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- PDB-1zdu: The Crystal Structure of Human Liver Receptor Homologue-1 -

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Basic information

Entry
Database: PDB / ID: 1zdu
TitleThe Crystal Structure of Human Liver Receptor Homologue-1
Components
  • Nuclear receptor coactivator 2
  • Orphan nuclear receptor NR5A2
KeywordsTRANSCRIPTION / Liver Receptor Homologue-1 / LRH-1 / Nuclear Receptor / phospholipid / phosphatidylethanolamine
Function / homology
Function and homology information


Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / embryo development ending in birth or egg hatching / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / homeostatic process / locomotor rhythm ...Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / embryo development ending in birth or egg hatching / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / homeostatic process / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of viral genome replication / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / cellular response to leukemia inhibitory factor / transcription coregulator binding / response to progesterone / cholesterol homeostasis / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / phospholipid binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / regulation of cell population proliferation / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / nuclear body / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / chromatin / 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 / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear hormone receptor family 5 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 ...Nuclear hormone receptor family 5 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATIDYLGLYCEROL-PHOSPHOGLYCEROL / Nuclear receptor subfamily 5 group A member 2 / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, W. / Zhang, C. / Marimuthu, A. / Krupka, H.I. / Tabrizizad, M. / Shelloe, R. / Mehra, U. / Eng, K. / Nguyen, H. / Settachatgul, C. ...Wang, W. / Zhang, C. / Marimuthu, A. / Krupka, H.I. / Tabrizizad, M. / Shelloe, R. / Mehra, U. / Eng, K. / Nguyen, H. / Settachatgul, C. / Powell, B. / Milburn, M.V. / West, B.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: The crystal structures of human steroidogenic factor-1 and liver receptor homologue-1
Authors: Wang, W. / Zhang, C. / Marimuthu, A. / Krupka, H.I. / Tabrizizad, M. / Shelloe, R. / Mehra, U. / Eng, K. / Nguyen, H. / Settachatgul, C. / Powell, B. / Milburn, M.V. / West, B.L.
History
DepositionApr 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Orphan nuclear receptor NR5A2
P: Nuclear receptor coactivator 2
Q: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0085
Polymers31,0133
Non-polymers9952
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-30 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.010, 67.000, 78.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Orphan nuclear receptor NR5A2 / Alpha-1-fetoprotein transcription factor / Hepatocytic transcription factor / B1-binding factor / ...Alpha-1-fetoprotein transcription factor / Hepatocytic transcription factor / B1-binding factor / hB1F / CYP7A promoter binding factor


Mass: 28313.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O00482
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Transcriptional intermediary factor 2


Mass: 1349.576 Da / Num. of mol.: 2 / Fragment: residues 741-751 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: Q15596
#3: Chemical ChemComp-P3A / PHOSPHATIDYLGLYCEROL-PHOSPHOGLYCEROL


Mass: 872.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78O15P2 / Comment: phospholipid*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NaH2PO4, K2HPO4, pH 7.5, temperature 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 10968 / Num. obs: 10899 / % possible obs: 99.37 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 65.5 Å2 / Rsym value: 0.054 / Net I/σ(I): 10
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 4 % / Mean I/σ(I) obs: 0.6 / Rsym value: 0.01247 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.25refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.924 / SU B: 12.874 / SU ML: 0.272 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.603 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28129 595 5.2 %RANDOM
Rwork0.23942 ---
all0.24161 10968 --
obs0.24161 10899 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.206 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20 Å2
2---2.04 Å20 Å2
3---3.32 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 66 35 2170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222167
X-RAY DIFFRACTIONr_bond_other_d0.0020.022021
X-RAY DIFFRACTIONr_angle_refined_deg1.0341.9992913
X-RAY DIFFRACTIONr_angle_other_deg0.72234722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2615250
X-RAY DIFFRACTIONr_chiral_restr0.0530.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022298
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02405
X-RAY DIFFRACTIONr_nbd_refined0.1790.2507
X-RAY DIFFRACTIONr_nbd_other0.1920.22284
X-RAY DIFFRACTIONr_nbtor_other0.0870.21324
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1360.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3720.24
X-RAY DIFFRACTIONr_mcbond_it0.2031.51268
X-RAY DIFFRACTIONr_mcangle_it0.39622037
X-RAY DIFFRACTIONr_scbond_it0.7293899
X-RAY DIFFRACTIONr_scangle_it1.2134.5876
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.349 32
Rwork0.331 777
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)
14.1042-1.0404-1.20194.86042.1423.32260.05520.4310.2096-0.28740.14820.0435-0.16070.1279-0.20340.2196-0.11560.0150.2025-0.01640.12716.55728.9039.473
213.386616.509620.96578.46526.51282.3797-0.21233.438-2.46950.4630.00370.3701-0.45951.32610.20860.3899-0.0069-0.0080.3846-0.00280.39171.88313.95110.395
327.0359-11.53086.941812.88989.75763.0488-0.1796-0.78110.03280.09810.6418-0.9020.32580.3699-0.46220.3312-0.12480.00350.3836-0.24820.188525.24424.00910.778
412.27128.7367-1.518236.0604-6.393429.03570.2279-0.5890.3514-0.2928-0.1347-0.9119-1.28060.5486-0.09320.36410.0231-0.02870.7886-0.37370.32242.09714.632-9.754
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA253 - 2843 - 34
2X-RAY DIFFRACTION1AA292 - 49242 - 242
3X-RAY DIFFRACTION1AD101
4X-RAY DIFFRACTION1AE103
5X-RAY DIFFRACTION1AF1 - 26
6X-RAY DIFFRACTION2AF27 - 30
7X-RAY DIFFRACTION3PB741 - 7511 - 11
8X-RAY DIFFRACTION3PG31 - 33
9X-RAY DIFFRACTION4QC742 - 7512 - 11
10X-RAY DIFFRACTION4QH34

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