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- PDB-1zdt: The Crystal Structure of Human Steroidogenic Factor-1 -

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Basic information

Entry
Database: PDB / ID: 1zdt
TitleThe Crystal Structure of Human Steroidogenic Factor-1
Components
  • Nuclear receptor coactivator 2
  • Steroidogenic factor 1
KeywordsTRANSCRIPTION / Steroidogenic Factor-1 / Nuclear Receptor / pholpholipid / phosphatidylethanolamine
Function / homology
Function and homology information


primary sex determination / response to gonadotropin-releasing hormone / Sertoli cell differentiation / negative regulation of female gonad development / luteinization / regulation of steroid biosynthetic process / sex determination / positive regulation of male gonad development / Transcriptional regulation of testis differentiation / tissue development ...primary sex determination / response to gonadotropin-releasing hormone / Sertoli cell differentiation / negative regulation of female gonad development / luteinization / regulation of steroid biosynthetic process / sex determination / positive regulation of male gonad development / Transcriptional regulation of testis differentiation / tissue development / Transcriptional regulation of pluripotent stem cells / Leydig cell differentiation / male sex determination / maintenance of protein location in nucleus / hormone metabolic process / adrenal gland development / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / female gonad development / locomotor rhythm / aryl hydrocarbon receptor binding / calcineurin-mediated signaling / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / regulation of lipid metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / Recycling of bile acids and salts / transcription regulator inhibitor activity / cellular response to hormone stimulus / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / response to progesterone / Activation of gene expression by SREBF (SREBP) / nuclear receptor binding / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of smoothened signaling pathway / SUMOylation of intracellular receptors / circadian regulation of gene expression / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / phospholipid binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / mRNA transcription by RNA polymerase II / RNA polymerase II transcription regulator complex / male gonad development / 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 / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / enzyme binding / 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 / cytosol
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 / 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Steroidogenic factor 1 / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / Refinement description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Steroidogenic factor 1
B: Steroidogenic factor 1
P: Nuclear receptor coactivator 2
Q: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6046
Polymers58,2204
Non-polymers1,3842
Water4,234235
1
A: Steroidogenic factor 1
P: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8023
Polymers29,1102
Non-polymers6921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-26 kcal/mol
Surface area12970 Å2
MethodPISA
2
B: Steroidogenic factor 1
Q: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8023
Polymers29,1102
Non-polymers6921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-26 kcal/mol
Surface area12980 Å2
MethodPISA
3
A: Steroidogenic factor 1
P: Nuclear receptor coactivator 2
hetero molecules

B: Steroidogenic factor 1
Q: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6046
Polymers58,2204
Non-polymers1,3842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area6530 Å2
ΔGint-60 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.601, 73.601, 195.678
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Steroidogenic factor 1 / STF-1 / SF-1 / Adrenal 4 binding protein / Steroid hormone receptor Ad4BP / Fushi tarazu factor homolog 1


Mass: 27645.172 Da / Num. of mol.: 2 / Mutation: C247S, C412S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q13285
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Transcriptional intermediary factor 2


Mass: 1464.664 Da / Num. of mol.: 2 / Fragment: residues 741-752 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: Q15596
#3: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.65 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG3350, ammonium sulfate, sucrose, pH 5.5, temperature 277K, 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: Jan 29, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. all: 34885 / Num. obs: 34644 / % possible obs: 99.31 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 38.74 Å2 / Rsym value: 0.112 / Net I/σ(I): 3.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 0.8 / Rsym value: 0.77 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.1.25refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.778 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26532 1565 4.3 %RANDOM
Rwork0.21597 ---
all0.21823 34885 --
obs0.21823 34644 99.31 %-
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: 21.368 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20.67 Å20 Å2
2--1.34 Å20 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3991 0 94 235 4320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214150
X-RAY DIFFRACTIONr_bond_other_d0.0020.023959
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.9995585
X-RAY DIFFRACTIONr_angle_other_deg0.8739218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1065489
X-RAY DIFFRACTIONr_chiral_restr0.0830.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024450
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02771
X-RAY DIFFRACTIONr_nbd_refined0.2040.21036
X-RAY DIFFRACTIONr_nbd_other0.2220.24476
X-RAY DIFFRACTIONr_nbtor_other0.0950.22537
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2190
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2830.214
X-RAY DIFFRACTIONr_mcbond_it0.4831.52472
X-RAY DIFFRACTIONr_mcangle_it0.93923971
X-RAY DIFFRACTIONr_scbond_it1.53231678
X-RAY DIFFRACTIONr_scangle_it2.5794.51614
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.335 2494
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)
13.97981.054-1.48531.185-0.70883.8661-0.20730.0305-0.2304-0.13650.1174-0.14670.46250.10310.08990.14750.04240.03940.043-0.00730.09664.633315.740477.4678
22.3171-0.1019-0.9182.34180.14514.76060.0958-0.067-0.04570.148-0.1934-0.0795-0.18810.42970.09750.0364-0.0393-0.04070.06420.01650.136513.8346-26.510196.2497
30.1838-0.10970.21120.9466-0.30930.1083-0.02010.0012-0.03690.00320.0667-0.1284-0.026-0.031-0.04650.1945-0.03510.06240.2987-0.04770.19193.9384-7.149486.0037
428.84257.07651.36234.4555-4.446326.0428-0.34510.0365-0.04570.22280.0521-0.7244-0.44841.15570.2930.12060.0220.00910.203-0.01440.063212.843422.017893.3912
520.579-1.15966.8311-4.0154-2.60234.20510.2938-0.62261.05660.3209-0.7442-1.7446-0.13870.68120.45040.524-0.3155-0.08790.53170.10240.5729.1754-18.1701101.331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A221 - 248
2X-RAY DIFFRACTION1A256 - 460
3X-RAY DIFFRACTION1A1001
4X-RAY DIFFRACTION1A1002 - 1096
5X-RAY DIFFRACTION1B1003
6X-RAY DIFFRACTION2B221 - 459
7X-RAY DIFFRACTION2B1002
8X-RAY DIFFRACTION2B1004 - 1096
9X-RAY DIFFRACTION3A1097 - 1115
10X-RAY DIFFRACTION3Q199
11X-RAY DIFFRACTION3B1097 - 1115
12X-RAY DIFFRACTION4P741 - 752
13X-RAY DIFFRACTION4P230 - 232
14X-RAY DIFFRACTION5Q741 - 751
15X-RAY DIFFRACTION5A1116 - 1117
16X-RAY DIFFRACTION5B1116

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