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- PDB-6xzk: Structure of zVDR LBD-Calcitriol in complex with chimera 13 -

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Basic information

Entry
Database: PDB / ID: 6xzk
TitleStructure of zVDR LBD-Calcitriol in complex with chimera 13
Components
  • GLU-ASN-ALA-UIA-URL-URY-URV-UZN-LYS
  • Vitamin D3 receptor A
KeywordsGENE REGULATION / Nuclear Receptor / Foldamer / Helix mimicry / Protein-protein Interaction
Function / homology
Function and homology information


heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / lithocholic acid binding / hematopoietic stem cell proliferation / heart looping / calcium ion homeostasis / intracellular receptor signaling pathway ...heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / lithocholic acid binding / hematopoietic stem cell proliferation / heart looping / calcium ion homeostasis / intracellular receptor signaling pathway / ossification / nuclear receptor activity / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
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 ...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
Similarity search - Domain/homology
ACETATE ION / Chem-VDX / Vitamin D3 receptor A
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBuratto, J. / Belorusova, A.Y. / Rochel, N. / Guichard, G.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Structural Basis for alpha-Helix Mimicry and Inhibition of Protein-Protein Interactions with Oligourea Foldamers.
Authors: Cussol, L. / Mauran-Ambrosino, L. / Buratto, J. / Belorusova, A.Y. / Neuville, M. / Osz, J. / Fribourg, S. / Fremaux, J. / Dolain, C. / Goudreau, S.R. / Rochel, N. / Guichard, G.
History
DepositionFeb 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vitamin D3 receptor A
B: GLU-ASN-ALA-UIA-URL-URY-URV-UZN-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7625
Polymers35,2272
Non-polymers5353
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-4 kcal/mol
Surface area11740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.112, 66.112, 262.488
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-683-

HOH

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Components

#1: Protein Vitamin D3 receptor A / VDR-A / 1 / 25-dihydroxyvitamin D3 receptor A / Nuclear receptor subfamily 1 group I member 1-A


Mass: 34060.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: vdra, nr1i1a, vdr / Production host: Escherichia coli (E. coli) / References: UniProt: Q9PTN2
#2: Protein/peptide GLU-ASN-ALA-UIA-URL-URY-URV-UZN-LYS


Mass: 1166.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-VDX / 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL / 1,25 DIHYDROXY VITAMIN D3


Mass: 416.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: Lithium sulfate 1.8 M, Mes 100 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→14.931 Å / Num. obs: 23222 / % possible obs: 96.24 % / Redundancy: 1.2 % / Rpim(I) all: 0.0127 / Net I/σ(I): 16.04
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 3.32 / Num. unique obs: 1833 / Rpim(I) all: 0.332 / % possible all: 78.57

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HC4

2hc4


Resolution: 2→14.931 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.15
RfactorNum. reflection% reflection
Rfree0.2235 1128 4.87 %
Rwork0.2011 --
obs0.2023 23167 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.56 Å2 / Biso mean: 49.0136 Å2 / Biso min: 27 Å2
Refinement stepCycle: final / Resolution: 2→14.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 38 100 2083
Biso mean--36.27 54.37 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032027
X-RAY DIFFRACTIONf_angle_d0.7082733
X-RAY DIFFRACTIONf_chiral_restr0.038314
X-RAY DIFFRACTIONf_plane_restr0.005348
X-RAY DIFFRACTIONf_dihedral_angle_d16.0421231
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0001-2.09090.2543890.2573223880
2.0909-2.20080.27611480.2449268196
2.2008-2.33820.24761350.2287275799
2.3382-2.5180.22981470.2232782100
2.518-2.76990.25561460.22362832100
2.7699-3.16740.27031420.22392840100
3.1674-3.97810.20871580.1946286499
3.9781-14.9310.19791630.174304598
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8298-0.877-1.16393.40092.89473.8304-0.0091-0.25410.1088-0.20350.04010.039-0.30740.1258-0.00450.2382-0.03890.01290.408-0.01290.3037-33.392430.0256-5.0982
24.3053-0.3658-2.23864.73111.5377.8515-0.2725-0.4789-0.78120.17220.04010.31480.9201-0.05140.26560.3871-0.01920.08530.38480.08810.4123-32.770912.8711-0.8425
35.66621.3811-1.59325.09910.33224.5074-0.0844-0.90420.25740.16260.263-0.2013-0.39590.4657-0.16760.30980.0164-0.0110.6887-0.13790.3493-29.67635.73628.6662
43.2704-1.37-1.72281.86051.77547.2659-0.123-0.6501-0.08970.09150.2321-0.09570.17550.6984-0.14440.188-0.00110.00690.4085-0.02610.343-20.766221.9032-5.6104
57.44813.428-2.0647.07182.36112.57010.0953-0.45710.6761-0.73410.00240.2808-1.86631.0134-0.10050.56-0.12030.04090.3992-0.0620.407-24.386536.9803-17.8869
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 154 through 305 )A154 - 305
2X-RAY DIFFRACTION2chain 'A' and (resid 306 through 351 )A306 - 351
3X-RAY DIFFRACTION3chain 'A' and (resid 352 through 404 )A352 - 404
4X-RAY DIFFRACTION4chain 'A' and (resid 405 through 452 )A405 - 452
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 9 )B1 - 9

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