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- PDB-4kzm: Crystal Structure of TR3 LBD S553A Mutant -

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Basic information

Entry
Database: PDB / ID: 4kzm
TitleCrystal Structure of TR3 LBD S553A Mutant
ComponentsNuclear receptor subfamily 4 group A member 1
KeywordsTRANSCRIPTION / ORPHAN NUCLEAR RECEPTOR
Function / homology
Function and homology information


neurotransmitter secretion involved in regulation of skeletal muscle contraction / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / cellular response to corticotropin-releasing hormone stimulus / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis ...neurotransmitter secretion involved in regulation of skeletal muscle contraction / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / cellular response to corticotropin-releasing hormone stimulus / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis / fat cell differentiation / skeletal muscle cell differentiation / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of cell cycle / cellular response to vascular endothelial growth factor stimulus / response to electrical stimulus / positive regulation of endothelial cell proliferation / response to amphetamine / lipopolysaccharide binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / presynapse / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / apoptotic process / chromatin / regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Orphan nuclear receptor, HMR type / Orphan nuclear receptor / Retinoid X Receptor / Retinoid X 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 ...Orphan nuclear receptor, HMR type / Orphan nuclear receptor / Retinoid X Receptor / Retinoid X 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear receptor subfamily 4immunitygroup A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, F. / Zhang, Q. / Li, A. / Tian, X. / Cai, Q. / Wang, W. / Wang, Y. / Chen, H. / Xing, Y. / Wu, Q. / Lin, T.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Orphan nuclear receptor TR3 acts in autophagic cell death via mitochondrial signaling pathway.
Authors: Wang, W.J. / Wang, Y. / Chen, H.Z. / Xing, Y.Z. / Li, F.W. / Zhang, Q. / Zhou, B. / Zhang, H.K. / Zhang, J. / Bian, X.L. / Li, L. / Liu, Y. / Zhao, B.X. / Chen, Y. / Wu, R. / Li, A.Z. / Yao, ...Authors: Wang, W.J. / Wang, Y. / Chen, H.Z. / Xing, Y.Z. / Li, F.W. / Zhang, Q. / Zhou, B. / Zhang, H.K. / Zhang, J. / Bian, X.L. / Li, L. / Liu, Y. / Zhao, B.X. / Chen, Y. / Wu, R. / Li, A.Z. / Yao, L.M. / Chen, P. / Zhang, Y. / Tian, X.Y. / Beermann, F. / Wu, M. / Han, J. / Huang, P.Q. / Lin, T. / Wu, Q.
History
DepositionMay 30, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.3Mar 20, 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
B: Nuclear receptor subfamily 4 group A member 1
A: Nuclear receptor subfamily 4 group A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7355
Polymers57,4592
Non-polymers2763
Water2,738152
1
B: Nuclear receptor subfamily 4 group A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8212
Polymers28,7291
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nuclear receptor subfamily 4 group A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9133
Polymers28,7291
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.481, 76.345, 128.443
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nuclear receptor subfamily 4 group A member 1 / Early response protein NAK1 / Nuclear hormone receptor NUR/77 / Nur77 / Orphan nuclear receptor HMR ...Early response protein NAK1 / Nuclear hormone receptor NUR/77 / Nur77 / Orphan nuclear receptor HMR / Orphan nuclear receptor TR3 / ST-59 / Testicular receptor 3


Mass: 28729.305 Da / Num. of mol.: 2 / Fragment: ligand binding domain, UNP residues 351-598 / Mutation: S553A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GFRP1, HMR, NAK1, NR4A1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22736
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.18 Å3/Da / Density % sol: 61.29 % / Mosaicity: 0.896 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.2
Details: PEG 4000, Sodium citrate, Glycerol, pH 4.2, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2013 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 32947 / Num. obs: 29916 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.073 / Χ2: 1.205 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.343.90.49114821.089191.3
2.34-2.3840.4614911.101191.5
2.38-2.433.90.38414531.102191.4
2.43-2.483.90.33414831.132190.6
2.48-2.533.90.30814741.137191
2.53-2.593.90.27114661.113191.3
2.59-2.663.90.20915051.181191.2
2.66-2.7340.18714581.194189.8
2.73-2.8140.15914761.25190.4
2.81-2.940.13914741.282191.7
2.9-340.11514781.261190.8
3-3.124.10.10415071.299191
3.12-3.264.10.08215081.374191.5
3.26-3.444.20.06915111.363191.9
3.44-3.654.40.06215121.255192.5
3.65-3.934.50.06215371.401191.9
3.93-4.334.70.05815061.251191.3
4.33-4.954.80.0515291.081190
4.95-6.244.80.04915471.186190.9
6.24-504.60.04915191.019184.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→37.37 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.2444 / WRfactor Rwork: 0.191 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8351 / SU B: 5.591 / SU ML: 0.136 / SU R Cruickshank DPI: 0.253 / SU Rfree: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 1544 5.2 %RANDOM
Rwork0.1946 ---
obs0.1973 29888 89.86 %-
all-32947 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.65 Å2 / Biso mean: 47.106 Å2 / Biso min: 15.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å2-0 Å20 Å2
2--1.72 Å20 Å2
3----2.51 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 18 152 3788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193707
X-RAY DIFFRACTIONr_bond_other_d0.0060.023678
X-RAY DIFFRACTIONr_angle_refined_deg1.842.0025016
X-RAY DIFFRACTIONr_angle_other_deg1.29138462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6555458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36723.203153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.6415643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4311528
X-RAY DIFFRACTIONr_chiral_restr0.1010.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214067
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02811
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 101 -
Rwork0.236 1799 -
all-1900 -
obs--78.64 %

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