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(-) Description

Title :  TRANSLATION INITIATION FACTOR EIF5B (517-858) FROM C. THERMOPHILUM, BOUND TO GTPGAMMAS AND SODIUM
 
Authors :  B. Kuhle, R. Ficner
Date :  02 Jun 14  (Deposition) - 24 Sep 14  (Release) - 24 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Keywords :  Ribosome, Translation, Initiation Factor, Gtpase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Kuhle, R. Ficner
A Monovalent Cation Acts As Structural And Catalytic Cofactor In Translational Gtpases.
Embo J. V. 33 2547 2014
PubMed-ID: 25225612  |  Reference-DOI: 10.15252/EMBJ.201488517

(-) Compounds

Molecule 1 - EIF5B
    Chains: B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA2
    Expression System Vector Type: PLASMID
    Fragment: G DOMAIN AND DOMAIN II
    Organism Scientific: CHAETOMIUM THERMOPHILUM
    Organism Taxid: 209285

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x):  B
Biological Unit 2 (1x): A 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL
2GSP2Ligand/Ion5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
4NA2Ligand/IonSODIUM ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2GSP1Ligand/Ion5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2GSP1Ligand/Ion5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4NA-1Ligand/IonSODIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL B:532 , ASP B:533 , THR B:534 , GLY B:535 , LYS B:536 , THR B:537 , LYS B:538 , GLN B:549 , GLY B:555 , ILE B:556 , THR B:557 , GLY B:597 , ASN B:648 , LYS B:649 , ASP B:651 , ARG B:652 , SER B:716 , ALA B:717 , HIS B:718 , MG B:902 , NA B:903 , HOH B:1074 , HOH B:1075 , HOH B:1126 , HOH B:1159 , HOH B:1162 , HOH B:1224binding site for residue GSP B 901
02AC2SOFTWARETHR B:537 , THR B:557 , GSP B:901 , HOH B:1074 , HOH B:1075binding site for residue MG B 902
03AC3SOFTWAREASP B:533 , GLY B:555 , GSP B:901binding site for residue NA B 903
04AC4SOFTWAREARG B:522 , LEU B:611 , ASN B:613 , SER B:770 , ASN B:771 , HOH B:1206 , HOH B:1294binding site for residue GOL B 904
05AC5SOFTWAREARG B:639 , LYS B:640 , PRO B:642 , ARG B:737 , MET B:738 , ALA B:739 , HOH B:1107 , HOH B:1244binding site for residue GOL B 905
06AC6SOFTWAREHIS B:814 , GLU B:816 , VAL B:817 , HOH B:1110 , HOH B:1153binding site for residue GOL B 906
07AC7SOFTWARELEU B:748 , GLY B:772 , ILE B:773 , ARG B:775 , HOH B:1140 , HOH B:1155binding site for residue GOL B 907
08AC8SOFTWAREVAL A:532 , ASP A:533 , THR A:534 , GLY A:535 , LYS A:536 , THR A:537 , LYS A:538 , GLN A:549 , GLY A:555 , ILE A:556 , THR A:557 , GLY A:597 , ASN A:648 , LYS A:649 , ASP A:651 , SER A:716 , ALA A:717 , HIS A:718 , MG A:902 , NA A:903 , HOH A:1057 , HOH A:1058 , HOH A:1100 , HOH A:1159 , HOH A:1170 , HOH A:1235binding site for residue GSP A 901
09AC9SOFTWARETHR A:537 , THR A:557 , GSP A:901 , HOH A:1057 , HOH A:1058binding site for residue MG A 902
10AD1SOFTWAREASP A:533 , GLY A:555 , GSP A:901binding site for residue NA A 903
11AD2SOFTWARELYS A:542 , ILE A:543 , GLN A:545 , LYS A:573 , HOH A:1064 , HOH A:1103 , HOH A:1193 , HOH B:1097binding site for residue GOL A 904
12AD3SOFTWAREARG A:779 , VAL A:842 , GLY A:843 , PRO A:844 , GLU A:848 , HOH A:1005 , HOH A:1024 , HOH A:1025binding site for residue GOL A 905
13AD4SOFTWAREARG A:779 , LYS A:790 , THR A:791 , PRO A:828 , HOH A:1011 , HOH A:1123 , HOH A:1284binding site for residue GOL A 906

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:527 -A:612
2B:527 -B:612

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala B:819 -Ala B:820
2Ala A:819 -Ala A:820

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TMV)

(-) 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:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhhhh.hhhhhhhhhh....eeeeeehhhhhhhhhhhh..........eeeeee...hhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhhh..eeeeeehhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eee.hhh......eeeee.......hhhhhhhhhhhhhhhh.hhhhhh....eeeeeeeeee...eeeeeeeeee.eee...eeeeee..eeeeee..eeee.............ee..eee..eeeeee............eee.....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tmv A 518 KDNLRSPICCILGHVDTGKTKLLDKIRQTNVQEGEAGGITQQIGATYFPVEAIKQKTAVVNKDGKFEFKVPGLLIIDTPGHESFSNLRSRGSSLCNIAILVVDIMHGLEPQTIESLRLLRERKTPFVVALNKIDRLYGWKKIENNGFRESFALQNKAVQNEFRNRLDQVKLQFAEQGFNSELFYENKNFARYVSLVPTSAHTGEGIPDMLKLIVQLCQERMASSLMYLSELQATVLEVKAIEGFGVTIDVILSNGILREGDRIVLCGLEGPIKTNIRALLTPAPMRELRIKGQYIHHKEVKAAQGVKISAPGLEGAIAGSRLLVVGPDDDEEELEEEVE 856
                                   527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847         


Chain B from PDB  Type:PROTEIN  Length:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee....hhhhhhhhhhh.hhhhhhhhhh....eeeeeehhhhhhhhhhhh..........eeeeee...hhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhh...eeeeeehhhhh.........hhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eee.hhh......eeeee.......hhhhhhhhhhhhhhhh.hhhhhh....eeeeeeeeee...eeeeeeeeee.eee...eeee......eeee..eeeee...........eee..eee..eeeeee...........eeee.....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tmv B 514 GHMNKDNLRSPICCILGHVDTGKTKLLDKIRQTNVQEGEAGGITQQIGATYFPVEAIKQKTAVVNKDGKFEFKVPGLLIIDTPGHESFSNLRSRGSSLCNIAILVVDIMHGLEPQTIESLRLLRERKTPFVVALNKIDRLYGWKKIENNGFRESFALQNKAVQNEFRNRLDQVKLQFAEQGFNSELFYENKNFARYVSLVPTSAHTGEGIPDMLKLIVQLCQERMASSLMYLSELQATVLEVKAIEGFGVTIDVILSNGILREGDRIVLCGLEGPIKTNIRALLTPAPMRELRIKGQYIHHKEVKAAQGVKISAPGLEGAIAGSRLLVVGPDDDEEELEEEVESD 858
                                   523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853
   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 4TMV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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        IF2P_CHATD | G0S8G9: 4n3g 4n3n 4ncl 4ncn 4tmt 4tmw 4tmx 4tmz 4tn1

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