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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF OCT-1 BOUND TO DNA AS A DIMER
 
Authors :  A. Remenyi, A. Tomilin, E. Pohl, H. R. Scholer, M. Wilmanns
Date :  27 Nov 00  (Deposition) - 10 Nov 01  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,M,N
Keywords :  Transcription, Oct-1, Pou Domain, Dimer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Remenyi, A. Tomilin, E. Pohl, K. Lins, A. Philippsen, R. Reinbold, H. R. Scholer, M. Wilmanns
Differential Dimer Activities Of The Transcription Factor Oct-1 By Dna-Induced Interface Swapping
Mol. Cell V. 8 569 2001
PubMed-ID: 11583619  |  Reference-DOI: 10.1016/S1097-2765(01)00336-7

(-) Compounds

Molecule 1 - OCTAMER-BINDING TRANSCRIPTION FACTOR 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: DNA-BINDING DOMAIN
    Mutation: YES
    Organelle: NUCLEUS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - DNA 5'-D(*CP*AP*CP*AP*TP*TP*TP*GP*AP*AP*AP*GP*GP* CP*AP*AP*AP*TP*GP*GP*AP*G)-3'
    Chains: M
    Synthetic: YES
 
Molecule 3 - DNA 5'-D(*CP*TP*CP*CP*AP*TP*TP*TP*GP*CP*CP*TP*TP* TP*CP*AP*AP*AP*TP*GP*TP*G)-3'
    Chains: N
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABMN

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1HF0)

(-) Sites  (0, 0)

(no "Site" information available for 1HF0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HF0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HF0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HF0)

(-) PROSITE Motifs  (4, 8)

Asymmetric/Biological Unit (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1POU_1PS00035 POU-specific (POUs) domain signature 1.PO2F1_HUMAN298-310
 		  2A:19-31
B:19-31
2POU_2PS00465 POU-specific (POUs) domain signature 2.PO2F1_HUMAN322-335
 		  2A:43-56
B:43-56
3HOMEOBOX_2PS50071 'Homeobox' domain profile.PO2F1_HUMAN377-437
 		  2A:102-159
B:102-159
4HOMEOBOX_1PS00027 'Homeobox' domain signature.PO2F1_HUMAN412-435
 		  2A:134-157
B:134-157

(-) Exons   (0, 0)

(no "Exon" information available for 1HF0)

(-) 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:128
 aligned with PO2F1_HUMAN | P14859 from UniProtKB/Swiss-Prot  Length:743

    Alignment length:153
                                   294       304       314       324       334       344       354       364       374       384       394       404       414       424       434   
          PO2F1_HUMAN   285 LEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLEKWLNDAENLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRI 437
               SCOP domains d1hf0a2 A:6-75 Oct-1                                                  -------------------------d1hf0a1 A:102-159 Oct-1 POU Homeodomain                    SCOP domains
               CATH domains 1hf0A01 A:6-75 lambda repressor-like DNA-binding domains              -------------------------1hf0A02 A:102-158 Homeodomain-like                       - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh-------------------------.......hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------POU_1        -----------POU_2         -----------------------------------------HOMEOBOX_2  PDB: A:102-159 UniProt: 377-437                   PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------HOMEOBOX_1              -- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hf0 A   6 LEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMSKLKPLLEKWLNDAE-------------------------RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEKRI 159
                                    15        25        35        45        55        65        75         -         -     | 106       116       126       136       146       156   
                                                                                                75                       102                                                         


Chain B from PDB  Type:PROTEIN  Length:128
 aligned with PO2F1_HUMAN | P14859 from UniProtKB/Swiss-Prot  Length:743

    Alignment length:153
                                   294       304       314       324       334       344       354       364       374       384       394       404       414       424       434   
          PO2F1_HUMAN   285 LEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLEKWLNDAENLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRI 437
               SCOP domains d1hf0b2 B:6-75 Oct-1                                                  -------------------------d1hf0b1 B:102-159 Oct-1 POU Homeodomain                    SCOP domains
               CATH domains 1hf0B01 B:6-75 lambda repressor-like DNA-binding domains              -------------------------1hf0B02 B:102-158 Homeodomain-like                       - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh-------------------------.......hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------POU_1        -----------POU_2         -----------------------------------------HOMEOBOX_2  PDB: B:102-159 UniProt: 377-437                   PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------HOMEOBOX_1              -- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hf0 B   6 LEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMSKLKPLLEKWLNDAE-------------------------RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEKRI 159
                                    15        25        35        45        55        65        75         -         -     | 106       116       126       136       146       156   
                                                                                                75                       102                                                         


Chain M from PDB  Type:DNA  Length:22
                                                      
                 1hf0 M   1 CACATTTGAAAGGCAAATGGAG  22
                                    10        20  


Chain N from PDB  Type:DNA  Length:22
                                                      
                 1hf0 N   1 CTCCATTTGCCTTTCAAATGTG  22
                                    10        20
   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  (2, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HF0)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PO2F1_HUMAN | P14859)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    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: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.
biological process
    GO:0097421    liver regeneration    The regrowth of lost or destroyed liver.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0042795    snRNA transcription from RNA polymerase II promoter    The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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: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: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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PO2F1_HUMAN | P14859: 1cqt 1e3o 1gt0 1o4x 1oct 1pog 1pou

(-) Related Entries Specified in the PDB File

1cqt CRYSTAL STRUCTURE OF A TERNARY COMPLEX CONTAINING AN OCA-B PEPTIDE, THE OCT-1 POU DOMAIN, AND AN OCTAMER ELEMENT
1e3o CRYSTAL STRUCTURE OF OCT-1 POU DIMER BOUND TO MORE