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- PDB-6xzj: Structure of zVDR LBD-Calcitriol in complex with chimera 12 -

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Basic information

Entry
Database: PDB / ID: 6xzj
TitleStructure of zVDR LBD-Calcitriol in complex with chimera 12
Components
  • ARG-HIS-LYS-ILE-LEU-URR-UIL-URL-GLN
  • 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: 2.1 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 / 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 13, 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

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Assembly

Deposited unit
A: Vitamin D3 receptor A
B: ARG-HIS-LYS-ILE-LEU-URR-UIL-URL-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8044
Polymers35,3282
Non-polymers4762
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-5 kcal/mol
Surface area11100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.200, 66.200, 254.220
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 ARG-HIS-LYS-ILE-LEU-URR-UIL-URL-GLN


Mass: 1267.612 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.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: NaAcetate 3M, 0.1 M Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→38.04 Å / Num. obs: 19740 / % possible obs: 97.19 % / Redundancy: 14 % / Rpim(I) all: 0.024 / Net I/σ(I): 16.74
Reflection shellResolution: 2.1→2.18 Å / Num. unique obs: 1757 / Rpim(I) all: 0.722

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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: 2.1→38.04 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.41
RfactorNum. reflection% reflection
Rfree0.2468 986 5 %
Rwork0.202 --
obs0.2042 19738 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.16 Å2 / Biso mean: 64.9284 Å2 / Biso min: 39.22 Å2
Refinement stepCycle: final / Resolution: 2.1→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 34 25 1995
Biso mean--54.05 67.66 -
Num. residues----248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042009
X-RAY DIFFRACTIONf_angle_d0.7362713
X-RAY DIFFRACTIONf_chiral_restr0.04314
X-RAY DIFFRACTIONf_plane_restr0.005339
X-RAY DIFFRACTIONf_dihedral_angle_d15.5421217
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.21070.34321310.3166247392
2.2107-2.34920.29631350.2711257997
2.3492-2.53060.3261390.2445263398
2.5306-2.78520.27291400.2342265598
2.7852-3.1880.29791410.2275268898
3.188-4.01580.23571440.1928273898
4.0158-38.040.22061560.1798298699
Refinement TLS params.Method: refined / Origin x: -31.9537 Å / Origin y: 26.3781 Å / Origin z: -1.5954 Å
111213212223313233
T0.4266 Å2-0.034 Å20.0101 Å2-0.5566 Å2-0.1017 Å2--0.4684 Å2
L1.4053 °2-0.5085 °2-0.9589 °2-0.7581 °20.2891 °2--1.1796 °2
S-0.0767 Å °-0.1876 Å °0.0111 Å °0.0855 Å °0.0905 Å °-0.0554 Å °0.076 Å °0.058 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA154 - 452
2X-RAY DIFFRACTION1allD525
3X-RAY DIFFRACTION1allB686 - 694
4X-RAY DIFFRACTION1allE1428
5X-RAY DIFFRACTION1allS1 - 25

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