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- PDB-2vz5: Structure of the PDZ domain of Tax1 (human T-cell leukemia virus ... -

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Basic information

Entry
Database: PDB / ID: 2vz5
TitleStructure of the PDZ domain of Tax1 (human T-cell leukemia virus type I) binding protein 3
ComponentsTAX1-BINDING PROTEIN 3
KeywordsPROTEIN BINDING / WNT SIGNALING PATHWAY / NUCLEUS / CYTOPLASM / PDZ DOMAIN
Function / homology
Function and homology information


negative regulation of protein localization to cell surface / RHO GTPases Activate Rhotekin and Rhophilins / activation of GTPase activity / negative regulation of Wnt signaling pathway / Rho protein signal transduction / fibrillar center / beta-catenin binding / Wnt signaling pathway / actin cytoskeleton / negative regulation of cell population proliferation ...negative regulation of protein localization to cell surface / RHO GTPases Activate Rhotekin and Rhophilins / activation of GTPase activity / negative regulation of Wnt signaling pathway / Rho protein signal transduction / fibrillar center / beta-catenin binding / Wnt signaling pathway / actin cytoskeleton / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tax1-binding protein 3 / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
IMIDAZOLE / Tax1-binding protein 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.738 Å
AuthorsMurray, J.W. / Shafqat, N. / Yue, W. / Pilka, E. / Johannsson, C. / Salah, E. / Cooper, C. / Elkins, J.M. / Pike, A.C. / Roos, A. ...Murray, J.W. / Shafqat, N. / Yue, W. / Pilka, E. / Johannsson, C. / Salah, E. / Cooper, C. / Elkins, J.M. / Pike, A.C. / Roos, A. / Filippakopoulos, P. / von Delft, F. / Wickstroem, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Oppermann, U.
CitationJournal: To be Published
Title: The Structure of the Pdz Domain of Tax1BP
Authors: Murray, J.W. / Shafqat, N. / Yue, W. / Pilka, E. / Johannsson, C. / Salah, E. / Cooper, C. / Elkins, J.M. / Pike, A.C. / Roos, A. / Filippakopoulos, P. / von Delft, F. / Wickstroem, M. / ...Authors: Murray, J.W. / Shafqat, N. / Yue, W. / Pilka, E. / Johannsson, C. / Salah, E. / Cooper, C. / Elkins, J.M. / Pike, A.C. / Roos, A. / Filippakopoulos, P. / von Delft, F. / Wickstroem, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Oppermann, U.
History
DepositionJul 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Atomic model / Non-polymer description ...Atomic model / Non-polymer description / Other / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Dec 13, 2023Group: 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TAX1-BINDING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9606
Polymers15,6561
Non-polymers3045
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.813, 59.813, 121.289
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1133-

CL

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Components

#1: Protein TAX1-BINDING PROTEIN 3 / TAX INTERACTION PROTEIN 1 / TIP-1 / GLUTAMINASE-INTERACTING PROTEIN / HUMAN T-CELL LEUKEMIA VIRUS ...TAX INTERACTION PROTEIN 1 / TIP-1 / GLUTAMINASE-INTERACTING PROTEIN / HUMAN T-CELL LEUKEMIA VIRUS TYPE I BINDING PROTEIN 3


Mass: 15655.637 Da / Num. of mol.: 1 / Fragment: PDZ DOMAIN, RESIDUES 13-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA-R3 / References: UniProt: O14907
#2: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growDetails: 15% W/V PEG 3350, 0.15 M ZN ACETATE, 0.1 M NA ACETATE PH 3.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9764
DetectorType: MARRESEARCH / Detector: CCD / Date: May 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 1.74→23.82 Å / Num. obs: 13938 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.82 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.94
Reflection shellResolution: 1.74→1.83 Å / Redundancy: 11.66 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 0.88 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HE2

2he2


Resolution: 1.738→23.819 Å / SU ML: 0.23 / σ(F): 0.03 / Phase error: 18.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 666 5 %
Rwork0.1735 --
obs0.1761 13415 96.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.29 Å2 / ksol: 0.409 e/Å3
Refinement stepCycle: LAST / Resolution: 1.738→23.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms857 0 13 115 985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071764
X-RAY DIFFRACTIONf_angle_d0.9423175
X-RAY DIFFRACTIONf_dihedral_angle_d15.459468
X-RAY DIFFRACTIONf_chiral_restr0.074139
X-RAY DIFFRACTIONf_plane_restr0.004274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7381-1.87220.25941170.19932325X-RAY DIFFRACTION91
1.8722-2.06050.19481300.15112445X-RAY DIFFRACTION95
2.0605-2.35840.18051530.1442530X-RAY DIFFRACTION98
2.3584-2.97050.2231320.14472616X-RAY DIFFRACTION99
2.9705-23.82080.23571340.19312833X-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)
10.6933-0.28530.1562.4638-0.26471.70890.02450.06140.12090.1205-0.06430.027-0.03080.06300.1104-0.0162-0.00680.12210.01930.121222.24630.5716.0768
20.0203-0.03150.01390.0008-0.00370.03720.06490.3974-0.0177-0.3001-0.07710.0359-0.0205-0.15760.00060.18930.007300.19610.04050.150737.812131.558327.0576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 11:113
2X-RAY DIFFRACTION2CHAIN A AND RESID 123:128

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