium fluoride, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.15→63.87 Å / Num. obs: 30758 / % possible obs: 97.3 % / Redundancy: 8.6 % / Net I/σ(I): 6.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EMA

1ema


Resolution: 2.15→63.87 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.908 / SU B: 14.26 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29818 1504 5 %RANDOM
Rwork0.23422 ---
obs0.23737 28380 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.342 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2--1.27 Å20 Å2
3----0.86 Å2
Refinement stepCycle: 1 / Resolution: 2.15→63.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4092 0 2 175 4269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224196
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0421.9575662
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5525500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20825.094212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.19215712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5211514
X-RAY DIFFRACTIONr_chiral_restr0.1540.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027024
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_it1.0051.52514
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77724064
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.01431682
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.664.51598
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: 2.153→2.208 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 102 -
Rwork0.253 2007 -
obs--95.3 %
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)
11.29940.41170.25641.02410.02111.02990.0716-0.07940.00210.0271-0.0568-0.04910.07870.0025-0.01480.0088-0.0085-0.00170.23980.00020.178422.71934.74734.038
26.84952.1871-3.83490.8604-0.24655.4196-0.42620.4252-0.2614-0.1450.1799-0.14280.3055-0.42250.24640.0532-0.06680.01110.3822-0.03920.225825.68573.50337.492
31.62770.4344-0.10391.06320.19321.24170.0078-0.01740.0194-0.0728-0.00980.0549-0.09520.0640.00190.010.0008-0.00630.23060.00410.17370.03553.84834.083
44.90842.87712.0973.0926-1.66826.4489-0.37360.05910.3043-0.26150.16520.1709-0.0936-0.43160.20840.0276-0.01890.00390.3966-0.02780.2094-2.99415.38637.577
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 229
2X-RAY DIFFRACTION2A235 - 261
3X-RAY DIFFRACTION3B1 - 229
4X-RAY DIFFRACTION4B235 - 261

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