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- PDB-1kb4: Crystal Structure of VDR DNA-binding Domain Bound to a Canonical ... -

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Basic information

Entry
Database: PDB / ID: 1kb4
TitleCrystal Structure of VDR DNA-binding Domain Bound to a Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element
Components
  • 5'-D(*CP*AP*CP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*A)-3'
  • 5'-D(*TP*GP*AP*CP*CP*TP*TP*CP*GP*TP*GP*AP*CP*CP*TP*GP*TP*G)-3'
  • Vitamin D3 Receptor
KeywordsTRANSCRIPTION/DNA / VDR / NUCLEAR RECEPTOR / PROTEIN-DNA COMPLEX / VITAMIN D / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


: / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / positive regulation of keratinocyte differentiation ...: / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / positive regulation of keratinocyte differentiation / phosphate ion transmembrane transport / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / intestinal absorption / mammary gland branching involved in pregnancy / decidualization / nuclear steroid receptor activity / negative regulation of keratinocyte proliferation / positive regulation of bone mineralization / nuclear retinoid X receptor binding / retinoic acid receptor signaling pathway / intracellular receptor signaling pathway / lactation / skeletal system development / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / cell morphogenesis / intracellular calcium ion homeostasis / calcium ion transport / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / receptor complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Vitamin D receptor / VDR, DNA-binding domain / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. ...Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Vitamin D receptor / VDR, DNA-binding domain / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Vitamin D3 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsShaffer, P.L. / Gewirth, D.T.
CitationJournal: EMBO J. / Year: 2002
Title: Structural basis of VDR-DNA interactions on direct repeat response elements.
Authors: Shaffer, P.L. / Gewirth, D.T.
History
DepositionNov 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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: 5'-D(*CP*AP*CP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*A)-3'
D: 5'-D(*TP*GP*AP*CP*CP*TP*TP*CP*GP*TP*GP*AP*CP*CP*TP*GP*TP*G)-3'
A: Vitamin D3 Receptor
B: Vitamin D3 Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2018
Polymers36,9404
Non-polymers2624
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.50, 61.50, 241.97
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 5534.607 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Canonical Direct Repeat with 3 Base Pair Spacer (DR3) Response Element
#2: DNA chain 5'-D(*TP*GP*AP*CP*CP*TP*TP*CP*GP*TP*GP*AP*CP*CP*TP*GP*TP*G)-3'


Mass: 5498.551 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Canonical Direct Repeat with 3 Base Pair Spacer (DR3) Response Element
#3: Protein Vitamin D3 Receptor / VDR / 1 / 25-DIHYDROXYVITAMIN D3 RECEPTOR


Mass: 12953.305 Da / Num. of mol.: 2 / Fragment: DNA-binding Domain (Residues 16-125)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VDR / Plasmid: PET11A-VDR-N1-RPLKS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11473
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 59.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 8000, magnesium chloride, MES, glycerol, DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2MgCl211
3MES11
4glycerol11
5DTT11
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.33-0.66 mMprotein1drop
25 mMTris1droppH7.6
350 mM1dropNaCl
42 mMdithiothreitol1drop
54-6 %PEG40001reservoir
650 mMMES1reservoirpH5.6
75 mM1reservoirMgCl2
810 %glycerol1reservoir
910 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0332 Å
DetectorType: APS-1 / Detector: CCD / Date: Sep 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 12384 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 79.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 27.2
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1173 / % possible all: 99
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.39

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TR Half-Complex from PDB Entry 2NLL

2nll


Resolution: 2.8→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 464135.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD FUNCTION
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1124 10 %RANDOM
Rwork0.214 ---
all-11200 --
obs-11200 91.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.5931 Å2 / ksol: 0.309478 e/Å3
Displacement parametersBiso mean: 76 Å2
Baniso -1Baniso -2Baniso -3
1-24.32 Å20 Å20 Å2
2--24.32 Å20 Å2
3----48.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.78 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 732 4 31 2235
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.31
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it1.542
X-RAY DIFFRACTIONc_scangle_it2.532.5
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.486 81 8.9 %
Rwork0.472 828 -
obs--77 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5PARAM_ZN
Refinement
*PLUS
Lowest resolution: 50 Å / Num. reflection obs: 9350 / % reflection Rfree: 10 % / Rfactor obs: 0.214 / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0154
X-RAY DIFFRACTIONc_angle_deg1.69
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.31
LS refinement shell
*PLUS
Rfactor Rfree: 0.486 / Rfactor Rwork: 0.472 / Rfactor obs: 0.472

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