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- PDB-5aiz: The PIAS-like coactivator Zmiz1 is a direct and selective cofacto... -

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Basic information

Entry
Database: PDB / ID: 5aiz
TitleThe PIAS-like coactivator Zmiz1 is a direct and selective cofactor of Notch1 in T-cell development and leukemia
ComponentsZINC FINGER MIZ DOMAIN-CONTAINING PROTEIN 1
KeywordsZINC-BINDING PROTEIN / PROTEIN
Function / homology
Function and homology information


pyramidal neuron migration to cerebral cortex / SUMO ligase activity / vitellogenesis / SMAD protein signal transduction / positive regulation of T cell differentiation / artery morphogenesis / positive regulation of Notch signaling pathway / SMAD binding / androgen receptor signaling pathway / protein sumoylation ...pyramidal neuron migration to cerebral cortex / SUMO ligase activity / vitellogenesis / SMAD protein signal transduction / positive regulation of T cell differentiation / artery morphogenesis / positive regulation of Notch signaling pathway / SMAD binding / androgen receptor signaling pathway / protein sumoylation / developmental growth / vasculogenesis / heart morphogenesis / transforming growth factor beta receptor signaling pathway / : / positive regulation of fibroblast proliferation / cellular senescence / in utero embryonic development / transcription coactivator activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Zmiz1, N-terminal tetratricopeptide repeat domain / Zmiz1 N-terminal tetratricopeptide repeat domain / MIZ/SP-RING zinc finger / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
ACETATE ION / Zinc finger MIZ domain-containing protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsCho, H.J. / Murai, M. / Chiang, M. / Cierpicki, T.
CitationJournal: Immunity / Year: 2015
Title: The Pias-Like Coactivator Zmiz1 is a Direct and Selective Cofactor of Notch1 in T-Cell Development and Leukemia
Authors: Cho, H.J. / Chiang, M. / Cierpicki, T.
History
DepositionFeb 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: ZINC FINGER MIZ DOMAIN-CONTAINING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3494
Polymers14,2281
Non-polymers1213
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.472, 45.040, 57.518
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 ZINC FINGER MIZ DOMAIN-CONTAINING PROTEIN 1 / PIAS-LIKE PROTEIN ZIMP10 / RETINOIC ACID-INDUCED PROTEIN 17 / ZMIZ1 N-TERMINAL DOMAIN


Mass: 14227.590 Da / Num. of mol.: 1 / Fragment: TPR DOMAIN, UNP RESIDUES 1-118
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: MODIFIED PET32A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: Q9ULJ6
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsZMIZ1 NTD WITH ADDITIONAL GPAMAH SEQUENCE AT THE N- TERMINUS DUE TO CLONING PROCEDURE.

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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: 2.3 Å3/Da / Density % sol: 46.67 %
Description: THE STRUCTURE WAS SOLVED BY SAD PHASING AND AN INITIAL MODEL WAS GENERATED USING AN EARLY VERSION HKL3000
Crystal growpH: 4.5
Details: 2.5 M SODIUM CHLORIDE, 0.2 M LITHIUM SULFATE AND 0.1 M SODIUM ACETATE PH4.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97928
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 11, 2012
RadiationMonochromator: KOHZU MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 12677 / % possible obs: 98.2 % / Observed criterion σ(I): -2 / Redundancy: 10.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 32.85
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.65 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.7→35.46 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.946 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20441 622 4.9 %RANDOM
Rwork0.15839 ---
obs0.16061 12026 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.335 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 9 131 1010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.019899
X-RAY DIFFRACTIONr_bond_other_d0.0020.02855
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.9561215
X-RAY DIFFRACTIONr_angle_other_deg0.95331953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8965111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.37324.04347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54215146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.958158
X-RAY DIFFRACTIONr_chiral_restr0.1170.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021043
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02225
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_it1.71.442442
X-RAY DIFFRACTIONr_mcbond_other1.6361.427440
X-RAY DIFFRACTIONr_mcangle_it2.472.142550
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7921.921457
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.702→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 54 -
Rwork0.184 838 -
obs--93.89 %

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