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- PDB-4bmj: Structure of the UBZ1and2 tandem of the ubiquitin-binding adaptor... -

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Basic information

Entry
Database: PDB / ID: 4bmj
TitleStructure of the UBZ1and2 tandem of the ubiquitin-binding adaptor protein TAX1BP1
ComponentsTAX1-BINDING PROTEIN 1
KeywordsAPOPTOSIS / UBZ DOMAINS / UBIQUITIN / INFLAMMATION
Function / homology
Function and homology information


protein localization to phagocytic vesicle / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / phagophore assembly site / negative regulation of NF-kappaB transcription factor activity / autophagosome / Negative regulators of DDX58/IFIH1 signaling / Regulation of TNFR1 signaling / autophagy / kinase binding ...protein localization to phagocytic vesicle / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / phagophore assembly site / negative regulation of NF-kappaB transcription factor activity / autophagosome / Negative regulators of DDX58/IFIH1 signaling / Regulation of TNFR1 signaling / autophagy / kinase binding / protein-macromolecule adaptor activity / cytoplasmic vesicle / innate immune response / apoptotic process / negative regulation of apoptotic process / mitochondrion / extracellular exosome / metal ion binding / cytosol
Similarity search - Function
Double Stranded RNA Binding Domain - #40 / Calcium binding and coiled-coil domain-like / Calcium binding and coiled-coil domain (CALCOCO1) like / Autophagy receptor zinc finger-C2H2 domain / Double Stranded RNA Binding Domain / SKICH domain / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / Other non-globular / Special
Similarity search - Domain/homology
Tax1-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsCeregido, M.A. / Spinola-Amilibia, M. / Buts, L. / Rivera, J. / Bravo, J. / van Nuland, N.A.J.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: The Structure of Tax1BP1 Ubz1 + 2 Provides Insight Into Target Specificity and Adaptability
Authors: Ceregido, M.A. / Spinola-Amilibia, M. / Buts, L. / Rivera-Torres, J. / Garcia-Pino, A. / Bravo, J. / Van Nuland, N.A.J.
History
DepositionMay 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Aug 9, 2017Group: Data collection / Refinement description / Category: diffrn_detector / refine / Item: _diffrn_detector.type / _refine.pdbx_starting_model
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: TAX1-BINDING PROTEIN 1
B: TAX1-BINDING PROTEIN 1
C: TAX1-BINDING PROTEIN 1
D: TAX1-BINDING PROTEIN 1
E: TAX1-BINDING PROTEIN 1
F: TAX1-BINDING PROTEIN 1
G: TAX1-BINDING PROTEIN 1
H: TAX1-BINDING PROTEIN 1
I: TAX1-BINDING PROTEIN 1
J: TAX1-BINDING PROTEIN 1
K: TAX1-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,52045
Polymers91,65511
Non-polymers1,86434
Water1,65792
1
A: TAX1-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4994
Polymers8,3321
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TAX1-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5345
Polymers8,3321
Non-polymers2024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TAX1-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4994
Polymers8,3321
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TAX1-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4994
Polymers8,3321
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: TAX1-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4994
Polymers8,3321
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: TAX1-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4994
Polymers8,3321
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: TAX1-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4994
Polymers8,3321
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: TAX1-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4994
Polymers8,3321
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: TAX1-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4994
Polymers8,3321
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: TAX1-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4994
Polymers8,3321
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: TAX1-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4994
Polymers8,3321
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.878, 118.878, 327.345
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
31B
41D
51E
61F
71G
81H
91I
101J
111K

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 4 / Auth seq-ID: 16 - 60 / Label seq-ID: 16 - 60

Dom-IDAuth asym-IDLabel asym-ID
1CC
2AA
3BB
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK

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Components

#1: Protein
TAX1-BINDING PROTEIN 1 / TRAF6-BINDING PROTEIN / TAX1BP1


Mass: 8332.310 Da / Num. of mol.: 11 / Fragment: RESIDUES 725-789
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28-6XHIS-PP/TAX1BP1_725-789 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q86VP1
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.65 Å3/Da / Density % sol: 66.3 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.1 M TRIS PH 8.5, 1 M LISO4

