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- PDB-1qp9: STRUCTURE OF HAP1-PC7 COMPLEXED TO THE UAS OF CYC7 -

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Basic information

Entry
Database: PDB / ID: 1qp9
TitleSTRUCTURE OF HAP1-PC7 COMPLEXED TO THE UAS OF CYC7
Components
  • CYP1(HAP1-PC7) ACTIVATORY PROTEIN
  • DNA (5'-D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*T)-3')
  • DNA (5'-D(*AP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*T)-3')
KeywordsTRANSCRIPTION/DNA / ZINC BINUCLEAR CLUSTER / COILED-COIL / HEPTAD REPEAT / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Zn(2)-C6 fungal-type DNA-binding domain / Transcription factor domain, fungi / Fungal specific transcription factor domain / CD2-Gal4 / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain ...Zn(2)-C6 fungal-type DNA-binding domain / Transcription factor domain, fungi / Fungal specific transcription factor domain / CD2-Gal4 / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Few Secondary Structures / Irregular / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Heme-responsive zinc finger transcription factor HAP1 / Heme-responsive zinc finger transcription factor HAP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsLukens, A. / King, D. / Marmorstein, R.
Citation
Journal: Nucleic Acids Res. / Year: 2000
Title: Structure of HAP1-PC7 bound to DNA: implications for DNA recognition and allosteric effects of DNA-binding on transcriptional activation.
Authors: Lukens, A.K. / King, D.A. / Marmorstein, R.
#1: Journal: Nat.Struct.Biol. / Year: 1999
Title: Structure of a HAP1-DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein
Authors: King, D. / Zhang, L. / Guarente, L. / Marmorstein, R.
#2: Journal: Nat.Struct.Biol. / Year: 1999
Title: Structure of HAP-18-DNA implicates direct allosteric effect of protein-DNA interactions on transcriptional activation
Authors: King, D. / Zhang, L. / Guarente, L. / Marmorstein, R.
#3: Journal: Thesis / Year: 1999
Title: Asymmetric binding and transactivation properties of the HAP1 DNA binding domain
Authors: King, D.
History
DepositionJun 1, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: DNA (5'-D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*T)-3')
F: DNA (5'-D(*AP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*T)-3')
G: DNA (5'-D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*T)-3')
H: DNA (5'-D(*AP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*T)-3')
A: CYP1(HAP1-PC7) ACTIVATORY PROTEIN
B: CYP1(HAP1-PC7) ACTIVATORY PROTEIN
C: CYP1(HAP1-PC7) ACTIVATORY PROTEIN
D: CYP1(HAP1-PC7) ACTIVATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,47017
Polymers60,8818
Non-polymers5899
Water1,72996
1
E: DNA (5'-D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*T)-3')
F: DNA (5'-D(*AP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*T)-3')
A: CYP1(HAP1-PC7) ACTIVATORY PROTEIN
B: CYP1(HAP1-PC7) ACTIVATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7689
Polymers30,4414
Non-polymers3275
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: DNA (5'-D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*T)-3')
H: DNA (5'-D(*AP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*T)-3')
C: CYP1(HAP1-PC7) ACTIVATORY PROTEIN
D: CYP1(HAP1-PC7) ACTIVATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7028
Polymers30,4414
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.900, 90.900, 96.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*T)-3') / DNA TARGET OF CYC7


Mass: 6098.964 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SEQUENCE NATURALLY OCCURING IN YEAST
#2: DNA chain DNA (5'-D(*AP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*T)-3') / DNA TARGET OF CYC7


Mass: 6166.030 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SEQUENCE NATURALLY OCCURING IN YEAST
#3: Protein
CYP1(HAP1-PC7) ACTIVATORY PROTEIN


Mass: 9087.827 Da / Num. of mol.: 4 / Fragment: HAP1-PC7 DNA BINDING DOMAIN, RESIDUES 55-130 / Mutation: S63G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PRSET-A / Production host: Escherichia coli (E. coli) / References: UniProt: P12351, UniProt: P0CS82*PLUS
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 11% PEG 400, 10 MM MGSO4, 200 MM KCL, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2MGSO411
3KCL11
4PEG 40012
5MGSO412
6KCL12
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.3 mMprotein1drop
20.4 mMDNA duplex1drop
325 mMMES1drop
45.5 %PEG4001drop
55 mM1dropMgSO4
6100 mM1dropKCl
711 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.917
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 11, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 27006 / Num. obs: 27006 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 14.77 % / Biso Wilson estimate: 60.054 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 28.8
Reflection shellResolution: 2.75→2.86 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.167 / % possible all: 100
Reflection
*PLUS
Num. obs: 14650 / Num. measured all: 27006 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.8→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.294 1812 -
Rwork0.255 --
obs0.255 18115 99.6 %
all-27006 -
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 1571 9 96 4116
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.529
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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