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(-) Description

Title :  CRYSTAL STRUCTURE OF A TERNARY COMPLEX CONTAINING AN OCA-B PEPTIDE, THE OCT-1 POU DOMAIN, AND AN OCTAMER ELEMENT
 
Authors :  D. I. Chasman, K. Cepek, P. A. Sharp, C. O. Pabo
Date :  11 Aug 99  (Deposition) - 15 Nov 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,I,J,M,N,O,P
Biol. Unit 1:  A,I,M,N  (1x)
Biol. Unit 2:  B,J,O,P  (1x)
Keywords :  Pou Domain, Protein-Dna Complex, Oct1, Oca-B, Protein-Dna Interface, Gene Regulation/Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Chasman, K. Cepek, P. A. Sharp, C. O. Pabo
Crystal Structure Of An Oca-B Peptide Bound To An Oct-1 Pou Domain/Octamer Dna Complex: Specific Recognition Of A Protein-Dna Interface.
Genes Dev. V. 13 2650 1999
PubMed-ID: 10541551  |  Reference-DOI: 10.1101/GAD.13.20.2650
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*TP*AP*AP*GP*G)-3')
    ChainsM, O
    EngineeredYES
    SyntheticYES
 
Molecule 2 - DNA (5'- D(*AP*CP*CP*TP*TP*AP*TP*TP*TP*GP*CP*AP*TP*AP*C)-3')
    ChainsN, P
    EngineeredYES
    SyntheticYES
 
Molecule 3 - POU DOMAIN, CLASS 2, TRANSCRIPTION FACTOR 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidSEE REFERENCE 1
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentOCT-1 POU DOMAIN, RESIDUES 278-439
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymOCTAMER-BINDING TRANSCRIPTION FACTOR 1, OTF-1, NF- A1
 
Molecule 4 - POU DOMAIN, CLASS 2, ASSOCIATING FACTOR 1
    CellB-CELL
    ChainsI, J
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentOCA-B PEPTIDE, RESIDUES 1-44
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymOCT-BINDING FACTOR, OCA-B, OBF-1, BOB1

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABIJMNOP
Biological Unit 1 (1x)A I MN  
Biological Unit 2 (1x) B J  OP

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1CQT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (4, 8)

Asymmetric Unit (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1POU_1PS00035 POU-specific (POUs) domain signature 1.PO2F1_HUMAN298-310
 
  2A:19-31
B:519-531
2POU_2PS00465 POU-specific (POUs) domain signature 2.PO2F1_HUMAN322-335
 
  2A:43-56
B:543-556
3HOMEOBOX_2PS50071 'Homeobox' domain profile.PO2F1_HUMAN377-437
 
  2A:102-159
B:602-659
4HOMEOBOX_1PS00027 'Homeobox' domain signature.PO2F1_HUMAN412-435
 
  2A:134-157
B:634-657
Biological Unit 1 (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1POU_1PS00035 POU-specific (POUs) domain signature 1.PO2F1_HUMAN298-310
 
  1A:19-31
-
2POU_2PS00465 POU-specific (POUs) domain signature 2.PO2F1_HUMAN322-335
 
  1A:43-56
-
3HOMEOBOX_2PS50071 'Homeobox' domain profile.PO2F1_HUMAN377-437
 
  1A:102-159
-
4HOMEOBOX_1PS00027 'Homeobox' domain signature.PO2F1_HUMAN412-435
 
  1A:134-157
-
Biological Unit 2 (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1POU_1PS00035 POU-specific (POUs) domain signature 1.PO2F1_HUMAN298-310
 
  1-
B:519-531
2POU_2PS00465 POU-specific (POUs) domain signature 2.PO2F1_HUMAN322-335
 
  1-
B:543-556
3HOMEOBOX_2PS50071 'Homeobox' domain profile.PO2F1_HUMAN377-437
 
  1-
B:602-659
4HOMEOBOX_1PS00027 'Homeobox' domain signature.PO2F1_HUMAN412-435
 
  1-
B:634-657

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.11aENST0000039306711aENSE00002141635chr11:111250417-111249887531OBF1_HUMAN1-660--
1.16cENST0000039306716cENSE00000795575chr11:111229643-111229513131OBF1_HUMAN6-49442I:300-321
J:800-822
22
23
1.17ENST0000039306717ENSE00000746836chr11:111228562-11122852043OBF1_HUMAN50-64150--
1.18bENST0000039306718bENSE00000746835chr11:111228435-111228170266OBF1_HUMAN64-152890--
1.19cENST0000039306719cENSE00002175136chr11:111225300-1112229772324OBF1_HUMAN153-2561040--

