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(-) Description

Title :  RECOGNITION OF EIF4G BY ROTAVIRUS NSP3 REVEALS A BASIS FOR MRNA CIRCULARIZATION
 
Authors :  C. M. Groft, S. K. Burley
Date :  18 Apr 02  (Deposition) - 05 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Nsp3; Homodimer; Eif4G; Rotavirus; Translation; Mrna; Closed Loop; Coiled Coil, Viral Protein/ Translation Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Groft, S. K. Burley
Recognition Of Eif4G By Rotavirus Nsp3 Reveals A Basis For Mrna Circularization.
Mol. Cell V. 9 1273 2002
PubMed-ID: 12086624  |  Reference-DOI: 10.1016/S1097-2765(02)00555-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NONSTRUCTURAL RNA-BINDING PROTEIN 34
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Mutation: YES
    Organism Scientific: SIMIAN ROTAVIRUS A/SA11
    Organism Taxid: 10923
    Synonym: NSP3-C;
NS34;
NCVP4;
NON-STRUCTURAL PROTEIN NCVP4
 
Molecule 2 - EUKARYOTIC PROTEIN SYNTHESIS INITIATION FACTOR
    Chains: C, D
    Engineered: YES
    Fragment: RESIDUES 132-159 OF AAC82471
    Other Details: SEQUENCE APPEAR NATURALLY IN HOMO SAPIENS
    Synonym: EIF4GI
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1AU3Ligand/IonGOLD ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:1101 , GLY D:149 , HOH D:1100BINDING SITE FOR RESIDUE AU D 1
2AC2SOFTWARESER B:208BINDING SITE FOR RESIDUE AU B 2
3AC3SOFTWAREHOH B:1223BINDING SITE FOR RESIDUE AU B 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LJ2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LJ2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LJ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LJ2)

(-) Exons   (2, 4)

Asymmetric/Biological Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003461691aENSE00001957337chr3:184032283-184032462180IF4G1_HUMAN-00--
1.2eENST000003461692eENSE00001364164chr3:184033277-18403333357IF4G1_HUMAN-00--
1.2fENST000003461692fENSE00002150918chr3:184033551-18403364494IF4G1_HUMAN1-20200--
1.2iENST000003461692iENSE00001640019chr3:184033920-18403400687IF4G1_HUMAN21-49290--
1.4bENST000003461694bENSE00001660690chr3:184035109-184035285177IF4G1_HUMAN50-108590--
1.5bENST000003461695bENSE00001754377chr3:184035505-184035604100IF4G1_HUMAN109-142340--
1.7cENST000003461697cENSE00002187218chr3:184037477-184037589113IF4G1_HUMAN142-179382C:138-139
D:133-139		2
7
1.8fENST000003461698fENSE00002192598chr3:184038418-18403851093IF4G1_HUMAN180-210312C:140-159
D:140-159		20
20
1.9bENST000003461699bENSE00001731325chr3:184038715-18403878167IF4G1_HUMAN211-233230--
1.10gENST0000034616910gENSE00001669160chr3:184039070-184039891822IF4G1_HUMAN233-5072750--
1.11ENST0000034616911ENSE00001609185chr3:184040150-18404023889IF4G1_HUMAN507-536300--
1.12ENST0000034616912ENSE00001719210chr3:184040332-184040518187IF4G1_HUMAN537-599630--
1.13ENST0000034616913ENSE00001656080chr3:184040609-184040742134IF4G1_HUMAN599-643450--
1.14ENST0000034616914ENSE00001783634chr3:184040871-184041029159IF4G1_HUMAN644-696530--
1.15bENST0000034616915bENSE00001615721chr3:184041196-184041381186IF4G1_HUMAN697-758620--
1.16ENST0000034616916ENSE00001678763chr3:184041568-184041765198IF4G1_HUMAN759-824660--
1.17cENST0000034616917cENSE00001769552chr3:184041989-184042135147IF4G1_HUMAN825-873490--
1.18bENST0000034616918bENSE00001788274chr3:184042666-184042902237IF4G1_HUMAN874-952790--
1.19bENST0000034616919bENSE00001705319chr3:184043057-184043161105IF4G1_HUMAN953-987350--
1.19dENST0000034616919dENSE00001595277chr3:184043268-184043427160IF4G1_HUMAN988-1041540--
1.20aENST0000034616920aENSE00001651286chr3:184043639-184043739101IF4G1_HUMAN1041-1074340--
1.21ENST0000034616921ENSE00001632341chr3:184044315-184044417103IF4G1_HUMAN1075-1109350--
1.22bENST0000034616922bENSE00001746928chr3:184044669-184044771103IF4G1_HUMAN1109-1143350--
1.23bENST0000034616923bENSE00001711150chr3:184045004-184045236233IF4G1_HUMAN1143-1221790--
1.24aENST0000034616924aENSE00001672897chr3:184045374-184045492119IF4G1_HUMAN1221-1260400--
1.24dENST0000034616924dENSE00001757656chr3:184045618-184045790173IF4G1_HUMAN1261-1318580--
1.25cENST0000034616925cENSE00001596715chr3:184046419-184046544126IF4G1_HUMAN1318-1360430--
1.25eENST0000034616925eENSE00001717841chr3:184046697-18404677882IF4G1_HUMAN1360-1387280--
1.26aENST0000034616926aENSE00001597508chr3:184049054-18404915299IF4G1_HUMAN1388-1420330--
1.26dENST0000034616926dENSE00001690366chr3:184049260-184049394135IF4G1_HUMAN1421-1465450--
1.27bENST0000034616927bENSE00001666158chr3:184049516-18404959782IF4G1_HUMAN1466-1493280--
1.27eENST0000034616927eENSE00001690919chr3:184049734-184049874141IF4G1_HUMAN1493-1540480--
1.28gENST0000034616928gENSE00001687057chr3:184052515-184053141627IF4G1_HUMAN1540-1599600--

