[English] 日本語
Yorodumi
- PDB-1zdt: The Crystal Structure of Human Steroidogenic Factor-1 -

+
Open data


ID or keywords:

Loading...

-
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 / sex determination / regulation of steroid biosynthetic process / positive regulation of male gonad development / Transcriptional regulation of testis differentiation / luteinization / calcineurin-mediated signaling ...primary sex determination / response to gonadotropin-releasing hormone / Sertoli cell differentiation / negative regulation of female gonad development / sex determination / regulation of steroid biosynthetic process / positive regulation of male gonad development / Transcriptional regulation of testis differentiation / luteinization / calcineurin-mediated signaling / Transcriptional regulation of pluripotent stem cells / tissue development / 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 / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / 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 / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / response to progesterone / transcription coregulator binding / nuclear receptor binding / phospholipid binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / SUMOylation of intracellular receptors / Heme signaling / 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 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / transcription coactivator activity / protein dimerization activity / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / chromatin binding / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / 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 / PAS domain superfamily / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Phosphatidylethanolamine


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


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more