(-) Sequences/Alignments

Asymmetric 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:134
 aligned with PO2F1_HUMAN | P14859 from UniProtKB/Swiss-Prot  Length:743

    Alignment length:159
                                   290       300       310       320       330       340       350       360       370       380       390       400       410       420       430         
          PO2F1_HUMAN   281 EPSDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLEKWLNDAENLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRINP 439
               SCOP domains d1cqta2 A:2-75 Oct-1                                                      -------------------------d1cqta1 A:102-161 Oct-1 POU Homeodomain                      SCOP domains
               CATH domains ---1cqtA01 A:5-75 lambda repressor-like DNA-binding domains               -------------------------1cqtA02 A:102-161 Homeodomain-like                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..-------------------------.......hhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh. 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
                 1cqt A   2 EPSDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLEKWLNDAE-------------------------RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRINP 161
                                    11        21        31        41        51        61        71   |     -         -       102       112       122       132       142       152         
                                                                                                    75                       102                                                           

Chain B from PDB  Type:PROTEIN  Length:129
 aligned with PO2F1_HUMAN | P14859 from UniProtKB/Swiss-Prot  Length:743

    Alignment length:156
                                   293       303       313       323       333       343       353       363       373       383       393       403       413       423       433      
          PO2F1_HUMAN   284 DLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLEKWLNDAENLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRINP 439
               SCOP domains d1cqtb2 B:505-575 Oct-1                                                                         d1cqtb1 B:602-661 Oct-1  POU Homeodomain                     SCOP domains
               CATH domains 1cqtB01 B:505-575 lambda repressor -like DNA-binding domains                                    1cqtB02 B:602-661 Homeod omain-like                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...hhhhhhhh....-...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.-------------------------.......hhhhhhhhhhhhh....-...............hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------------POU_1        -----------POU_2         -----------------------------------------HOMEOBOX_2  PDB: B:602-659 UniProt: 377-437                  -- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------HOMEOBOX_1              ---- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cqt B 505 DLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLY-NDFSQTTISRFEALNLSFKNMCKLKPLLEKWLNDAE-------------------------RKKRTSIETNIRVALEKSFLENQK-TSEEITMIADQLNMEKEVIRVWFCNRRQKEKRINP 661
                                   514       524       534   | | 544       554       564       574|        -         -      |605       615       625 |     635       645       655      
                                                           538 |                                575                       602                    625 |                                  
                                                             540                                                                                   627                                  

Chain I from PDB  Type:PROTEIN  Length:22
 aligned with OBF1_HUMAN | Q16633 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:22
                                    25        35  
           OBF1_HUMAN    16 ARPYQGVRVKEPVKELLRRKRG  37
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
               Transcript 1 Exon 1.16c             Transcript 1
                 1cqt I 300 ARPYQGVRVKEPVKELLRRKRG 321
                                   309       319  

Chain J from PDB  Type:PROTEIN  Length:23
 aligned with OBF1_HUMAN | Q16633 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:23
                                    25        35   
           OBF1_HUMAN    16 ARPYQGVRVKEPVKELLRRKRGH  38
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
               Transcript 1 Exon 1.16c [INCOMPLETE] Transcript 1
                 1cqt J 800 ARPYQGVRVKEPVKELLRRKRGH 822
                                   809       819   

Chain M from PDB  Type:DNA  Length:15
                                               
                 1cqt M 201 TGTATGCAAATAAGG 215
                                   210     

Chain N from PDB  Type:DNA  Length:15
                                               
                 1cqt N 216 ACCTTATTTGCATAC 230
                                   225     

Chain O from PDB  Type:DNA  Length:14
                                              
                 1cqt O 702 GTATGCAAATAAGG 715
                                   711    

Chain P from PDB  Type:DNA  Length:14
                                              
                 1cqt P 717 CCTTATTTGCATAC 730
                                   726    

   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 Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 25)

Asymmetric 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.

Chain I,J   (OBF1_HUMAN | Q16633)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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:0003712    transcription cofactor activity    Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
biological process
    GO:0006959    humoral immune response    An immune response mediated through a body fluid.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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: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 | P148591e3o 1gt0 1hf0 1o4x 1oct 1pog 1pou

(-) Related Entries Specified in the PDB File

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