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- PDB-6xzv: Structure of zVDR LBD-Calcitriol in complex with chimera 18 -

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Basic information

Entry
Database: PDB / ID: 6xzv
TitleStructure of zVDR LBD-Calcitriol in complex with chimera 18
Components
  • URA-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 / vitamin D response element binding / lithocholic acid binding / hematopoietic stem cell proliferation / heart looping / calcium ion homeostasis ...heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / vitamin D response element binding / lithocholic acid binding / hematopoietic stem cell proliferation / heart looping / calcium ion homeostasis / 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 / Zinc finger, C4 type (two domains) / 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 ...Vitamin D receptor / VDR, DNA-binding domain / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / 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
Chem-VDX / Vitamin D3 receptor A
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 5, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,4303
Polymers35,0132
Non-polymers4171
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.244, 66.244, 252.522
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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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 URA-UIA-URL-URY-URV-UZN-LYS


Mass: 952.218 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: Lithium sulfate 1.5 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.03→19.92 Å / Num. obs: 15432 / % possible obs: 99.34 % / Redundancy: 37.1 % / Rpim(I) all: 0.018 / Net I/σ(I): 25.56
Reflection shellResolution: 2.03→2.38 Å / Redundancy: 40 % / Mean I/σ(I) obs: 2.06 / Num. unique obs: 1492 / Rpim(I) all: 0.372 / % possible all: 100

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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: 2.3→19.92 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 1404 9.1 %
Rwork0.1993 14028 -
obs0.2021 15432 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.88 Å2 / Biso mean: 74.0103 Å2 / Biso min: 43.48 Å2
Refinement stepCycle: final / Resolution: 2.3→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 30 38 1969
Biso mean--57.9 76.6 -
Num. residues----243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041977
X-RAY DIFFRACTIONf_angle_d0.7372670
X-RAY DIFFRACTIONf_chiral_restr0.045310
X-RAY DIFFRACTIONf_plane_restr0.005337
X-RAY DIFFRACTIONf_dihedral_angle_d13.5431200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.38230.33981360.288213571493100
2.3823-2.47760.25431350.25413601495100
2.4776-2.59030.31461370.249413671504100
2.5903-2.72680.31791370.234213741511100
2.7268-2.89760.25461390.236313821521100
2.8976-3.12110.26971350.23191349148497
3.1211-3.43490.28621400.214514021542100
3.4349-3.93130.20441420.173814181560100
3.9313-4.95030.17311450.157414491594100
4.9503-19.920.23251580.2071570172899
Refinement TLS params.Method: refined / Origin x: -31.6688 Å / Origin y: 25.9107 Å / Origin z: -1.6668 Å
111213212223313233
T0.4185 Å2-0.0455 Å20.0131 Å2-0.6372 Å2-0.1136 Å2--0.4845 Å2
L2.0727 °2-0.5958 °2-1.0662 °2-1.4004 °20.6417 °2--2.4717 °2
S-0.0032 Å °-0.4375 Å °-0.0326 Å °0.1943 Å °0.0816 Å °-0.1666 Å °0.0983 Å °0.1449 Å °0.0022 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA154 - 525
2X-RAY DIFFRACTION1allB1 - 7
3X-RAY DIFFRACTION1allS1 - 45

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