(-) 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:106
 aligned with NSP3_ROTS1 | P03536 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:106
                                   216       226       236       246       256       266       276       286       296       306      
           NSP3_ROTS1   207 HSLQNVIPQQQAHIAELQVYNNKLERDLQNKIGSLTSSIEWYLRSMELDPEIKADIEQQINSIDAINPLHAFDDLESVIRNLISDYDKLFLMFKGLIQRCNYQYSF 312
               SCOP domains d1lj2a_ A: NSP3 C-terminal domain, NS34                                                                    SCOP domains
               CATH domains 1lj2A00 A:207-312 Nonstructural RNA-binding protein                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1lj2 A 207 HSLQNVIPQQQAHIAELQVYNNKLERDLQNKIGSLTSSIEWYLRSMELDPEIKADIEQQINSIDAINPLHAFDDLESVIRNLISDYDKLFLMFKGLIQRSNYQYSF 312
                                   216       226       236       246       256       266       276       286       296       306      


Chain B from PDB  Type:PROTEIN  Length:110
 aligned with NSP3_ROTS1 | P03536 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:110
                                   215       225       235       245       255       265       275       285       295       305       315
           NSP3_ROTS1   206 MHSLQNVIPQQQAHIAELQVYNNKLERDLQNKIGSLTSSIEWYLRSMELDPEIKADIEQQINSIDAINPLHAFDDLESVIRNLISDYDKLFLMFKGLIQRCNYQYSFGCE 315
               SCOP domains d1lj2b_ B: NSP3 C-terminal domain, NS34                                                                        SCOP domains
               CATH domains 1lj2B00 B:206-315 Nonstructural RNA-binding protein                                                            CATH domains
           Pfam domains (1) Rota_NSP3-1lj2B01 B:206-282                                                  --------------------------------- Pfam domains (1)
           Pfam domains (2) Rota_NSP3-1lj2B02 B:206-282                                                  --------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1lj2 B 206 MHSLQNVIPQQQAHIAELQVYNNKLERDLQNKIGSLTSSIEWYLRSMELDPEIKADIEQQINSIDAINPLHAFDDLESVIRNLISDYDKLFLMFKGLIQRSNYQYSFGSE 315
                                   215       225       235       245       255       265       275       285       295       305       315


Chain C from PDB  Type:PROTEIN  Length:22
 aligned with IF4G1_HUMAN | Q04637 from UniProtKB/Swiss-Prot  Length:1599

    Alignment length:22
                                   187       197  
          IF4G1_HUMAN   178 KTIRIRDPNQGGKDITEEIMSG 199
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author ...eeehhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
               Transcript 1 1.Exon 1.8f            Transcript 1
                 1lj2 C 138 KTIRIRDPNQGGKDITEEIMSG 159
                                   147       157  


Chain D from PDB  Type:PROTEIN  Length:27
 aligned with IF4G1_HUMAN | Q04637 from UniProtKB/Swiss-Prot  Length:1599

    Alignment length:27
                                   182       192       
          IF4G1_HUMAN   173 PKRERKTIRIRDPNQGGKDITEEIMSG 199
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .....eeeeee........hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
               Transcript 1 1.7c   Exon 1.8f            Transcript 1
                 1lj2 D 133 PKRERKTIRIRDPNQGGKDITEEIMSG 159
                                   142       152
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Rota_NSP3] (1)

(-) Gene Ontology  (20, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NSP3_ROTS1 | P03536)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0039657    suppression by virus of host gene expression    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. 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 (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.

Chain C,D   (IF4G1_HUMAN | Q04637)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008190    eukaryotic initiation factor 4E binding    Interacting selectively and non-covalently with eukaryotic initiation factor 4E, a polypeptide factor involved in the initiation of ribosome-mediated translation.
    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:0008135    translation factor activity, RNA binding    Functions during translation by interacting selectively and non-covalently with RNA during polypeptide synthesis at the ribosome.
    GO:0003743    translation initiation factor activity    Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
    GO:0001662    behavioral fear response    An acute behavioral change resulting from a perceived external threat.
    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.
    GO:0000289    nuclear-transcribed mRNA poly(A) tail shortening    Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
    GO:0045666    positive regulation of neuron differentiation    Any process that activates or increases the frequency, rate or extent of neuron differentiation.
    GO:0043488    regulation of mRNA stability    Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0006446    regulation of translational initiation    Any process that modulates the frequency, rate or extent of translational initiation.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006413    translational initiation    The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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:0016281    eukaryotic translation initiation factor 4F complex    The eukaryotic translation initiation factor 4F complex is composed of eIF4E, eIF4A and eIF4G; it is involved in the recognition of the mRNA cap, ATP-dependent unwinding of the 5'-terminal secondary structure and recruitment of the mRNA to the ribosome.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IF4G1_HUMAN | Q04637: 1ug3 2w97 4aza 4f02 5ehc 5ei3 5eir 5t46
        NSP3_ROTS1 | P03536: 1knz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1LJ2)