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- PDB-6e33: Crystal Structure of Pho7-DNA complex -

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Basic information

Entry
Database: PDB / ID: 6.0E+33
TitleCrystal Structure of Pho7-DNA complex
Components
  • DNA (5'-D(*GP*AP*TP*TP*TP*GP*AP*AP*TP*GP*TP*CP*CP*GP*AP*AP*GP*GP*AP*T)-3')
  • DNA (5'-D(*TP*CP*CP*TP*TP*CP*GP*GP*AP*CP*AP*TP*TP*CP*AP*AP*AP*TP*CP*A)-3')
  • Uncharacterized transcriptional regulatory protein C27B12.11c
KeywordsTRANSCRIPTION / Zn2Cys6 / Zinc binuclear cluster transcription factor / transcription factor-DNA complex / Pho7
Function / homology
Function and homology information


intracellular phosphate ion homeostasis / cellular response to phosphate starvation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / cellular response to starvation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin ...intracellular phosphate ion homeostasis / cellular response to phosphate starvation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / cellular response to starvation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
DNA / DNA (> 10) / Uncharacterized transcriptional regulatory protein C27B12.11c
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.705 Å
AuthorsGarg, A. / Goldgur, Y. / Shuman, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 GM126945 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Distinctive structural basis for DNA recognition by the fission yeast Zn2Cys6 transcription factor Pho7 and its role in phosphate homeostasis.
Authors: Garg, A. / Goldgur, Y. / Schwer, B. / Shuman, S.
History
DepositionJul 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 2.0Nov 21, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct.title / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized transcriptional regulatory protein C27B12.11c
C: DNA (5'-D(*TP*CP*CP*TP*TP*CP*GP*GP*AP*CP*AP*TP*TP*CP*AP*AP*AP*TP*CP*A)-3')
B: DNA (5'-D(*GP*AP*TP*TP*TP*GP*AP*AP*TP*GP*TP*CP*CP*GP*AP*AP*GP*GP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4025
Polymers19,2713
Non-polymers1312
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-22 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.827, 40.682, 58.237
Angle α, β, γ (deg.)90.00, 105.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized transcriptional regulatory protein C27B12.11c


Mass: 7005.494 Da / Num. of mol.: 1 / Fragment: residues 279-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: pi067, SPBC27B12.11c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O13658
#2: DNA chain DNA (5'-D(*TP*CP*CP*TP*TP*CP*GP*GP*AP*CP*AP*TP*TP*CP*AP*AP*AP*TP*CP*A)-3')


Mass: 6052.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#3: DNA chain DNA (5'-D(*GP*AP*TP*TP*TP*GP*AP*AP*TP*GP*TP*CP*CP*GP*AP*AP*GP*GP*AP*T)-3')


Mass: 6213.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 3.01 Å3/Da / Density % sol: 59.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Tris-HCl pH 7.0, 0.2M NaOAc, 32.5% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2827, 0.97918
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 21, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28271
20.979181
ReflectionResolution: 1.7→50 Å / Num. obs: 24169 / % possible obs: 96.1 % / Redundancy: 5.5 % / CC1/2: 0.932 / Rpim(I) all: 0.04 / Net I/σ(I): 24.1
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1086 / CC1/2: 0.953 / % possible all: 87.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
Omodel building
RefinementMethod to determine structure: SAD / Resolution: 1.705→43.131 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.63
RfactorNum. reflection% reflection
Rfree0.2152 1121 4.66 %
Rwork0.1881 --
obs0.1893 24060 95.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.705→43.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms460 814 2 269 1545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061377
X-RAY DIFFRACTIONf_angle_d0.8862018
X-RAY DIFFRACTIONf_dihedral_angle_d25.024708
X-RAY DIFFRACTIONf_chiral_restr0.048221
X-RAY DIFFRACTIONf_plane_restr0.007120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7046-1.78220.30191330.25932635X-RAY DIFFRACTION88
1.7822-1.87610.22831530.21672932X-RAY DIFFRACTION98
1.8761-1.99370.25781300.21012967X-RAY DIFFRACTION99
1.9937-2.14760.21991320.20952940X-RAY DIFFRACTION98
2.1476-2.36370.22231490.19532954X-RAY DIFFRACTION99
2.3637-2.70570.22011530.19922960X-RAY DIFFRACTION98
2.7057-3.40870.21751260.20412789X-RAY DIFFRACTION92
3.4087-43.14520.19191450.15182762X-RAY DIFFRACTION90
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)
14.4228-1.21510.20136.0281-0.5984.1676-0.1727-0.1647-0.0716-0.04560.2255-0.0097-0.0105-0.028-0.06830.1406-0.01880.02380.12710.01240.105839.632-0.396135.2697
21.6299-1.33242.47523.5097-4.12758.9227-0.1798-0.0982-0.00310.31090.41340.2621-1.0682-1.0279-0.33810.27330.07910.05580.23670.04240.202534.54447.808138.9707
30.94250.4303-0.30820.8720.14424.5604-0.0342-0.3417-0.17240.47080.068-0.11380.2485-0.0385-0.01530.28530.0328-0.00580.180.02960.181541.5192-6.375360.334
43.60440.08111.37086.90992.88547.70020.30130.742-0.3899-0.62230.07510.2197-0.86190.0379-0.00480.2179-0.1098-0.14780.64450.03220.463327.2791-3.837623.3186
50.86110.38330.74111.5808-0.48225.3062-0.0218-0.0932-0.10580.07740.142-0.08080.02840.1928-0.19370.15320.02070.03560.14620.01310.201743.4775-7.977151.4916
68.0524-0.19154.1112.1731-1.02264.68150.0250.1289-0.15820.09850.0878-0.247-0.05380.5865-0.12910.15820.01990.03780.2568-0.02240.159247.3943-6.460356.365
75.09950.4893.40340.8310.26844.03670.24860.2205-0.5772-0.1440.00010.29660.4132-0.8046-0.23630.2539-0.0881-0.03110.412-0.02490.28828.9497-8.254228.1289
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 60 )
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 5 )
5X-RAY DIFFRACTION5chain 'C' and (resid 6 through 20 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 10 )
7X-RAY DIFFRACTION7chain 'B' and (resid 11 through 20 )

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