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- PDB-8hd3: Farnesoid X Receptor Agonists_FXR fused with a HD3 peptide -

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Basic information

Entry
Database: PDB / ID: 8hd3
TitleFarnesoid X Receptor Agonists_FXR fused with a HD3 peptide
ComponentsFarnesoid X Receptor
KeywordsNUCLEAR PROTEIN / Bile acid receptor / agonist / Farnesoid X-activated receptor
Function / homology
Function and homology information


regulation of urea metabolic process / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid / negative regulation of very-low-density lipoprotein particle remodeling / negative regulation of interleukin-1 production ...regulation of urea metabolic process / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid / negative regulation of very-low-density lipoprotein particle remodeling / negative regulation of interleukin-1 production / nuclear receptor-mediated bile acid signaling pathway / regulation of bile acid biosynthetic process / regulation of insulin secretion involved in cellular response to glucose stimulus / : / toll-like receptor 9 signaling pathway / negative regulation of monocyte chemotactic protein-1 production / bile acid nuclear receptor activity / bile acid metabolic process / cell-cell junction assembly / bile acid binding / cellular response to fatty acid / regulation of cholesterol metabolic process / negative regulation of interleukin-2 production / intracellular glucose homeostasis / positive regulation of interleukin-17 production / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / Synthesis of bile acids and bile salts / negative regulation of tumor necrosis factor-mediated signaling pathway / fatty acid homeostasis / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / negative regulation of canonical NF-kappaB signal transduction / positive regulation of insulin receptor signaling pathway / Recycling of bile acids and salts / Notch signaling pathway / positive regulation of adipose tissue development / cholesterol homeostasis / transcription coregulator binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / euchromatin / PPARA activates gene expression / negative regulation of inflammatory response / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription by RNA polymerase II / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium / inflammatory response / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / innate immune response / regulation of DNA-templated transcription / chromatin / negative regulation of apoptotic process / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Bile acid receptor, ligand binding domain / Thyroid hormone receptor / : / 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 ...Bile acid receptor, ligand binding domain / Thyroid hormone receptor / : / 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-XAW / Bile acid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsLu, X. / Zhang, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of FXR fused with a HD3 peptide in complex with agonist QT0127
Authors: Lu, X. / Zhang, H.
History
DepositionNov 3, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Farnesoid X Receptor
B: Farnesoid X Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6844
Polymers59,9362
Non-polymers7482
Water30617
1
A: Farnesoid X Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3422
Polymers29,9681
Non-polymers3741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Farnesoid X Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3422
Polymers29,9681
Non-polymers3741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.032, 34.408, 110.830
Angle α, β, γ (deg.)90.000, 91.324, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Farnesoid X Receptor


Mass: 29968.230 Da / Num. of mol.: 2 / Mutation: E45A, E118A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96RI1
#2: Chemical ChemComp-XAW / [(3s,5s,7s)-adamantan-1-yl][4-(2-amino-5-chlorophenyl)piperazin-1-yl]methanone


Mass: 373.920 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28ClN3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 51.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 50mM HEPES pH7.0, 3.5M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.29→64.42 Å / Num. obs: 27792 / % possible obs: 99.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 42.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06339 / Rpim(I) all: 0.03467 / Rrim(I) all: 0.07258 / Net I/σ(I): 9.9
Reflection shellResolution: 2.29→2.42 Å / Rmerge(I) obs: 0.5877 / Num. unique obs: 2715 / CC1/2: 0.85 / Rpim(I) all: 0.3228 / Rrim(I) all: 0.674 / % possible all: 99.96

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Processing

Software
NameVersionClassification
REFMAC7.0.078refinement
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WVD.

4wvd


Resolution: 2.29→55.4 Å / SU ML: 0.2907 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.1399
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 1418 5.11 %RANDOM
Rwork0.2055 26357 --
obs0.2078 27775 99.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.7 Å2
Refinement stepCycle: LAST / Resolution: 2.29→55.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3985 0 52 17 4054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784128
X-RAY DIFFRACTIONf_angle_d0.95125584
X-RAY DIFFRACTIONf_chiral_restr0.0481623
X-RAY DIFFRACTIONf_plane_restr0.0054712
X-RAY DIFFRACTIONf_dihedral_angle_d4.79672496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.370.33171400.25812580X-RAY DIFFRACTION99.96
2.37-2.470.29551400.24792656X-RAY DIFFRACTION99.96
2.47-2.580.32981570.25082597X-RAY DIFFRACTION100
2.58-2.720.33181200.24242628X-RAY DIFFRACTION99.96
2.72-2.890.30171320.24172656X-RAY DIFFRACTION99.93
2.89-3.110.26151400.24122645X-RAY DIFFRACTION100
3.11-3.420.30981450.22392659X-RAY DIFFRACTION99.93
3.42-3.920.26861370.19792530X-RAY DIFFRACTION95.56
3.92-4.940.17341470.16852677X-RAY DIFFRACTION99.58
4.94-36.930.22471600.18252729X-RAY DIFFRACTION98

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