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(-) Description

Title :  SOLUTION STRUCTURE OF THE FIRST TWO RRM DOMAINS OF FIR IN THE COMPLEX WITH FBP NBOX PEPTIDE
 
Authors :  C. D. Cukier, A. Ramos, D. Hollingworth, I. Diaz-Moreno, G. Kelly
Date :  05 May 10  (Deposition) - 18 Aug 10  (Release) - 18 Aug 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Rrm, Fir, Fbp, Protein-Protein Complex, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. D. Cukier, D. Hollingworth, S. R. Martin, G. Kelly, I. Diaz-Moreno, A. Ramos
Molecular Basis Of Fir-Mediated C-Myc Transcriptional Control
Nat. Struct. Mol. Biol. 2010
PubMed: search  |  Reference-DOI: 10.1038/NSMB.1883

(-) Compounds

Molecule 1 - POLY(U)-BINDING-SPLICING FACTOR PUF60
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System VectorPETM-30
    Expression System Vector TypeVECTOR
    FragmentUNP RESIDUES 119-314
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym60 KDA POLY(U)-BINDING-SPLICING FACTOR, FUSE-BINDING PROTEIN-INTERACTING REPRESSOR, FBP-INTERACTING REPRESSOR, SIAH- BINDING PROTEIN 1, SIAH-BP1, RO-BINDING PROTEIN 1, ROBP1
 
Molecule 2 - PEPTIDE OF FAR UPSTREAM ELEMENT-BINDING PROTEIN 1
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System VectorPETM-30
    Expression System Vector TypeVECTOR
    FragmentUNP RESIDUES 27-52
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFUSE-BINDING PROTEIN 1, FBP, DNA HELICASE V, HDH V

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2KXH)

(-) Sites  (0, 0)

(no "Site" information available for 2KXH)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KXH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KXH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_070939H169YPUF60_HUMANDisease (VRJS)398123001AH152Y

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_070939H169YPUF60_HUMANDisease (VRJS)398123001AH152Y

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.PUF60_HUMAN129-207
226-304
462-549
  2A:112-190
A:209-287
-
NMR Structure * (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.PUF60_HUMAN129-207
226-304
462-549
  2A:112-190
A:209-287
-

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1eENST000003707681eENSE00001815368chr1:78444770-78444569202FUBP1_HUMAN1-40401B:22-4019
1.2ENST000003707682ENSE00001066871chr1:78435699-7843560991FUBP1_HUMAN41-71311B:41-5212
1.4ENST000003707684ENSE00001066882chr1:78433887-7843384939FUBP1_HUMAN71-84140--
1.5ENST000003707685ENSE00001066879chr1:78433350-7843331140FUBP1_HUMAN84-97140--
1.6aENST000003707686aENSE00001349606chr1:78432785-7843273353FUBP1_HUMAN97-115190--
1.7ENST000003707687ENSE00001066887chr1:78432639-7843256872FUBP1_HUMAN115-139250--
1.8ENST000003707688ENSE00001066874chr1:78432435-7843237858FUBP1_HUMAN139-158200--
1.9ENST000003707689ENSE00002163081chr1:78430915-78430753163FUBP1_HUMAN158-212550--
1.10ENST0000037076810ENSE00001066888chr1:78430653-7843055599FUBP1_HUMAN213-245330--
1.11ENST0000037076811ENSE00001066872chr1:78430432-78430331102FUBP1_HUMAN246-279340--
1.12ENST0000037076812ENSE00001066883chr1:78430041-78429939103FUBP1_HUMAN280-314350--
1.13ENST0000037076813ENSE00001066884chr1:78429847-78429747101FUBP1_HUMAN314-347340--
1.14ENST0000037076814ENSE00001435529chr1:78429400-78429259142FUBP1_HUMAN348-395480--
1.15ENST0000037076815ENSE00001435707chr1:78428615-78428455161FUBP1_HUMAN395-448540--
1.16bENST0000037076816bENSE00001066870chr1:78426180-78426029152FUBP1_HUMAN449-499510--
1.17ENST0000037076817ENSE00001066877chr1:78425948-7842586980FUBP1_HUMAN499-526280--
1.18ENST0000037076818ENSE00001066876chr1:78422385-78422257129FUBP1_HUMAN526-569440--
1.19dENST0000037076819dENSE00001066889chr1:78421014-7842094075FUBP1_HUMAN569-594260--
1.20aENST0000037076820aENSE00001349579chr1:78414985-78414840146FUBP1_HUMAN594-642490--
1.21bENST0000037076821bENSE00001916670chr1:78414459-78414090370FUBP1_HUMAN643-64420--

