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- PDB-8y7v: Crystal structure of CP2c/LSF DNA-binding domain -

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Basic information

Entry
Database: PDB / ID: 8y7v
TitleCrystal structure of CP2c/LSF DNA-binding domain
ComponentsAlpha-globin transcription factor CP2
KeywordsTRANSCRIPTION / transcription factor CP2c complexes / transcriptional regulation
Function / homology
Function and homology information


mRNA transcription by RNA polymerase II / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / cytosol
Similarity search - Function
Transcription factor CP2, SAM domain / GRHL1-like, C-terminal domain / CP2 transcription factor / : / CP2 transcription factor / Grh/CP2 DNA-binding (DB) domain profile. / SAM domain / SAM domain (Sterile alpha motif) / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
Alpha-globin transcription factor CP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsPark, J. / Lee, S.J. / Won, H.S. / Lee, S.H. / Lee, S.H. / Kim, S.J. / Lee, S.I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of CP2c/LSF DNA-binding domain
Authors: Park, J. / Lee, S.H. / Lee, S.H. / Kim, S.J. / Lee, S.I. / Won, H.S. / Lee, S.J.
History
DepositionFeb 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-globin transcription factor CP2


Theoretical massNumber of molelcules
Total (without water)25,9541
Polymers25,9541
Non-polymers00
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11110 Å2
Unit cell
Length a, b, c (Å)57.093, 57.093, 130.642
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-466-

HOH

21A-504-

HOH

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Components

#1: Protein Alpha-globin transcription factor CP2


Mass: 25953.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Tfcp2, Tcfcp2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ERA0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.005 M Magnesium chloride hexahydrate, 0.05 M HEPES sodium pH 7.0, 25% v/v Polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→29.61 Å / Num. obs: 28993 / % possible obs: 98.67 % / Redundancy: 15.6 % / Biso Wilson estimate: 16.99 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 31.69
Reflection shellResolution: 1.6→1.657 Å / Mean I/σ(I) obs: 8.31 / Num. unique obs: 2775 / CC1/2: 0.984 / CC star: 0.996

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→29.61 Å / SU ML: 0.1457 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 20.7439
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2294 2000 6.9 %
Rwork0.1915 26993 -
obs0.1941 28993 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.54 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1681 0 0 231 1912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651719
X-RAY DIFFRACTIONf_angle_d0.91772323
X-RAY DIFFRACTIONf_chiral_restr0.0622254
X-RAY DIFFRACTIONf_plane_restr0.0072301
X-RAY DIFFRACTIONf_dihedral_angle_d6.2143222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.21471380.19021854X-RAY DIFFRACTION96.93
1.64-1.680.21831360.19761848X-RAY DIFFRACTION96.64
1.68-1.730.24211380.19221863X-RAY DIFFRACTION97.75
1.73-1.790.21731410.19911886X-RAY DIFFRACTION98.02
1.79-1.850.29421390.19621884X-RAY DIFFRACTION98.16
1.85-1.930.24811390.20831886X-RAY DIFFRACTION98.25
1.93-2.020.22791400.19241892X-RAY DIFFRACTION98.55
2.02-2.120.20061450.18831952X-RAY DIFFRACTION99.53
2.12-2.250.22591420.18891914X-RAY DIFFRACTION99.42
2.25-2.430.26141420.20471927X-RAY DIFFRACTION99.28
2.43-2.670.23441450.20981952X-RAY DIFFRACTION99.38
2.67-3.060.26261470.19621976X-RAY DIFFRACTION99.72
3.06-3.850.19541490.17882018X-RAY DIFFRACTION99.82
3.85-29.610.22711590.18332141X-RAY DIFFRACTION99.87

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