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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PABP-BINDING SITE OF EIF4G IN COMPLEX WITH RRM1-2 OF PABP AND POLY(A)
 
Authors :  N. Safaee, G. Kozlov, K. B. Gehring
Date :  03 May 12  (Deposition) - 08 Aug 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Translation Initiation, Mrna, Eukaryotic Initiation Factors (Eifs), Paip1 And Paip2, Translation-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Safaee, G. Kozlov, A. M. Noronha, J. Xie, C. J. Wilds, K. Gehring
Interdomain Allostery Promotes Assembly Of The Poly(A) Mrna Complex With Pabp And Eif4G.
Mol. Cell V. 48 375 2012
PubMed-ID: 23041282  |  Reference-DOI: 10.1016/J.MOLCEL.2012.09.001

(-) Compounds

Molecule 1 - POLYADENYLATE-BINDING PROTEIN 1
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PABPC1, PAB1, PABP1, PABPC2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PABP-1, POLY(A)-BINDING PROTEIN 1
 
Molecule 2 - RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
    Chains: B, E
    Engineered: YES
    Other Details: OLIGO-RA11
    Synthetic: YES
 
Molecule 3 - EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA 1
    Chains: C, F
    Engineered: YES
    Fragment: UNP RESIDUES 178-203
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EIF-4-GAMMA 1, EIF-4G 1, EIF-4G1, P220
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4F02)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:14 , ARG A:41 , ARG A:44 , ASP A:45 , MET A:46 , LEU A:52 , TYR A:54 , TYR A:56 , ASN A:58 , MET A:85 , TRP A:86 , SER A:87 , GLN A:88 , ARG A:89 , ARG A:94 , ASN A:100 , PHE A:102 , LYS A:104 , ASN A:105 , SER A:127 , LYS A:138 , GLY A:139 , TYR A:140 , PHE A:142 , HIS A:144 , ARG A:172 , PHE A:173 , LYS A:174 , SER A:175 , ARG A:176 , ARG A:179 , HOH A:318 , HOH A:321 , HOH A:325 , HOH B:101 , HOH B:102 , HOH B:103 , HOH B:104 , HOH B:105 , HOH B:106 , HOH B:108 , HOH B:109 , HOH B:112 , HOH B:113 , HOH B:114 , HOH B:119 , HOH B:120 , MET D:46 , A E:7BINDING SITE FOR CHAIN B OF RNA (5'-R(*AP*AP*AP* AP*AP*AP*AP*AP*AP*AP*A)-3')

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F02)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F02)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F02)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F02)

(-) Exons   (0, 0)

(no "Exon" information available for 4F02)

(-) 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:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeee....hhhhhhh..eeeee......hhhhhhhhhhhhh.eeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeee..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f02 A  10 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELG 184
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179     


Chain B from PDB  Type:RNA  Length:9
                                         
                 4f02 B   1 AAAAAAAAA   9


Chain C from PDB  Type:PROTEIN  Length:20
                                                    
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author ...eehhhhh...hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 4f02 C 179 TIRIRDPNQGGKDITEEIMS 198
                                   188       198


Chain D from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeee....hhhhhhh..eeeee......hhhhhhhhhhhhh.eeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeee..hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4f02 D  10 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 183
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    


Chain E from PDB  Type:RNA  Length:9
                                         
                 4f02 E   1 AAAAAAAAA   9


Chain F from PDB  Type:PROTEIN  Length:20
                                                    
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author ...eehhhhh...hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 4f02 F 179 TIRIRDPNQGGKDITEEIMS 198
                                   188       198
   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 4F02)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F02)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F02)

(-) Gene Ontology  (44, 53)

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  4f02
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  IF4G1_HUMAN | Q04637
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  PABP1_HUMAN | P11940
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 Related Entries

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

UniProtKB/Swiss-Prot
        IF4G1_HUMAN | Q04637: 1lj2 1ug3 2w97 4aza 5ehc 5ei3 5eir 5t46
        PABP1_HUMAN | P11940: 1cvj 1g9l 1jgn 1jh4 2k8g 2rqg 2rqh 2x04 3ktp 3ktr 3kui 3kuj 3kur 3kus 3kut 3pkn 3pth 4f25 4f26 5dx1 5dx8 5dxa 5lgp 5lgq 5lgr 5lgs

(-) Related Entries Specified in the PDB File

4f25 4f26