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- PDB-8hov: Crystal structure of Hms1p from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 8hov
TitleCrystal structure of Hms1p from Saccharomyces cerevisiae
Components
  • DNA (5'-D(*AP*TP*GP*CP*GP*TP*GP*A)-3')
  • DNA (5'-D(*TP*CP*AP*CP*GP*CP*AP*T)-3')
  • Transcription factor HMS1
KeywordsDNA BINDING PROTEIN/DNA / transcription factor / DNA binding domain / DNA binding protein / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


pseudohyphal growth / DNA-binding transcription activator activity / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
: / Helix-loop-helix DNA-binding domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / Probable transcription factor HMS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsKhan, M.H. / Wang, C.C. / Xue, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Molecular recognition of the promoter DNA signature sequence by Hms1p DBD.
Authors: Khan, M.H. / Chenchen, W. / Rahman, N. / Lu, X. / Zeng, F. / Zhu, Z. / Niu, L.
History
DepositionDec 11, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2Jan 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor HMS1
B: Transcription factor HMS1
C: Transcription factor HMS1
D: Transcription factor HMS1
E: Transcription factor HMS1
F: Transcription factor HMS1
G: DNA (5'-D(*TP*CP*AP*CP*GP*CP*AP*T)-3')
H: DNA (5'-D(*TP*CP*AP*CP*GP*CP*AP*T)-3')
I: DNA (5'-D(*AP*TP*GP*CP*GP*TP*GP*A)-3')
J: DNA (5'-D(*AP*TP*GP*CP*GP*TP*GP*A)-3')
K: DNA (5'-D(*TP*CP*AP*CP*GP*CP*AP*T)-3')
L: DNA (5'-D(*AP*TP*GP*CP*GP*TP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)90,05412
Polymers90,05412
Non-polymers00
Water95553
1
A: Transcription factor HMS1
C: Transcription factor HMS1
G: DNA (5'-D(*TP*CP*AP*CP*GP*CP*AP*T)-3')
J: DNA (5'-D(*AP*TP*GP*CP*GP*TP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)30,0184
Polymers30,0184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-46 kcal/mol
Surface area12270 Å2
MethodPISA
2
B: Transcription factor HMS1
F: Transcription factor HMS1
K: DNA (5'-D(*TP*CP*AP*CP*GP*CP*AP*T)-3')
L: DNA (5'-D(*AP*TP*GP*CP*GP*TP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)30,0184
Polymers30,0184
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-46 kcal/mol
Surface area12090 Å2
MethodPISA
3
D: Transcription factor HMS1
E: Transcription factor HMS1
H: DNA (5'-D(*TP*CP*AP*CP*GP*CP*AP*T)-3')
I: DNA (5'-D(*AP*TP*GP*CP*GP*TP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)30,0184
Polymers30,0184
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-46 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.416, 99.175, 79.998
Angle α, β, γ (deg.)90.000, 109.250, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Transcription factor HMS1 / High-copy MEP suppressor protein 1


Mass: 12582.369 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HMS1, YOR032C, OR26.22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12398
#2: DNA chain DNA (5'-D(*TP*CP*AP*CP*GP*CP*AP*T)-3')


Mass: 2386.593 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(*AP*TP*GP*CP*GP*TP*GP*A)-3')


Mass: 2466.641 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.26 Å3/Da / Density % sol: 62.28 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium citrate, pH 5.0, 8 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.77→50 Å / Num. obs: 28197 / % possible obs: 94.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 63.76 Å2 / CC1/2: 1 / Net I/σ(I): 16.47
Reflection shellResolution: 2.77→2.82 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 1224 / Rpim(I) all: 0.371 / Rrim(I) all: 0.913 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIXdev_4778refinement
PHENIXdev_4778model building
HKL-2000data reduction
Cootmodel building
PHASERphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→33.66 Å / SU ML: 0.4615 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.6316
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2736 1324 4.83 %
Rwork0.2336 26113 -
obs0.2355 27435 92.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.71 Å2
Refinement stepCycle: LAST / Resolution: 2.77→33.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4148 966 0 53 5167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045274
X-RAY DIFFRACTIONf_angle_d0.69477301
X-RAY DIFFRACTIONf_chiral_restr0.0679862
X-RAY DIFFRACTIONf_plane_restr0.003759
X-RAY DIFFRACTIONf_dihedral_angle_d18.35462125
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.880.4141360.38092699X-RAY DIFFRACTION87.15
2.88-3.010.41470.35613064X-RAY DIFFRACTION98.26
3.01-3.170.38671360.32553045X-RAY DIFFRACTION97.88
3.17-3.370.34871340.29632950X-RAY DIFFRACTION94.43
3.37-3.610.32931600.27332770X-RAY DIFFRACTION96
3.65-3.990.35411180.28852173X-RAY DIFFRACTION74.82
3.99-4.570.21371680.18773096X-RAY DIFFRACTION99.91
4.57-5.750.22111690.20453133X-RAY DIFFRACTION99.91
5.75-33.660.22691560.17053183X-RAY DIFFRACTION99.76

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