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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SECOND MIF4G DOMAIN OF HUMAN NONSENSE MEDIATED DECAY FACTOR UPF2
 
Authors :  M. Clerici, A. Deniaud, V. Boehm, N. H. Gehring, C. Schaffitzel, S. Cusa
Date :  11 Nov 13  (Deposition) - 11 Dec 13  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Clerici, A. Deniaud, V. Boehm, N. H. Gehring, C. Schaffitzel, S. Cusack
Structural And Functional Analysis Of The Three Mif4G Domains Of Nonsense-Mediated Decay Factor Upf2.
Nucleic Acids Res. V. 42 2673 2014
PubMed-ID: 24271394  |  Reference-DOI: 10.1093/NAR/GKT1197

(-) Compounds

Molecule 1 - REGULATOR OF NONSENSE TRANSCRIPTS 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantSTAR
    Expression System VectorPPROEXHTB
    Expression System Vector TypePLASMID
    FragmentMIF4G2, RESIDUES 455-757
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNONSENSE MRNA REDUCING FACTOR 2, UP-FRAMESHIFT SUPPRESSOR 2 HOMOLOG, HUPF2, UPF2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4CEK)

(-) Sites  (0, 0)

(no "Site" information available for 4CEK)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CEK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CEK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CEK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CEK)

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003970531bENSE00001402467chr10:12085023-12084913111RENT2_HUMAN-00--
1.3cENST000003970533cENSE00002187710chr10:12077440-12077058383RENT2_HUMAN1-1221220--
1.4ENST000003970534ENSE00000999707chr10:12071523-12070744780RENT2_HUMAN122-3822610--
1.5ENST000003970535ENSE00001349465chr10:12056183-12056023161RENT2_HUMAN382-436550--
1.6ENST000003970536ENSE00001213473chr10:12046726-12046529198RENT2_HUMAN436-502671A:457-48024
1.7ENST000003970537ENSE00001213468chr10:12043824-12043675150RENT2_HUMAN502-552511A:529-548 (gaps)21
1.8bENST000003970538bENSE00001213463chr10:12042008-12041905104RENT2_HUMAN552-586351A:559-58628
1.9ENST000003970539ENSE00001754391chr10:12039756-1203967186RENT2_HUMAN587-615291A:587-61529
1.10ENST0000039705310ENSE00001649308chr10:12021164-12021056109RENT2_HUMAN615-651371A:615-65137
1.11ENST0000039705311ENSE00001649100chr10:12009453-12009340114RENT2_HUMAN652-689381A:652-689 (gaps)38
1.12ENST0000039705312ENSE00001742008chr10:12006124-12006008117RENT2_HUMAN690-728391A:690-72839
1.13ENST0000039705313ENSE00001617394chr10:12001355-12001170186RENT2_HUMAN729-790621A:729-75729
1.14ENST0000039705314ENSE00001724518chr10:11998522-11998319204RENT2_HUMAN791-858680--
1.15ENST0000039705315ENSE00001595330chr10:11997506-11997231276RENT2_HUMAN859-950920--
1.16ENST0000039705316ENSE00001647744chr10:11994248-11994065184RENT2_HUMAN951-1012620--
1.17ENST0000039705317ENSE00001662463chr10:11990507-11990368140RENT2_HUMAN1012-1058470--
1.18ENST0000039705318ENSE00001754512chr10:11985167-11985063105RENT2_HUMAN1059-1093350--
1.19ENST0000039705319ENSE00001760455chr10:11984762-1198466499RENT2_HUMAN1094-1126330--
1.20ENST0000039705320ENSE00001094605chr10:11978711-11978544168RENT2_HUMAN1127-1182560--
1.21bENST0000039705321bENSE00001094602chr10:11973781-11973640142RENT2_HUMAN1183-1230480--
1.22ENST0000039705322ENSE00001094595chr10:11971984-11971864121RENT2_HUMAN1230-1270410--
1.23aENST0000039705323aENSE00001213550chr10:11963306-119620221285RENT2_HUMAN1270-127230--

(-) 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:240
 aligned with RENT2_HUMAN | Q9HAU5 from UniProtKB/Swiss-Prot  Length:1272

    Alignment length:301
                                   466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756 
          RENT2_HUMAN   457 GIWEDEDARNFYENLIDLKAFVPAILFKDNEKSCQNKESNKDDTKEAKESKENKEVSSPDDLELELENLEINDDTLELEGGDEAEDLTKKLLDEQEQEDEEASTGSHLKLIVDAFLQQLPNCVNRDLIDKAAMDFCMNMNTKANRKKLVRALFIVPRQRLDLLPFYARLVATLHPCMSDVAEDLCSMLRGDFRFHVRKKDQINIETKNKTVRFIGELTKFKMFTKNDTLHCLKMLLSDFSHHHIEMACTLLETCGRFLFRSPESHLRTSVLLEQMMRKKQAMHLDARYVTMVENAYYYCNP 757
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh..hhhhh...--------------------------------------------------....--.hhhhhhhhhhhhh.-------hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.--.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:457-480 UniProt: 436-502     -------------------------------------------------Exon 1.8b  PDB: A:559-586          ----------------------------Exon 1.10  PDB: A:615-651            Exon 1.11  PDB: A:652-689 (gaps)      Exon 1.12  PDB: A:690-728              Exon 1.13  PDB: A:729-757     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.7  PDB: A:529-548 (gaps) UniProt: 502-552   ----------------------------------Exon 1.9  PDB: A:587-615     ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 4cek A 457 GIWEDEDARNFYENLIDLKAFVPA--------------------------------------------------TLEL--GDEAEDLTKKLLDEQ-------STGSHLKLIVDAFLQQLPNCVNRDLIDKAAMDFCMNMNTKANRKKLVRALFIVPRQRLDLLPFYARLVATLHPCMSDVAEDLCSMLRGDFRFHVRKK--INIETKNKTVRFIGELTKFKMFTKNDTLHCLKMLLSDFSHHHIEMACTLLETCGRFLFRSPESHLRTSVLLEQMMRKKQAMHLDARYVTMVENAYYYCNP 757
                                   466       476   |     -         -         -         -         -    |  | -|      543    |    -  |    566       576       586       596       606       616       626       636       646        |- |     666       676       686       696       706       716       726       736       746       756 
                                                 480                                                529  |  |           548     559                                                                                             655  |                                                                                                   
                                                                                                       532  |                                                                                                                      658                                                                                                   
                                                                                                          534                                                                                                                                                                                                                            

   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 4CEK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CEK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CEK)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RENT2_HUMAN | Q9HAU5)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0042162    telomeric DNA binding    Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.
biological process
    GO:0031100    animal organ regeneration    The regrowth of a lost or destroyed animal organ.
    GO:0001889    liver development    The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
    GO:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    GO:0000184    nuclear-transcribed mRNA catabolic process, nonsense-mediated decay    The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0035145    exon-exon junction complex    A multi-subunit complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RENT2_HUMAN | Q9HAU51uw4 2wjv 4cem

(-) Related Entries Specified in the PDB File

4cem CRYSTAL STRUCTURE OF THE FIRST MIF4G DOMAIN OF HUMAN NONSENSE MEDIATED DECAY FACTOR UPF2