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- PDB-7qpp: High resolution structure of human VDR ligand binding domain in c... -

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Basic information

Entry
Database: PDB / ID: 7qpp
TitleHigh resolution structure of human VDR ligand binding domain in complex with calcitriol
ComponentsVitamin D3 receptor
KeywordsTRANSCRIPTION / VDR / calcitriol
Function / homology
Function and homology information


regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding ...regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding / positive regulation of keratinocyte differentiation / vitamin D receptor signaling pathway / positive regulation of vitamin D receptor signaling pathway / bile acid signaling pathway / intestinal absorption / mammary gland branching involved in pregnancy / decidualization / negative regulation of keratinocyte proliferation / positive regulation of bone mineralization / nuclear retinoid X receptor binding / lactation / skeletal system development / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / cell morphogenesis / Nuclear Receptor transcription pathway / intracellular calcium ion homeostasis / RNA polymerase II transcription regulator complex / nuclear receptor activity / calcium ion transport / cell differentiation / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / 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
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 ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsRochel, N.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: J.Med.Chem. / Year: 2022
Title: Advances in Vitamin D Receptor Function and Evolution Based on the 3D Structure of the Lamprey Ligand-Binding Domain.
Authors: Sigueiro, R. / Bianchetti, L. / Peluso-Iltis, C. / Chalhoub, S. / Dejaegere, A. / Osz, J. / Rochel, N.
History
DepositionJan 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3183
Polymers29,8051
Non-polymers5132
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-11 kcal/mol
Surface area12220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.926, 51.317, 132.317
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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


Mass: 29805.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VDR, NR1I1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P11473
#2: 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.56 Å3/Da / Density % sol: 51.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: Ammonium Sulfate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 2, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.52→20.1 Å / Num. obs: 46307 / % possible obs: 96.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 11.22 Å2 / Rsym value: 0.005 / Net I/σ(I): 20.7
Reflection shellResolution: 1.52→1.56 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 9.8 / Num. unique obs: 46136 / % possible all: 66.6

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PHENIX1.17_3644refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DB1

