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(-) Description

Title :  TRANSLATION INITIATION FACTOR 4E IN COMPLEX WITH M7GPPPPG MRNA 5' CAP ANALOG
 
Authors :  M. Warminski, E. Nowak, A. M. Rydzik, J. Kowalska, J. Jemielity, M. Nowo
Date :  03 Apr 16  (Deposition) - 10 May 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Protein-Ligand Complex, Translation Initiation Factor, Eif4E, M7Gppppg, Mrna 5' Cap Analog, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Rydzik, M. Warminski, P. J. Sikorski, M. R. Baranowski, S. Walczak, J. Kowalska, J. Zuberek, M. Lukaszewicz, E. Nowak, T. D. W Claridge, E. Darzynkiewicz, M. Nowotny, J. Jemielity
Mrna Cap Analogues Substituted In The Tetraphosphate Chain With Cx2: Identification Of O-To-Ccl2 As The First Bridging Modification That Confers Resistance To Decapping Without Impairing Translation.
Nucleic Acids Res. 2017
PubMed-ID: 28666355  |  Reference-DOI: 10.1093/NAR/GKX569

(-) Compounds

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 28-217
    Gene: EIF4E
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: MRNA CAP-BINDING PROTEIN,EIF-4F 25 KDA SUBUNIT

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
16G04Ligand/Ion5'-O-[(R)-HYDROXY{[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]OXY}PHOSPHORYL]-7-METHYLGUANOSINE
2GOL2Ligand/IonGLYCEROL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
16G01Ligand/Ion5'-O-[(R)-HYDROXY{[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]OXY}PHOSPHORYL]-7-METHYLGUANOSINE
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
16G01Ligand/Ion5'-O-[(R)-HYDROXY{[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]OXY}PHOSPHORYL]-7-METHYLGUANOSINE
2GOL1Ligand/IonGLYCEROL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
16G01Ligand/Ion5'-O-[(R)-HYDROXY{[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]OXY}PHOSPHORYL]-7-METHYLGUANOSINE
2GOL-1Ligand/IonGLYCEROL
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
16G01Ligand/Ion5'-O-[(R)-HYDROXY{[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]OXY}PHOSPHORYL]-7-METHYLGUANOSINE
2GOL-1Ligand/IonGLYCEROL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:56 , MET A:101 , TRP A:102 , GLU A:103 , ARG A:157 , LYS A:162 , HOH A:409 , HOH A:413 , HOH A:427 , HOH A:429 , HOH A:438 , HOH A:477 , HOH A:480 , HOH A:482 , HOH A:491binding site for residue 6G0 A 301
2AC2SOFTWAREILE A:115 , THR A:116 , GLN A:121 , ILE A:195 , HOH A:407 , HOH A:420binding site for residue GOL A 302
3AC3SOFTWARETRP B:56 , MET B:101 , TRP B:102 , GLU B:103 , ARG B:157 , LYS B:159 , LYS B:162 , HOH B:403 , HOH B:413 , HOH B:427 , HOH B:467 , HOH B:468 , HOH B:476 , HOH B:477binding site for residue 6G0 B 301
4AC4SOFTWARELYS B:95 , ILE B:98 , LYS B:106 , GLN B:120 , ASP B:147 , VAL B:149 , HOH B:405binding site for residue GOL B 302
5AC5SOFTWARETRP C:56 , PRO C:100 , MET C:101 , TRP C:102 , GLU C:103 , ARG C:157 , LYS C:162binding site for residue 6G0 C 300
6AC6SOFTWARETRP D:56 , MET D:101 , TRP D:102 , GLU D:103 , ARG D:157 , LYS D:162binding site for residue 6G0 D 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J5O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5J5O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J5O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J5O)

(-) Exons   (0, 0)

(no "Exon" information available for 5J5O)

(-) 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:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee.......hhh.eeeeeeeeehhhhhhhhh...hhhhh....eeeeee...............eeeeee...hhhhhhhhhhhhhhhhhhhh..hhhhhh.eeeeeee......eeeeee....hhhhhhhhhhhhhhhh.......eeeeehhhhh....eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j5o A  31 PEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALYNHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDYSDDVCGAVVNVRAKGDKIAIWTTECENRDAVTHIGRVYKERLGLPPKIVIGYQSHADTATKNRFVV 217
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    || 216 
                                                                                                                                                                                                        205|     
                                                                                                                                                                                                         212     


Chain B from PDB  Type:PROTEIN  Length:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee...........eeeeeeeeehhhhhhhhh...hhhhh....eeeeee...............eeeeee...hhhhhhhhhhhhhhhhhhhh..hhhhhh.eeeeeee......eeeeee....hhhhhhhhhhhhhhhhh......eeeeehhhhh....eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j5o B  31 PEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALYNHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDYSDDVCGAVVNVRAKGDKIAIWTTECENRDAVTHIGRVYKERLGLPPKIVIGYQSHADTATKNRFVV 217
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    || 216 
                                                                                                                                                                                                        205|     
                                                                                                                                                                                                         212     


Chain C from PDB  Type:PROTEIN  Length:179
                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee......hhhhheeeeeeeeehhhhhhhhhhh.hhhhh...eeeeeee...............eeeeee...hhhhhhhhhhhhhhhhhhhh..hhhhhh.eeeeeeee.....eeeeee....hhhhhhhhhhhhhhhhh......eeeee.hhh...eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j5o C  31 PEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALYNHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDYSDDVCGAVVNVRAKGDKIAIWTTECENRDAVTHIGRVYKERLGLPPKIVIGYQSHADTKNRFVV 217
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  ||     
                                                                                                                                                                                                      203|     
                                                                                                                                                                                                       212     


Chain D from PDB  Type:PROTEIN  Length:179
                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee.......hhh.eeeeeeeeehhhhhhhhhhh.hhhhh...eeeeeee........hhhhhh.eeeeee...hhhhhhhhhhhhhhhhhhhh..hhhhhh.eeeeeeee.....eeeeee....hhhhhhhhhhhhhhhhh.......eehhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j5o D  31 PEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALYNHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDYSDDVCGAVVNVRAKGDKIAIWTTECENRDAVTHIGRVYKERLGLPPKIVYQSHADTATKNRFVV 217
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   ||  202 ||      
                                                                                                                                                                                             194|    204|      
                                                                                                                                                                                              197     211
   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 5J5O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J5O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J5O)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

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UniProtKB/Swiss-Prot
        IF4E_MOUSE | P63073: 1ej1 1ej4 1ejh 1l8b 5bxv 5j5y

(-) Related Entries Specified in the PDB File

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