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- PDB-1cs3: STRUCTURE OF BTB/POZ TRANSCRIPTION REPRESSION DOMAIN FROM PROMELO... -

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Basic information

Entry
Database: PDB / ID: 1cs3
TitleSTRUCTURE OF BTB/POZ TRANSCRIPTION REPRESSION DOMAIN FROM PROMELOCYTIC LEUKEMIA ZINC FINGER ONCOPROTEIN
ComponentsZINC FINGER PROTEIN PLZF
KeywordsTRANSCRIPTION / BTB/POZ / PLZF / TRANSCRIPTION REPRESSION / ONCOPROTEIN / GENE REGULATION
Function / homology
Function and homology information


male germ-line stem cell asymmetric division / type 2 angiotensin receptor binding / forelimb morphogenesis / positive regulation of cartilage development / negative regulation of myeloid cell differentiation / positive regulation of chondrocyte differentiation / mesonephros development / positive regulation of NK T cell differentiation / embryonic pattern specification / myeloid cell differentiation ...male germ-line stem cell asymmetric division / type 2 angiotensin receptor binding / forelimb morphogenesis / positive regulation of cartilage development / negative regulation of myeloid cell differentiation / positive regulation of chondrocyte differentiation / mesonephros development / positive regulation of NK T cell differentiation / embryonic pattern specification / myeloid cell differentiation / positive regulation of ossification / embryonic hindlimb morphogenesis / cartilage development / ossification involved in bone maturation / anterior/posterior pattern specification / embryonic digit morphogenesis / hemopoiesis / protein localization to nucleus / positive regulation of fat cell differentiation / transcription repressor complex / transcription corepressor binding / male germ cell nucleus / central nervous system development / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / DNA-binding transcription activator activity, RNA polymerase II-specific / cell population proliferation / protein ubiquitination / nuclear body / nuclear speck / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / apoptotic process / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / DNA binding / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
C2H2-type zinc finger / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. ...C2H2-type zinc finger / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Zinc finger and BTB domain-containing protein 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsLi, X. / Rauscher III, F.J. / Marmorstein, R.
CitationJournal: Cancer Res. / Year: 1999
Title: Structure-function studies of the BTB/POZ transcriptional repression domain from the promyelocytic leukemia zinc finger oncoprotein.
Authors: Li, X. / Peng, H. / Schultz, D.C. / Lopez-Guisa, J.M. / Rauscher III, F.J. / Marmorstein, R.
History
DepositionAug 16, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.6Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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 PROTEIN PLZF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4413
Polymers13,3241
Non-polymers1162
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ZINC FINGER PROTEIN PLZF
hetero molecules

A: ZINC FINGER PROTEIN PLZF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8816
Polymers26,6492
Non-polymers2334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area4550 Å2
ΔGint-46 kcal/mol
Surface area11260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)38.800, 78.200, 85.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1007-

HOH

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Components

#1: Protein ZINC FINGER PROTEIN PLZF / / PROMYELOCYTIC LEUKEMIA ZINC FINGER PROTEIN


Mass: 13324.340 Da / Num. of mol.: 1 / Fragment: BTB/POZ
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PQE-30 T5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05516
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.42 Å3/Da / Density % sol: 40 %
Crystal growMethod: vapor diffusion / pH: 8
Details: VAPOR DIFFUSION BY 8% ISOPROPANOL, 600mM MAGNESIUM CHLORIDE, 50mM HEPES 7.5 and 50mM TRIS 8.5, pH 8.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: reservoir contains two times the concentration of salts, buffer, and precipitating agent
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
28 %isopropanol1drop
3600 mM1dropMgCl2
450 mMTris-HCl1drop
550 mMHEPES1drop

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9879,0.9795,0.9791, 0.9667
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 3, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98791
20.97951
30.97911
40.96671
ReflectionResolution: 2→20 Å / Num. obs: 8790 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 13 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 35.5
Reflection shellResolution: 2→2.06 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 24 / % possible all: 95
Reflection
*PLUS
Num. measured all: 115110
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
SCALEPACKdata scaling
RefinementResolution: 2→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.272 844 10 %RANDOM
Rwork0.228 ---
obs0.228 8749 96 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.682 Å20 Å20 Å2
2--7.487 Å20 Å2
3----6.936 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 7 61 999
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.09
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.35 89 10 %
Rwork0.336 708 -
obs--70.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1GOL.PARGOL.TOP
X-RAY DIFFRACTION2MG.PAR

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