1db1


Resolution: 1.52→19.8 Å / SU ML: 0.0872 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 13.8881
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1662 4655 10.05 %
Rwork0.1389 41652 -
obs0.1416 46307 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.37 Å2
Refinement stepCycle: LAST / Resolution: 1.52→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 35 410 2466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01142135
X-RAY DIFFRACTIONf_angle_d1.26812901
X-RAY DIFFRACTIONf_chiral_restr0.2382333
X-RAY DIFFRACTIONf_plane_restr0.0087368
X-RAY DIFFRACTIONf_dihedral_angle_d21.9487818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.540.17081240.13641092X-RAY DIFFRACTION77.6
1.54-1.560.16061450.13471298X-RAY DIFFRACTION90.24
1.56-1.580.13871410.12481260X-RAY DIFFRACTION92.05
1.58-1.60.15281390.13481349X-RAY DIFFRACTION92.88
1.6-1.620.17131300.1261332X-RAY DIFFRACTION93
1.62-1.640.17861310.13141334X-RAY DIFFRACTION94.7
1.64-1.660.15781650.13051345X-RAY DIFFRACTION94.02
1.66-1.690.1571380.12821329X-RAY DIFFRACTION95.69
1.69-1.710.16521460.13051395X-RAY DIFFRACTION96.37
1.71-1.740.16741850.13351336X-RAY DIFFRACTION97.38
1.74-1.770.17331480.12841388X-RAY DIFFRACTION97.34
1.77-1.80.16261410.12981415X-RAY DIFFRACTION98.11
1.8-1.840.15941520.13261402X-RAY DIFFRACTION98.54
1.84-1.880.15161550.13571400X-RAY DIFFRACTION98.29
1.88-1.920.16861550.13621394X-RAY DIFFRACTION98.6
1.92-1.960.17181650.13121419X-RAY DIFFRACTION99.19
1.96-2.010.15911790.12981382X-RAY DIFFRACTION99.24
2.01-2.060.15371650.12951428X-RAY DIFFRACTION99.07
2.06-2.130.16261590.12591416X-RAY DIFFRACTION99.49
2.13-2.190.15771540.12321419X-RAY DIFFRACTION99.49
2.19-2.270.15931570.12131420X-RAY DIFFRACTION99.43
2.27-2.360.1541890.12151430X-RAY DIFFRACTION99.57
2.36-2.470.16911800.12541386X-RAY DIFFRACTION99.43
2.47-2.60.15251580.12651432X-RAY DIFFRACTION99.31
2.6-2.760.16111610.13571439X-RAY DIFFRACTION99.56
2.76-2.980.16391670.14591455X-RAY DIFFRACTION99.57
2.98-3.270.16261630.14481457X-RAY DIFFRACTION99.75
3.27-3.740.1661490.14281477X-RAY DIFFRACTION99.03
3.74-4.710.16681580.1371477X-RAY DIFFRACTION98.91
4.71-19.80.22191560.20791546X-RAY DIFFRACTION97.15
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)
11.838156243410.7903434972351.284185989340.6442226556570.4275450269111.827846079460.117661423165-0.195492926055-0.1921900763250.3436632121950.0410286988341-0.1251428336240.3333589357720.237071276937-0.1435680754370.1769836232030.0443429640896-0.06251474127240.132534562295-0.01011634106920.10255976364223.32196152657.6404170984153.9263889634
20.983202628235-0.7835605277160.1979897230891.70636355925-0.3149319993140.9790668101130.1191160911440.1599841123210.107018845166-0.243381851903-0.12850210240.00808213896623-0.0380792640130.0329176472750.02240391539480.06956655924480.00569787647405-0.008944834859720.09404957073110.002892661245730.09410398533998.8867262879723.217092697824.5323083332
30.7255714726-0.2394128258240.4203502596311.039640416190.003886591798561.288642111150.0179750671851-0.0826142687678-0.006242905314350.0920351627408-0.0507460477780.08035063075720.160980326914-0.108468455939-0.04839924406720.0517798410483-0.01727040642760.000428352312490.053050424871-0.005291574320580.07305636424377.5140639381112.241971705742.205305894
43.007747129980.869363138784-2.083963394461.55892566697-0.9999906987443.87565530762-0.00902894801551-0.0001436943708670.1141977532710.0457126918388-0.02980513422280.00791711835422-0.0414331842994-0.1176796862160.02921269878330.0475819729252-0.00613769405931-0.02553768123730.0421586641084-0.0125079520290.061140002983613.513461885320.084185379839.7481994011
53.49165134668-1.396442877780.7346651343036.661984746820.4516475247352.528574221550.01131534244850.2718857746630.148252270276-0.324387175784-0.0685574421669-0.133854100316-0.1221601048220.162504399730.03012328747340.0842360976065-0.0273066850758-0.03384777824040.110173806930.03407968821330.086013688905913.165402158726.622748046926.230255683
65.5678303231-2.401833232811.413142234653.42440687219-1.170682198123.52210746703-0.1490978424240.1801657308390.6895715814210.0324148162195-0.127737696716-0.174535551347-0.2231970049750.1021656806640.2076529102130.0834011478148-0.0234582640374-0.03882184222310.0546808693240.02059529766740.15593083320319.187333728930.45878000339.1130915638
74.00268119444-0.280925844962-1.038170482151.742622414080.09074359365962.775686825450.0717953510741-0.004854333804080.1255850691460.140913898904-0.05080577971630.00645188717971-0.0214079869232-0.1578523631430.008563264224140.0763914117455-0.00213604886894-0.02185155058280.0490595835342-0.01421768859110.039929669993514.354278012217.881504660551.7092397078
84.14000759530.331095152041-0.903334750521.63935271959-0.1837521217312.62638687282-0.0202674858815-0.2735744528390.1678052714810.2247178011250.014587248365-0.2477526775450.02620837743150.3172545597290.02164458696710.1372544956640.0143615773026-0.04518126540910.117898812767-0.01409660666440.099319582080523.04344339516.802628231657.5641480646
96.44438867413-1.476545333865.398564605790.839769981935-1.099566932884.85606862784-0.282895275475-0.3726550706210.4493144349610.08992624595180.0541539441128-0.0978369338949-0.288570353638-0.3080128017370.2037513804380.09204010901140.00837055811808-0.02002998053410.0865191261292-0.02359888918690.12247106236710.139064948529.245564690244.8288350338
102.47103610745-2.083927058110.9140447506745.72190358851-2.849425374032.64133536998-0.0645906894456-0.24113138945-0.07487663309210.1825455967640.1386046725430.298847432733-0.0916738684107-0.242112011994-0.07689795321440.05568350326830.00798203515207-0.004148936089990.10983938535-0.01298051916030.147401770054-3.470298527222.816893782733.4179754904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 119 through 142 )
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 226 )
3X-RAY DIFFRACTION3chain 'A' and (resid 227 through 255 )
4X-RAY DIFFRACTION4chain 'A' and (resid 256 through 290 )
5X-RAY DIFFRACTION5chain 'A' and (resid 291 through 306 )
6X-RAY DIFFRACTION6chain 'A' and (resid 307 through 323 )
7X-RAY DIFFRACTION7chain 'A' and (resid 324 through 348 )
8X-RAY DIFFRACTION8chain 'A' and (resid 349 through 378 )
9X-RAY DIFFRACTION9chain 'A' and (resid 379 through 406 )
10X-RAY DIFFRACTION10chain 'A' and (resid 407 through 424 )

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