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- PDB-7t91: Crystal structure of Zinc finger motif 1 and 2 of GLI1 DNA bindin... -

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Basic information

Entry
Database: PDB / ID: 7t91
TitleCrystal structure of Zinc finger motif 1 and 2 of GLI1 DNA binding region
ComponentsIsoform 2 of Zinc finger protein GLI1
KeywordsDNA BINDING PROTEIN / GLI1 / DNA-binding / Zinc finger binding motif / Cancer
Function / homology
Function and homology information


notochord regression / GLI proteins bind promoters of Hh responsive genes to promote transcription / regulation of hepatocyte proliferation / GLI-SUFU complex / ventral midline development / epidermal cell differentiation / pituitary gland development / prostate gland development / proximal/distal pattern formation / ciliary tip ...notochord regression / GLI proteins bind promoters of Hh responsive genes to promote transcription / regulation of hepatocyte proliferation / GLI-SUFU complex / ventral midline development / epidermal cell differentiation / pituitary gland development / prostate gland development / proximal/distal pattern formation / ciliary tip / positive regulation of cell cycle G1/S phase transition / cerebellar cortex morphogenesis / regulation of smoothened signaling pathway / positive regulation of smoothened signaling pathway / dorsal/ventral pattern formation / regulation of osteoblast differentiation / ciliary base / digestive tract morphogenesis / smoothened signaling pathway / axoneme / spermatid development / Hedgehog 'off' state / positive regulation of cardiac muscle cell proliferation / positive regulation of DNA replication / liver regeneration / Degradation of GLI1 by the proteasome / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hedgehog 'on' state / lung development / negative regulation of canonical Wnt signaling pathway / response to wounding / osteoblast differentiation / microtubule binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
C2H2-type zinc-finger protein GLI-like / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Zinc finger protein GLI1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsWu, M. / Zhang, S. / Augelli-Szanfran, C.E. / Boohaker, R.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5RO1CA183921-05 United States
CitationJournal: To Be Published
Title: Crystal structure of Zinc finger motif 1 and 2 of GLI1 DNA binding region
Authors: Wu, M. / Zhang, S. / Augelli-Szafran, C.E. / Boohaker, R.J.
History
DepositionDec 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Zinc finger protein GLI1
B: Isoform 2 of Zinc finger protein GLI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1576
Polymers16,8952
Non-polymers2624
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-17 kcal/mol
Surface area8630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.728, 66.728, 65.909
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Isoform 2 of Zinc finger protein GLI1 / Glioma-associated oncogene / Oncogene GLI


Mass: 8447.468 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLI1, GLI / Production host: Escherichia coli (E. coli) / References: UniProt: P08151
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 291 K / Method: evaporation / Details: 29-32% PEG3350, 0.1M Bis-Tris pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→57.79 Å / Num. obs: 10542 / % possible obs: 100 % / Redundancy: 11.4 % / Rpim(I) all: 0.034 / Net I/σ(I): 17.3
Reflection shellResolution: 2.05→2.1 Å / Num. unique obs: 818 / Rpim(I) all: 0.283

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GLI

2gli


Resolution: 2.05→57.79 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.132 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 510 4.8 %RANDOM
Rwork0.1915 ---
obs0.194 10027 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.65 Å2 / Biso mean: 45.175 Å2 / Biso min: 30.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å2-0.32 Å2-0 Å2
2---0.64 Å20 Å2
3---2.07 Å2
Refinement stepCycle: final / Resolution: 2.05→57.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 4 72 1160
Biso mean--39.66 50.03 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131115
X-RAY DIFFRACTIONr_bond_other_d0.0010.018967
X-RAY DIFFRACTIONr_angle_refined_deg1.241.6391496
X-RAY DIFFRACTIONr_angle_other_deg1.2661.592228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.70620.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38715194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.41512
X-RAY DIFFRACTIONr_chiral_restr0.0540.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021274
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02294
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 40 -
Rwork0.251 732 -
all-772 -
obs--100 %

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