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- PDB-9smq: Crystal structure of LRH-1/TIF-2 peptide in complex with CP4 -

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Basic information

Entry
Database: PDB / ID: 9smq
TitleCrystal structure of LRH-1/TIF-2 peptide in complex with CP4
Components
  • Nuclear receptor coactivator 2
  • Nuclear receptor subfamily 5 group A member 2
KeywordsTRANSCRIPTION / Nuclear receptor subfamily 5 group A member 2 / LRH-1 / TIF-2 / Nuclear receptor / NR5A2
Function / homology
Function and homology information


positive regulation of glucocorticoid biosynthetic process / zygotic genome activation / positive regulation of tendon cell differentiation / morula formation / Regulation of gene expression in early pancreatic precursor cells / primary ovarian follicle growth / pancreas morphogenesis / inner cell mass cell differentiation / tissue development / acinar cell differentiation ...positive regulation of glucocorticoid biosynthetic process / zygotic genome activation / positive regulation of tendon cell differentiation / morula formation / Regulation of gene expression in early pancreatic precursor cells / primary ovarian follicle growth / pancreas morphogenesis / inner cell mass cell differentiation / tissue development / acinar cell differentiation / Sertoli cell development / positive regulation of T cell anergy / positive regulation of stem cell differentiation / embryonic cleavage / bile acid metabolic process / embryo development ending in birth or egg hatching / exocrine pancreas development / cartilage development / negative regulation of chondrocyte differentiation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / homeostatic process / locomotor rhythm / calcineurin-mediated signaling / aryl hydrocarbon receptor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / somatic stem cell population maintenance / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of viral genome replication / cellular response to hormone stimulus / Recycling of bile acids and salts / transcription regulator inhibitor activity / hormone-mediated signaling pathway / : / positive regulation of adipose tissue development / neurogenesis / Regulation of lipid metabolism by PPARalpha / positive regulation of T cell proliferation / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / cholesterol homeostasis / cellular response to leukemia inhibitory factor / nuclear receptor binding / transcription coregulator binding / negative regulation of smoothened signaling pathway / SUMOylation of intracellular receptors / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PPARA activates gene expression / Cytoprotection by HMOX1 / phospholipid binding / positive regulation of T cell activation / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / : / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / transcription cis-regulatory region binding / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / 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 / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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
: / PHOSPHATE ION / 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: 2.2 Å
AuthorsKim, Y. / Ildefeld, N. / Heering, J. / Proschak, E. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of LRH-1/TIF-2 peptide in complex with CP4
Authors: Kim, Y. / Ildefeld, N. / Heering, J. / Proschak, E. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
History
DepositionSep 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor subfamily 5 group A member 2
C: Nuclear receptor coactivator 2
E: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3396
Polymers31,7893
Non-polymers5503
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-23 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.950, 68.375, 82.770
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 Nuclear receptor subfamily 5 group A member 2 / Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor ...Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor / Hepatocytic transcription factor / Liver receptor homolog 1 / LRH-1


Mass: 28370.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR5A2, B1F, CPF, FTF / Production host: Escherichia coli (E. coli) / References: UniProt: O00482
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1708.931 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA2, BHLHE75, SRC2, TIF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15596
#3: Chemical ChemComp-A1JOT / 3-[5-phenyl-1-[3-(trifluoromethyl)phenyl]pyrazol-3-yl]propanoic acid


Mass: 360.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15F3N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.25 M Ammonium phosphate monobasic 0.9 Ammonium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 20, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.2→52.71 Å / Num. obs: 20392 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.021 / Rrim(I) all: 0.078 / Χ2: 0.91 / Net I/σ(I): 17.4
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 1.074 / Num. measured all: 21788 / Num. unique obs: 1618 / CC1/2: 0.885 / Rpim(I) all: 0.301 / Rrim(I) all: 1.116 / Χ2: 0.84 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→52.71 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.456 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 1078 5 %RANDOM
Rwork0.21439 ---
obs0.21591 20392 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.065 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å20 Å20 Å2
2---3.3 Å2-0 Å2
3---0.49 Å2
Refinement stepCycle: 1 / Resolution: 2.2→52.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 36 31 2175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122186
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162080
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.822963
X-RAY DIFFRACTIONr_angle_other_deg0.4581.7594761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4215264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.51859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82510385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022581
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02500
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2135.7451062
X-RAY DIFFRACTIONr_mcbond_other4.2075.7451062
X-RAY DIFFRACTIONr_mcangle_it5.95710.3041324
X-RAY DIFFRACTIONr_mcangle_other5.95510.3071325
X-RAY DIFFRACTIONr_scbond_it5.1896.2181124
X-RAY DIFFRACTIONr_scbond_other5.1346.1871117
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.98711.191628
X-RAY DIFFRACTIONr_long_range_B_refined9.98456.662481
X-RAY DIFFRACTIONr_long_range_B_other9.98256.672482
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.27 Å
RfactorNum. reflection% reflection
Rfree0.333 71 -
Rwork0.33 1493 -
obs--99.94 %

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