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 13, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.59→51.5 Å / Num. obs: 43605 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.38
Reflection shellResolution: 2.59→2.73 Å / Redundancy: 10.44 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 0.96 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→103.14 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.915 / SU B: 20.779 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.436 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25459 1823 5 %RANDOM
Rwork0.21471 ---
obs0.21673 34714 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.732 Å2
Baniso -1Baniso -2Baniso -3
1--3.79 Å2-1.89 Å20 Å2
2---3.79 Å20 Å2
3---5.68 Å2
Refinement stepCycle: LAST / Resolution: 2.75→103.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5761 0 34 92 5887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215977
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.9148104
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6225666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15225.359362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.35315971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.0941511
X-RAY DIFFRACTIONr_chiral_restr0.090.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0224826
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_it0.4471.53443
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87225658
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.16332534
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8434.52446
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 389 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Cmedium positional0.330.5
2Amedium positional0.320.5
3Bmedium positional0.320.5
4Dmedium positional0.390.5
5Emedium positional0.360.5
6Fmedium positional0.470.5
7Gmedium positional0.410.5
8Hmedium positional0.440.5
9Imedium positional0.340.5
10Jmedium positional0.360.5
11Kmedium positional0.30.5
1Cmedium thermal0.492
2Amedium thermal0.582
3Bmedium thermal0.632
4Dmedium thermal0.522
5Emedium thermal0.532
6Fmedium thermal0.512
7Gmedium thermal0.42
8Hmedium thermal0.522
9Imedium thermal0.632
10Jmedium thermal0.722
11Kmedium thermal0.572
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 126 -
Rwork0.32 2521 -
obs--99.96 %
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)
11.4834-0.0029-0.03463.84743.054612.2321-0.1996-0.0092-0.2604-0.13910.00870.21830.30850.21390.1909-0.5266-0.0048-0.01420.08520.0142-0.064392.721424.374167.1227
23.6193-2.1936-2.10837.26954.92039.8326-0.3646-0.3789-0.1190.03580.42090.2224-0.40550.4471-0.0563-0.66850.0245-0.00240.29230.0512-0.12981.832233.1302175.2845
30.9795-0.4147-0.193311.20314.56445.0122-0.16920.0522-0.19390.31240.13020.48110.38580.03070.039-0.5827-0.01470.010.17950.03840.14571.427422.0284170.6485
40.94490.0067-0.248912.84084.15134.9899-0.09420.03690.0681-0.3670.03830.2744-0.39080.06170.056-0.488-0.012-0.01520.18540.01670.124260.105534.9199172.6433
51.21020.8981-0.000815.17321.90483.9073-0.02910.0131-0.07390.29840.0898-0.31730.38910.1556-0.0608-0.57250.0316-0.00610.19950.02830.225349.369522.691173.6835
60.99670.0408-0.278814.5954-2.22434.6348-0.09180.0660.1867-0.6810.1093-0.3409-0.20850.1537-0.0174-0.5678-0.0224-0.03550.16220.02320.143138.469633.0926168.8973
72.42760.51460.014710.7016-4.03035.8616-0.1299-0.0835-0.12820.5584-0.0251-0.44920.06130.09140.1549-0.59340.0552-0.00430.14730.0556-0.009127.819424.2417176.6165
80.8647-0.82760.57839.8497-6.85749.004-0.22010.13170.1418-0.695-0.0375-0.45050.15910.03410.2576-0.5773-0.0223-0.00320.18180.0663-0.098116.769232.8874164.3383
91.5508-0.02581.02554.932-2.870110.9506-0.3118-0.0414-0.08420.66570.0227-0.2295-0.2315-0.20220.289-0.54350.01610.01170.15440.0273-0.20736.907227.4038179.8661
101.4159-0.4201-1.05173.141-0.83812.4524-0.17870.0704-0.035-0.304-0.0526-0.0490.34120.14350.2313-0.5058-0.0498-0.02270.117-0.0006-0.1329-4.264727.6723164.3534
112.15320.34960.31213.21440.354212.9631-0.1936-0.18320.03280.2769-0.0370.1532-0.36240.0780.2306-0.5340.0170.00240.1121-0.0011-0.1102-15.552830.8696177.3749
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 69
2X-RAY DIFFRACTION2B1 - 69
3X-RAY DIFFRACTION3C1 - 69
4X-RAY DIFFRACTION4D1 - 69
5X-RAY DIFFRACTION5E1 - 69
6X-RAY DIFFRACTION6F1 - 69
7X-RAY DIFFRACTION7G1 - 69
8X-RAY DIFFRACTION8H1 - 69
9X-RAY DIFFRACTION9I1 - 69
10X-RAY DIFFRACTION10J1 - 69
11X-RAY DIFFRACTION11K1 - 69

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