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(-) Description

Title :  HUMAN SREBP-1A BOUND TO LDL RECEPTOR PROMOTER
 
Authors :  A. Parraga, S. K. Burley
Date :  25 Jun 97  (Deposition) - 10 Jul 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Sterol Regulatory Element Binding Protein, Basic-Helix-Loop- Helix-Leucine Zipper, Srebp, Transcription Factor, Complex (Transcription Regulation/Dna), Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Parraga, L. Bellsolell, A. R. Ferre-D'Amare, S. K. Burley
Co-Crystal Structure Of Sterol Regulatory Element Binding Protein 1A At 2. 3 A Resolution.
Structure V. 6 661 1998
PubMed-ID: 9634703  |  Reference-DOI: 10.1016/S0969-2126(98)00067-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*TP*TP*GP*CP*AP*GP*TP*GP*GP*GP*GP*TP*GP*AP*TP*CP*T )-3')
    Chains: E, G
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*CP*AP*TP*GP*AP*GP*AP*TP*CP*AP*CP*CP*CP*CP*AP*CP*T P*GP*CP*AP*A)-3')
    Chains: F, H
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - PROTEIN (STEROL REGULATORY ELEMENT BINDING PROTEIN 1A)
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: DNA BINDING DOMAIN
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SREBP-1A

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH D:2003 , HOH D:2004 , HOH D:2005 , HOH D:2006 , HOH D:2007 , HOH D:2008BINDING SITE FOR RESIDUE MG C 2001
2AC2SOFTWAREHOH A:2009 , HOH A:2012 , HOH A:2013 , HOH B:2010 , HOH B:2011 , HOH B:2014BINDING SITE FOR RESIDUE MG B 2002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1AM9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1AM9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AM9)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BHLHPS50888 Myc-type, basic helix-loop-helix (bHLH) domain profile.SRBP1_HUMAN323-373
 
 
 		  4A:323-373
B:323-373
C:323-373
D:323-373

(-) Exons   (3, 10)

Asymmetric/Biological Unit (3, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002616461bENSE00001883965chr17:17740316-17740041276SRBP1_HUMAN1-31310--
1.3bENST000002616463bENSE00001596459chr17:17723835-17723404432SRBP1_HUMAN31-1751450--
1.4bENST000002616464bENSE00001776681chr17:17723039-17722852188SRBP1_HUMAN175-237630--
1.5ENST000002616465ENSE00001687138chr17:17722768-17722634135SRBP1_HUMAN238-282450--
1.6ENST000002616466ENSE00001767426chr17:17722548-17722327222SRBP1_HUMAN283-356744A:319-356
B:320-356
C:319-356
D:319-356		38
37
38
38
1.7bENST000002616467bENSE00001654308chr17:17721688-17721574115SRBP1_HUMAN357-395394A:357-395
B:357-394
C:357-395
D:357-394		39
38
39
38
1.8bENST000002616468bENSE00001704753chr17:17721230-17721010221SRBP1_HUMAN395-468742A:395-398
-
C:395-400
-		4
-
6
-
1.8hENST000002616468hENSE00001284623chr17:17720771-17720570202SRBP1_HUMAN469-536680--
1.9ENST000002616469ENSE00001284618chr17:17720450-17720272179SRBP1_HUMAN536-595600--
1.10bENST0000026164610bENSE00001284615chr17:17720032-17719771262SRBP1_HUMAN596-683880--
1.11cENST0000026164611cENSE00001017795chr17:17719687-17719521167SRBP1_HUMAN683-738560--
1.12ENST0000026164612ENSE00000693018chr17:17719342-17719174169SRBP1_HUMAN739-795570--
1.13ENST0000026164613ENSE00000946283chr17:17718643-17718535109SRBP1_HUMAN795-831370--
1.14ENST0000026164614ENSE00000341628chr17:17718258-17718149110SRBP1_HUMAN831-868380--
1.15bENST0000026164615bENSE00000341629chr17:17718061-17717929133SRBP1_HUMAN868-912450--
1.16bENST0000026164616bENSE00000693009chr17:17717724-17717559166SRBP1_HUMAN912-967560--
1.17ENST0000026164617ENSE00000341631chr17:17717083-17716883201SRBP1_HUMAN968-1034670--
1.18aENST0000026164618aENSE00000946284chr17:17716793-17716682112SRBP1_HUMAN1035-1072380--
1.19bENST0000026164619bENSE00001522720chr17:17716165-17715387779SRBP1_HUMAN1072-1147760--

(-) 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:80
 aligned with SRBP1_HUMAN | P36956 from UniProtKB/Swiss-Prot  Length:1147

    Alignment length:80
                                   328       338       348       358       368       378       388       398
          SRBP1_HUMAN   319 QSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSKSLK 398
               SCOP domains d1am9a_ A: SREBP-1a                                                              SCOP domains
               CATH domains 1am9A00 A:319-398 MYOD Basic-Helix-Loop-Helix Domain, subunit B                  CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----BHLH  PDB: A:323-373 UniProt: 323-373              ------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:319-356 [INCOMPLETE] Exon 1.7b  PDB: A:357-395              --- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------1.8b Transcript 1 (2)
                 1am9 A 319 QSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSKSLK 398
                                   328       338       348       358       368       378       388       398


Chain B from PDB  Type:PROTEIN  Length:75
 aligned with SRBP1_HUMAN | P36956 from UniProtKB/Swiss-Prot  Length:1147

