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(-) Description

Title :  CRYSTAL STRUCTURE OF EUKARYOTIC TRANSLATION INITIATION FACTOR EIF5B (517-970) FROM CHAETOMIUM THERMOPHILUM IN COMPLEX WITH GDP
 
Authors :  B. Kuhle, R. Ficner
Date :  24 Oct 13  (Deposition) - 09 Jul 14  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Translation Initiation, Gtpase, Eif5B/If2, Subunit Joining, Ribosome, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Kuhle, R. Ficner
Eif5B Employs A Novel Domain Release Mechanism To Catalyze Ribosomal Subunit Joining.
Embo J. V. 33 1177 2014
PubMed-ID: 24686316  |  Reference-DOI: 10.1002/EMBJ.201387344

(-) Compounds

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION FACTOR 5B-LIKE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 516-946
    Gene: CTHT_0029840
    Organism Scientific: CHAETOMIUM THERMOPHILUM VAR. THERMOPHILUM
    Organism Taxid: 759272
    Strain: DSM 1495

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:531 , VAL A:532 , ASP A:533 , THR A:534 , GLY A:535 , LYS A:536 , THR A:537 , LYS A:538 , ASN A:648 , LYS A:649 , ASP A:651 , ARG A:652 , SER A:716 , ALA A:717 , HIS A:718 , MG A:1002 , HOH A:1171 , HOH A:1192 , ASP B:845 , HOH B:1199BINDING SITE FOR RESIDUE GDP A 1001
2AC2SOFTWARELYS A:536 , THR A:537 , GDP A:1001 , HOH A:1192BINDING SITE FOR RESIDUE MG A 1002
3AC3SOFTWAREASP B:533 , THR B:534 , GLY B:535 , LYS B:536 , THR B:537 , LYS B:538 , ASN B:648 , LYS B:649 , ASP B:651 , ARG B:652 , SER B:716 , ALA B:717 , HIS B:718 , MG B:1002 , HOH B:1154 , HOH B:1167 , HOH B:1195BINDING SITE FOR RESIDUE GDP B 1001
4AC4SOFTWARETHR B:537 , GDP B:1001 , HOH B:1154 , HOH B:1167BINDING SITE FOR RESIDUE MG B 1002

(-) 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 A:819 -Ala A:820
2Ala B:819 -Ala B:820

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NCL)

(-) 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:428
                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhh......eee..eeeeehhhhhhhhhhhh..........eeeeee...hhhhh.hhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhh...eeeeeehhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eee..........eeeee.......hhhhhhhhhhhhhhhhhh..eeeeeeee...eeeeeeee.eee...eeee......eeee..eeeee.....eeee.eee..eeeeee............eee.....hhhhhhhhhhhhhhhhhh........eeeee.hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ncl A 521 LRSPICCILGHVDTGKTKLLDKIRQTNVGGITQQIGATYFPVEAIKQKTAVVNKDGKFEFKVPGLLIIDTPGHESFSNLRSRGSSLCNIAILVVDIMHGLEPQTIESLRLLRERKTPFVVALNKIDRLYGWKKIENNGFRESFALQNKAVQNEFRNRLDQVKLQFAEQGFNSELFYENKNFARYVSLVPTSAHTGEGIPDMLKLIVQLCQERMAELQATVLEVKAGVTIDVILSNGILREGDRIVLCGLEGPIKTNIRALLTPAPKGQYIHHKEVKAAQGVKISAPGLEGAIAGSRLLVVGPDDDEEELEEEVESDLQSLFSRVEKTGKGVSVQASTLGSLEALLDFLKDCKIPVANVGIGPVYKRDVMQCGIMLEKAPDYAVMLCFDVKVDKEAQQYADENGIKIFTADIIYHLFDQFTKHMQEQLE 970
                                   530       540       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735   ||  752    || 766       776       786       796    || 812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962        
                                                     548|                                                                                                                                                                                      739|       757|                                    801|                                                                                                                                                                  
                                                      554                                                                                                                                                                                       747        762                                     808                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:435
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee....hhhhhhhhhhh....eee..eeeeehhhhhhhhhhhh..........eeeeeeee.hhhhh.hhhhhhhh..eeeeeee.....hhhhhhhhhhhhhh...eeeeeehhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..eeee.........eeeeee.......hhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeee...eeeeeeeeee.eee...eeee......eeee..eeeee....eeee.eee..eeeeee............eee.....hhhhhhhhhhhhhhhhhh........eeeee.hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ncl B 520 NLRSPICCILGHVDTGKTKLLDKIRQTGGITQQIGATYFPVEAIKQKTAVVNKDGKFEFKVPGLLIIDTPGHESFSNLRSRGSSLCNIAILVVDIMHGLEPQTIESLRLLRERKTPFVVALNKIDRLYGWKKIENNGFRESFALQNKAVQNEFRNRLDQVKLQFAEQGFNSELFYENKNFARYVSLVPTSAHTGEGIPDMLKLIVQLCQERMASSLMYLSELQATVLEVKAIEGFGVTIDVILSNGILREGDRIVLCGLEGPIKTNIRALLTPAPGQYIHHKEVKAAQGVKISAPGLEGAIAGSRLLVVGPDDDEEELEEEVESDLQSLFSRVEKTGKGVSVQASTLGSLEALLDFLKDCKIPVANVGIGPVYKRDVMQCGIMLEKAPDYAVMLCFDVKVDKEAQQYADENGIKIFTADIIYHLFDQFTKHMQEQ 968
                                   529       539      |556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796    || 813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963     
                                                    546|                                                                                                                                                                                                                                                    801|                                                                                                                                                               
                                                     554                                                                                                                                                                                                                                                     809
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  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 4NCL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        IF2P_CHATD | G0S8G9: 4n3g 4n3n 4ncn 4tmt 4tmv 4tmw 4tmx 4tmz 4tn1

(-) Related Entries Specified in the PDB File

4ncf 4ncn