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- PDB-1hwt: STRUCTURE OF A HAP1/DNA COMPLEX REVEALS DRAMATICALLY ASYMMETRIC D... -

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Basic information

Entry
Database: PDB / ID: 1hwt
TitleSTRUCTURE OF A HAP1/DNA COMPLEX REVEALS DRAMATICALLY ASYMMETRIC DNA BINDING BY A HOMODIMERIC PROTEIN
Components
  • DNA (5'-D(*GP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*C)-3')
  • PROTEIN (HEME ACTIVATOR PROTEIN)
KeywordsGENE REGULATION/DNA / TRANSCRIPTION FACTOR / ASYMMETRY / GAL4 / COMPLEX ACTIVATOR-DNA / GENE REGULATION-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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKing, D.A. / Zhang, L. / Guarente, L. / Marmorstein, R.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Structure of a HAP1-DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein.
Authors: King, D.A. / Zhang, L. / Guarente, L. / Marmorstein, R.
History
DepositionSep 17, 1998Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*C)-3')
B: DNA (5'-D(*GP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*C)-3')
E: DNA (5'-D(*GP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*C)-3')
F: DNA (5'-D(*GP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*C)-3')
C: PROTEIN (HEME ACTIVATOR PROTEIN)
D: PROTEIN (HEME ACTIVATOR PROTEIN)
G: PROTEIN (HEME ACTIVATOR PROTEIN)
H: PROTEIN (HEME ACTIVATOR PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,62817
Polymers63,0408
Non-polymers5899
Water1,04558
1
A: DNA (5'-D(*GP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*C)-3')
B: DNA (5'-D(*GP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*C)-3')
C: PROTEIN (HEME ACTIVATOR PROTEIN)
D: PROTEIN (HEME ACTIVATOR PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8479
Polymers31,5204
Non-polymers3275
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*GP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*C)-3')
F: DNA (5'-D(*GP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*C)-3')
G: PROTEIN (HEME ACTIVATOR PROTEIN)
H: PROTEIN (HEME ACTIVATOR PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7818
Polymers31,5204
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.600, 85.700, 94.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper: (Code: given
Matrix: (-0.995828, 0.056911, 0.071327), (0.077273, 0.110232, 0.990897), (0.048531, 0.992275, -0.114169)
Vector: 16.938, 13.784, -17.15)

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Components

#1: DNA chain DNA (5'-D(*GP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*C)-3') / UAS CYC7


Mass: 6099.952 Da / Num. of mol.: 2 / Fragment: UPSTREAM ACTIVATION SEQUENCE / Source method: obtained synthetically / Details: SEQUENCE FROM SACCHAROMYCES CEREVISIAE
#2: DNA chain DNA (5'-D(*GP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*C)-3') / UAS CYC7


Mass: 6167.018 Da / Num. of mol.: 2 / Fragment: UPSTREAM ACTIVATION SEQUENCE / Source method: obtained synthetically / Details: SEQUENCE FROM SACCHAROMYCES CEREVISIAE
#3: Protein
PROTEIN (HEME ACTIVATOR PROTEIN) / HAP1 / CYP1 ACTIVATORY PROTEIN


Mass: 9626.401 Da / Num. of mol.: 4 / Fragment: DNA BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: BWG-1-7A-DCYC1 / Plasmid: PRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 LYSS / 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.: 58 / 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: 2.67 Å3/Da / Density % sol: 54.35 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: 0.3 MM PROTEIN, 0.4 MM DNA DUPLEX, 5% PEG 2000, 100 MM KCL 5 MM MGCL2, 0.1 MM CO(NH3)6CL3, 25 MM MES (PH 5.6), VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1KCL11
2MGCL211
3[CO(NH3)6]CL311
4MES11
5PEG 200011
6PEG 200012
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.3 mMprotein1drop
20.4 mMDNA duplex1drop
35 %PEG20001drop
4100 mM1dropKCl
55 mM1dropMgCl2
60.1 mM1dropCo(NH3)6Cl3
725 mMMES1drop
810 %PEG20001reservoir
9200 mM1reservoirKCl
1010 mM1reservoirMgCl2
110.2 mM1reservoirCo(NH3)6Cl3
1250 mMMES1reservoir

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 15, 1997 / Details: YALE MIRRORS
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→8 Å / Num. obs: 23274 / % possible obs: 91 % / Observed criterion σ(I): 1 / Redundancy: 1.7 % / Rsym value: 0.083
Reflection
*PLUS
% possible obs: 91.6 % / Num. measured all: 41241 / Rmerge(I) obs: 0.083

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HAP1_18

Resolution: 2.5→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.291 2098 10 %RANDOM
Rwork0.246 ---
obs0.246 20768 82.2 %-
Displacement parametersBiso mean: 26.6 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 1628 9 58 4062
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.4
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_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev Biso (Å2)Weight Biso Weight position
11RESTRAINTSX-RAY DIFFRACTION1.3321300
22X-RAY DIFFRACTION0.9591300
33X-RAY DIFFRACTION1.3391300
44X-RAY DIFFRACTION1.1331300
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.342 219 10 %
Rwork0.317 1975 -
obs--83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3PARAM.ZNCTOPH.ZNC
X-RAY DIFFRACTION4TOPH19.SOL

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