    Alignment length:75
                                   329       339       349       359       369       379       389     
          SRBP1_HUMAN   320 SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKS 394
               SCOP domains d1am9b_ B: SREBP-1a                                                         SCOP domains
               CATH domains 1am9B00 B:320-394 MYOD Basic-Helix-Loop-Helix Domain, subunit B             CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---BHLH  PDB: B:323-373 UniProt: 323-373              --------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: B:320-356 [INCOMPLETE]Exon 1.7b  PDB: B:357-394 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------- Transcript 1 (2)
                 1am9 B 320 SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKS 394
                                   329       339       349       359       369       379       389     


Chain C from PDB  Type:PROTEIN  Length:82
 aligned with SRBP1_HUMAN | P36956 from UniProtKB/Swiss-Prot  Length:1147

    Alignment length:82
                                   328       338       348       358       368       378       388       398  
          SRBP1_HUMAN   319 QSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSKSLKDL 400
               SCOP domains d1am9c_ C: SREBP-1a                                                                SCOP domains
               CATH domains 1am9C00 C:319-400 MYOD Basic-Helix-Loop-Helix Domain, subunit B                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----BHLH  PDB: C:323-373 UniProt: 323-373              --------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: C:319-356 [INCOMPLETE] Exon 1.7b  PDB: C:357-395              ----- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------1.8b   Transcript 1 (2)
                 1am9 C 319 QSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSKSLKDL 400
                                   328       338       348       358       368       378       388       398  


Chain D from PDB  Type:PROTEIN  Length:76
 aligned with SRBP1_HUMAN | P36956 from UniProtKB/Swiss-Prot  Length:1147

    Alignment length:76
                                   328       338       348       358       368       378       388      
          SRBP1_HUMAN   319 QSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKS 394
               SCOP domains d1am9d_ D: SREBP-1a                                                          SCOP domains
               CATH domains 1am9D00 D:319-394 MYOD Basic-Helix-Loop-Helix Domain, subunit B              CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----BHLH  PDB: D:323-373 UniProt: 323-373              --------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: D:319-356 [INCOMPLETE] Exon 1.7b  PDB: D:357-394 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------- Transcript 1 (2)
                 1am9 D 319 QSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKS 394
                                   328       338       348       358       368       378       388      


Chain E from PDB  Type:DNA  Length:17
                                                 
                 1am9 E   1 TTGCAGTGGGGTGATCT  17
                                    10       


Chain F from PDB  Type:DNA  Length:21
                                                     
                 1am9 F  18 CATGAGATCACCCCACTGCAA  38
                                    27        37 


Chain G from PDB  Type:DNA  Length:17
                                                 
                 1am9 G  39 TTGCAGTGGGGTGATCT  55
                                    48       


Chain H from PDB  Type:DNA  Length:21
                                                     
                 1am9 H  56 CATGAGATCACCCCACTGCAA  76
                                    65        75
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AM9)

(-) Gene Ontology  (69, 69)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (SRBP1_HUMAN | P36956)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for 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: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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    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:0032810    sterol response element binding    Interacting selectively and non-covalently with the sterol response element (SRE), a nonpalindromic sequence found in the promoters of genes involved in lipid metabolism.
    GO:0000982    transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter 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:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0071398    cellular response to fatty acid    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fatty acid stimulus.
    GO:0032869    cellular response to insulin stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0009267    cellular response to starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nourishment.
    GO:0008203    cholesterol metabolic process    The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
    GO:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0045444    fat cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat.
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    GO:0008610    lipid biosynthetic process    The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0042789    mRNA transcription from RNA polymerase II promoter    The cellular synthesis of messenger RNA (mRNA) from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter.
    GO:0046676    negative regulation of insulin secretion    Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of insulin.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045542    positive regulation of cholesterol biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cholesterol.
    GO:0031065    positive regulation of histone deacetylation    Any process that activates or increases the frequency, rate or extent of the removal of acetyl groups from histones.
    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:0010867    positive regulation of triglyceride biosynthetic process    Any process that increases the rate, frequency, or extent of triglyceride biosynthesis. Triglyceride biosynthesis is the collection of chemical reactions and pathways resulting in the formation of triglyceride, any triester of glycerol.
    GO:0019217    regulation of fatty acid metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving fatty acids.
    GO:0003062    regulation of heart rate by chemical signal    The regulation of the rate of heart contraction mediated by chemical signaling, hormonal, autocrine or paracrine.
    GO:0050796    regulation of insulin secretion    Any process that modulates the frequency, rate or extent of the regulated release of insulin.
    GO:1903146    regulation of mitophagy    Any process that modulates the frequency, rate or extent of mitochondrion degradation (mitophagy).
    GO:0031647    regulation of protein stability    Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation.
    GO:1903214    regulation of protein targeting to mitochondrion    Any process that modulates the frequency, rate or extent of protein targeting to mitochondrion.
    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:0051591    response to cAMP    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0070542    response to fatty acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fatty acid stimulus.
    GO:0032094    response to food    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a food stimulus; food is anything which, when taken into the body, serves to nourish or build up the tissues or to supply body heat.
    GO:0033762    response to glucagon    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucagon stimulus.
    GO:0009749    response to glucose    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
    GO:0033993    response to lipid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0043434    response to peptide hormone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
    GO:0032570    response to progesterone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a progesterone stimulus.
    GO:0032526    response to retinoic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0012507    ER to Golgi transport vesicle membrane    The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    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.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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