(-) Sequences/Alignments

NMR Structure
   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:199
 aligned with PUF60_HUMAN | Q9UHX1 from UniProtKB/Swiss-Prot  Length:559

    Alignment length:199
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305         
          PUF60_HUMAN   116 SMAAQRQRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPAT 314
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2kxhA01 A:99-208  [code=3.30.70.330, no name defined]                                                         2kxhA02 A:209-297  [code=3.30.70.330, no name defined]                                    CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------RRM_1-2kxhA01 A:211-281                                                ---------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------RRM_1-2kxhA02 A:211-281                                                ---------------- Pfam domains (2)
         Sec.struct. author ......hhhhhhhheeeee......hhhhhhhhh.....eeeeee............eeeee.hhhhhhhhhhh...........ee........hhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhh.eeeeee...........eeeeee.hhhhhhhhhhhhh.........eeee............. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------Y------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------RRM  PDB: A:112-190 UniProt: 129-207                                           ------------------RRM  PDB: A:209-287 UniProt: 226-304                                           ---------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2kxh A  99 GAMAQRQRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPAT 297
                                   108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288         

Chain B from PDB  Type:PROTEIN  Length:31
 aligned with FUBP1_HUMAN | Q96AE4 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:31
                                    31        41        51 
          FUBP1_HUMAN    22 GGGGGVNDAFKDALQRARQIAAKIGGDAGTS  52
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
               Transcript 1 Exon 1.1e          Exon 1.2     Transcript 1
                 2kxh B  22 GAMGYVNDAFKDALQRARQIAAKIGGDAGTS  52
                                    31        41        51 

   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 2KXH)

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: RRM (206)
(-)
Family: RRM_1 (131)
1aRRM_1-2kxhA01A:211-281
1bRRM_1-2kxhA02A:211-281

(-) Gene Ontology  (20, 28)

NMR Structure(hide GO term definitions)
Chain A   (PUF60_HUMAN | Q9UHX1)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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).
biological process
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0019907    cyclin-dependent protein kinase activating kinase holoenzyme complex    A cyclin-dependent kinase activating kinase complex capable of activating cyclin-dependent kinases by threonine phosphorylation, thus regulating cell cycle progression. consists of a kinase, cyclin and optional assembly factors, in human CDK7, CCNH and MNAT1. CAK activity is itself regulated throughout the cell cycle by T-loop phosphorylation of its kinase component (CDK7 in human). Phosphorylation of serine residues during mitosis inactivates the enzyme. Also capable of CAK phosphorylating the carboxyl-terminal domain (CTD) of RNA polymerase II and other transcription activating proteins, as part of the general transcription factor TFIIH.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    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 B   (FUBP1_HUMAN | Q96AE4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic 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:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
    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.
biological process
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    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: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
        FUBP1_HUMAN | Q96AE41j4w 4lij
        PUF60_HUMAN | Q9UHX12dny 2kxf 2qfj 3dxb 3ue2 3us5 3uwt

(-) Related Entries Specified in the PDB File

2kxf SOLUTION STRUCTURE OF THE FIRST TWO RRM DOMAINS OF FBP- INTERACTING REPRESSOR (FIR)