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- PDB-9j5e: Crystal structure of Hir2_WD40 in complex with Hpc2_NHRD -

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Basic information

Entry
Database: PDB / ID: 9j5e
TitleCrystal structure of Hir2_WD40 in complex with Hpc2_NHRD
Components
  • Peptide from Histone promoter control protein 2
  • Protein HIR2
KeywordsCHAPERONE / Complex
Function / homology
Function and homology information


negative regulation of chromatin organization / HIR complex / negative regulation of transcription by RNA polymerase III / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / transcription elongation-coupled chromatin remodeling / transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle / transcription corepressor activity / nucleosome assembly / chromatin organization ...negative regulation of chromatin organization / HIR complex / negative regulation of transcription by RNA polymerase III / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / transcription elongation-coupled chromatin remodeling / transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle / transcription corepressor activity / nucleosome assembly / chromatin organization / chromosome / chromatin remodeling / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Hpc2-related domain / HPC2 and ubinuclein domain / TUP1-like enhancer of split / WD repeat HIR1 / TUP1-like enhancer of split / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Protein HIR2 / Histone promoter control protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLin, C.-L.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST 111 - 2311 - B - 005 - 002 - MY2 Taiwan
CitationJournal: To Be Published
Title: Crystal structure of Hir2_WD40 in complex with Hpc2_NHRD
Authors: Lin, C.-L.
History
DepositionAug 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein HIR2
B: Peptide from Histone promoter control protein 2


Theoretical massNumber of molelcules
Total (without water)44,3062
Polymers44,3062
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-9 kcal/mol
Surface area15860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.541, 103.541, 108.503
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Protein HIR2 / Histone transcription regulator 2


Mass: 41881.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: HIR2, YOR038C, OR26.31 / Production host: Escherichia coli (E. coli) / References: UniProt: P32480
#2: Protein/peptide Peptide from Histone promoter control protein 2


Mass: 2423.648 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q01448
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.79 Å3/Da / Density % sol: 67.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 7.0, 1.2M Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 52168 / % possible obs: 99.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 33.69 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 34.11
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 3.95 / Num. unique obs: 5207

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→26.18 Å / SU ML: 0.191 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.7105
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1932 2002 3.84 %
Rwork0.175 50112 -
obs0.1757 52114 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.51 Å2
Refinement stepCycle: LAST / Resolution: 1.9→26.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 0 140 3056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732973
X-RAY DIFFRACTIONf_angle_d0.94654031
X-RAY DIFFRACTIONf_chiral_restr0.063475
X-RAY DIFFRACTIONf_plane_restr0.0071502
X-RAY DIFFRACTIONf_dihedral_angle_d6.3367390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.27461370.2333527X-RAY DIFFRACTION97.84
1.94-20.25471430.20463588X-RAY DIFFRACTION100
2-2.050.19281440.19823582X-RAY DIFFRACTION99.97
2.05-2.120.25521390.20733551X-RAY DIFFRACTION99.95
2.12-2.20.21711430.18323563X-RAY DIFFRACTION100
2.2-2.280.23431420.18733590X-RAY DIFFRACTION100
2.28-2.390.22831440.18983585X-RAY DIFFRACTION100
2.39-2.510.21951450.20293586X-RAY DIFFRACTION99.97
2.51-2.670.21781470.19973566X-RAY DIFFRACTION99.97
2.67-2.880.22711440.20313604X-RAY DIFFRACTION99.97
2.88-3.170.2521450.19643574X-RAY DIFFRACTION100
3.17-3.620.191410.16723593X-RAY DIFFRACTION99.95
3.62-4.560.15841490.14513614X-RAY DIFFRACTION99.97
4.56-26.180.14041390.15513589X-RAY DIFFRACTION98.23
Refinement TLS params.Method: refined / Origin x: -35.4769274102 Å / Origin y: -16.5494333507 Å / Origin z: 0.751806779867 Å
111213212223313233
T0.201223058263 Å20.0125506772996 Å20.00241511642974 Å2-0.179693124561 Å20.0103619204197 Å2--0.193973473626 Å2
L2.03581998595 °2-0.0320322006931 °2-0.208336414168 °2-1.93861125658 °20.21007166716 °2--1.67840361344 °2
S0.00818757771967 Å °0.157680950765 Å °-0.103601069958 Å °0.0590506022618 Å °-0.00969659501868 Å °-0.0884957087635 Å °-0.00592781871384 Å °-0.0293557766245 Å °0.00304825536057 Å °
Refinement TLS groupSelection details: all

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