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(-) Description

Title :  HUMAN STEROIDOGENIC FACTOR 1 LBD WITH BOUND CO-FACTOR PEPTIDE
 
Authors :  I. N. Krylova, E. P. Sablin, R. X. Xu, G. M. Waitt, D. Juzumiene, J. D. Williams, H. A. Ingraham, T. M. Willson, S. P. Williams, V. Montana, K. P. Madauss, J. Moore, J. M. Bynum, L. Lebedeva, J. A. Mackay, M. Suzawa, R. K. Guy, J. W. Thornton
Date :  28 Jan 05  (Deposition) - 10 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Steroidogenic Factor 1, Sf1, Phospholipid, Phosphatidyl Ethanolamine, Phosphatidyl Glycerol, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. N. Krylova, E. P. Sablin, R. X. Xu, G. M. Waitt, J. A. Mackay, D. Juzumiene, J. M. Bynum, K. P. Madauss, V. Montana, L. Lebedeva, M. Suzawa, J. D. Williams, S. P. Williams, R. K. Guy, J. W. Thornton, R. J. Fletterick, T. M. Willson, H. A. Ingraham
Structural Analyses Reveal Phosphatidyl Inositols As Ligands For The Nr5 Orphan Receptors Sf-1 And Lrh-1
Cell(Cambridge, Mass. ) V. 120 343 2005
PubMed-ID: 15707893  |  Reference-DOI: 10.1016/J.CELL.2005.01.024
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - STEROIDOGENIC FACTOR 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 [DE3]
    Expression System Taxid: 562
    Gene: NR5A1, AD4BP, FTZF1, SF1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: STF-1, SF-1, ADRENAL 4 BINDING PROTEIN, STEROID HORMONE RECEPTOR AD4BP, FUSHI TARAZU FACTOR HOMOLOG 1
 
Molecule 2 - TIF2 PEPTIDE
    Chains: B
    Engineered: YES
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1P0E1Ligand/IonPHOSPHATIDYL ETHANOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:262 , LEU A:265 , SER A:303 , LEU A:306 , VAL A:307 , HIS A:310 , ILE A:323 , VAL A:331 , THR A:335 , VAL A:336 , GLN A:339 , ALA A:340 , GLY A:341 , LEU A:344 , ALA A:351 , SER A:430 , ALA A:433 , TYR A:436 , LYS A:440BINDING SITE FOR RESIDUE P0E A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YOW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YOW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_065869D238NSTF1_HUMANDisease (SPGF8)780568525AD238N
2UniProtVAR_062970D293NSTF1_HUMANDisease (POF7)121918655AD293N
3UniProtVAR_063258L437QSTF1_HUMANDisease (SRXY3)104894120AL437Q
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YOW)

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003735881ENSE00001460970chr9:127269709-127269528182STF1_HUMAN-00--
1.3ENST000003735883ENSE00001460969chr9:127265689-127265573117STF1_HUMAN1-34340--
1.4ENST000003735884ENSE00000726938chr9:127265499-127265358142STF1_HUMAN35-82480--
1.6bENST000003735886bENSE00000726937chr9:127262994-127262369626STF1_HUMAN82-2902091A:221-290 (gaps)70
1.7ENST000003735887ENSE00000726936chr9:127255428-127255309120STF1_HUMAN291-330401A:291-33040
1.8ENST000003735888ENSE00000726934chr9:127253507-127253360148STF1_HUMAN331-380501A:331-38050
1.9bENST000003735889bENSE00001230484chr9:127245284-1272435161769STF1_HUMAN380-461821A:380-45879

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:230
 aligned with STF1_HUMAN | Q13285 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:238
                                   230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450        
           STF1_HUMAN   221 PNVPELILQLLQLEPDEDQVRARILGCLQEPTKSRPDQPAAFGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELTTVATQAGSLLHSLVLRAQELVLQLLALQLDRQEFVCLKFIILFSLDLKFLNNHILVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLCLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQA 458
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1yowA00 A:221-458 Retinoid X R        eceptor                                                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------Ho        rmone_recep-1yowA01 A:249-455                                                                                                                                                                        --- Pfam domains
         Sec.struct. author ...hhhhhhhhhh..hhhhhhhhhhhhhh.--------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------N------------------------------------------------------N-----------------------------------------------------------------------------------------------------------------------------------------------Q--------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6b  PDB: A:221-290 (gaps) UniProt: 82-290 [INCOMPLETE]         Exon 1.7  PDB: A:291-330                Exon 1.8  PDB: A:331-380 UniProt: 331-380         ------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9b  PDB: A:380-458 UniProt: 380-461 [INCOMPLETE]                         Transcript 1 (2)
                 1yow A 221 SNVPELMLQLLQLEPDEDQVRARILGCLQE--------PAAFGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELTTVATQAGSLLHSLVLRAQELVLQLLALQLDRQEFVCLKFIILFSLDLKFLNNHILVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLCLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQA 458
                                   230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450        
                                                       250      259                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 1yow B 598 AQALAALLAKA 608
                                   607
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1YOW)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Hormone_recep] (290)

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (STF1_HUMAN | Q13285)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000980    RNA polymerase II distal enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
    GO:0004879    RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding    Combining with a signal and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003707    steroid hormone receptor activity    Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function.
    GO:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0003705    transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0000976    transcription regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030325    adrenal gland development    The process whose specific outcome is the progression of the adrenal gland over time, from its formation to the mature structure. This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0008585    female gonad development    The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure.
    GO:0042445    hormone metabolic process    The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone.
    GO:0009755    hormone-mediated signaling pathway    A series of molecular signals mediated by the detection of a hormone.
    GO:0030522    intracellular receptor signaling pathway    Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
    GO:0001553    luteinization    The set of processes resulting in differentiation of theca and granulosa cells into luteal cells and in the formation of a corpus luteum after ovulation.
    GO:0051457    maintenance of protein location in nucleus    Any process in which a protein is maintained in the nucleus and prevented from moving elsewhere. These include sequestration within the nucleus, protein stabilization to prevent transport elsewhere and the active retrieval of proteins that escape the nucleus.
    GO:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:0010259    multicellular organism aging    An aging process that has as participant a whole multicellular organism. Multicellular organism aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Multicellular organisms aging includes processes like cellular senescence and organ senescence, but is more inclusive. May precede death (GO:0016265) of an organism and may succeed developmental maturation (GO:0021700).
    GO:2000195    negative regulation of female gonad development    Any process that stops, prevents, or reduces the frequency, rate or extent of female gonad development.
    GO:2000020    positive regulation of male gonad development    Any process that activates or increases the frequency, rate or extent of male gonad development.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007538    primary sex determination    The sex determination process that results in the initial specification of sexual status of an individual organism.
    GO:0050810    regulation of steroid biosynthetic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0022414    reproductive process    A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
    GO:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    GO:0009888    tissue development    The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006367    transcription initiation from RNA polymerase II promoter    Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0090575    RNA polymerase II transcription factor complex    A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase II.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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        STF1_HUMAN | Q13285: 1zdt 4qjr 4qk4

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