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- PDB-2gli: FIVE-FINGER GLI/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2gli
TitleFIVE-FINGER GLI/DNA COMPLEX
Components
  • DNA (5'-D(*AP*CP*GP*TP*GP*GP*AP*CP*CP*AP*CP*CP*CP*AP*AP*GP*AP*CP*GP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*CP*GP*TP*CP*TP*TP*GP*GP*GP*TP*GP*GP*TP*CP*CP*AP*CP*G)-3')
  • PROTEIN (FIVE-FINGER GLI)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX
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 / positive regulation of cell cycle G1/S phase transition / 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 / positive regulation of cell cycle G1/S phase transition / proximal/distal pattern formation / ciliary tip / prostate gland development / 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 / lung development / Hedgehog 'on' state / negative regulation of canonical Wnt signaling pathway / osteoblast differentiation / response to wounding / microtubule binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
C2H2-type zinc-finger protein GLI-like / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Zinc finger protein GLI1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsPavletich, N.P. / Pabo, C.O.
CitationJournal: Science / Year: 1993
Title: Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers.
Authors: Pavletich, N.P. / Pabo, C.O.
History
DepositionNov 9, 1993Deposition site: NDB / Processing site: NDB
Revision 1.0Nov 9, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*TP*TP*TP*CP*GP*TP*CP*TP*TP*GP*GP*GP*TP*GP*GP*TP*CP*CP*AP*CP*G)-3')
D: DNA (5'-D(*AP*CP*GP*TP*GP*GP*AP*CP*CP*AP*CP*CP*CP*AP*AP*GP*AP*CP*GP*AP*A)-3')
A: PROTEIN (FIVE-FINGER GLI)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3738
Polymers31,0783
Non-polymers2955
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.000, 50.200, 45.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*TP*TP*TP*CP*GP*TP*CP*TP*TP*GP*GP*GP*TP*GP*GP*TP*CP*CP*AP*CP*G)-3')


Mass: 6452.141 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*CP*GP*TP*GP*GP*AP*CP*CP*AP*CP*CP*CP*AP*AP*GP*AP*CP*GP*AP*A)-3')


Mass: 6435.192 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (FIVE-FINGER GLI)


Mass: 18190.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLI ONCOGENE / Gene (production host): GLI ONCOGENE / Production host: Escherichia coli (E. coli) / References: UniProt: P08151
#4: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 40011
3MGCL211
4BIS-TRIS-PROPANE_HCL11
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.5 mMprotein1drop
20.6 mMDNA1drop
360-100 mM1reservoirMgCl2
420-25 %PEG4001reservoir
550 mMBTP-HCl1reservoirpH7.0

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Data collection

DiffractionMean temperature: 98 K
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.6 Å / Num. all: 28039 / Num. obs: 10856
Reflection
*PLUS
Highest resolution: 2.6 Å / % possible obs: 97.9 % / Num. measured all: 28039 / Rmerge(I) obs: 0.0672

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.6→7 Å / σ(F): 2 /
RfactorNum. reflection
obs0.228 9187
Refinement stepCycle: LAST / Resolution: 2.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 855 5 44 2174
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg3.07
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 7 Å / Num. reflection obs: 9187 / σ(F): 2 / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg3.07

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