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(-) Description

Title :  CRYSTAL STRUCTURE OF THE G338E MUTANT OF HUMAN APOPTOSIS INDUCING FACTOR
 
Authors :  I. Sevrioukova
Date :  31 Dec 15  (Deposition) - 11 May 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Mitochondria, Flavoprotein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. F. Sevrioukova
Structure/Function Relations In Aifm1 Variants Associated With Neurodegenerative Disorders.
J. Mol. Biol. V. 428 3650 2016
PubMed-ID: 27178839  |  Reference-DOI: 10.1016/J.JMB.2016.05.004

(-) Compounds

Molecule 1 - APOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL
    ChainsA, B
    EC Number1.1.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPKK233-3
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN, RESIDUES 104-613
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsRESIDUES 104-125,531-558 AND 613-617 IN CHAIN A AND 104-125 AND 531-557 IN CHAIN B ARE DISORDERED. EACH CHAIN HAS 4 ADDITIONAL C-TERMINAL RESIDUES L614-V615- P616-R617, PART OF THE THROMBIN CLEAVAGE SITE
    SynonymPROGRAMMED CELL DEATH PROTEIN 8, APOPTOSIS INDUCING FACTOR

 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
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL2Ligand/IonGLYCEROL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:138 , GLY A:139 , GLY A:140 , THR A:141 , ALA A:142 , VAL A:162 , GLU A:164 , ARG A:172 , PRO A:173 , SER A:176 , LYS A:177 , LYS A:231 , LYS A:232 , VAL A:233 , ALA A:259 , THR A:260 , GLY A:261 , ARG A:285 , GLY A:437 , ASP A:438 , GLU A:453 , HIS A:454 , HIS A:455 , ALA A:458 , PHE A:482 , TRP A:483 , HOH A:2006 , HOH A:2009 , HOH A:2010 , HOH A:2012 , HOH A:2029 , HOH A:2089 , HOH A:2090 , HOH A:2133 , HOH A:2214 , HOH A:2274BINDING SITE FOR RESIDUE FAD A1000
2AC2SOFTWAREMET A:481 , SER A:530 , MET A:585 , ARG A:589 , HIS B:611BINDING SITE FOR RESIDUE GOL A1002
3AC3SOFTWAREGLY B:138 , GLY B:139 , GLY B:140 , THR B:141 , ALA B:142 , VAL B:162 , GLU B:164 , ASP B:165 , ARG B:172 , PRO B:173 , SER B:176 , LYS B:177 , LYS B:231 , VAL B:233 , ALA B:259 , THR B:260 , GLY B:261 , PHE B:284 , ARG B:285 , GLY B:437 , ASP B:438 , GLU B:453 , HIS B:454 , HIS B:455 , ALA B:458 , PHE B:482 , TRP B:483 , HOH B:2006 , HOH B:2007 , HOH B:2009 , HOH B:2072 , HOH B:2073 , HOH B:2117 , HOH B:2167 , HOH B:2207BINDING SITE FOR RESIDUE FAD B1000
4AC4SOFTWAREMET B:481 , ARG B:529 , SER B:530 , MET B:585 , PRO B:586 , ARG B:589 , HOH B:2275 , HOH B:2276 , HOH B:2277BINDING SITE FOR RESIDUE GOL B1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FS9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:524 -Gly A:525

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FS9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FS9)

(-) Exons   (0, 0)

(no "Exon" information available for 5FS9)

(-) 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:459
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee..hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhh....hhhhhheee.....eee....hhhhh............eeeee....eeeee....eeee....eeeeeeeee...eee..hhhhhhhhhhhhhheee..hhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhhhh..eee....eeeeeee..eeeeee....eeee.eeee...eee...hhhhhh.........ee.....eee..eee....eeeee...eeee..hhhhhhhhhhhhhhhhh..........eeeee.....eeeeee.......eeeeee......hhhhhhhhhh........eeeeeeee..eeeeeeee....hhhhhhhhhhhh....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fs9 A 126 DKAPSHVPFLLIGGGTAAFAAARSIRARDPGARVLIVSEDPELPYMRPPLSKELWFSDDPNVTKTLRFKQWNGKERSIYFQPPSFYVSAQDLPHIENGGVAVLTGKKVVQLDVRDNMVKLNDGSQITYEKCLIATGGTPRSLSAIDRAGAEVKSRTTLFRKIGDFRSLEKISREVKSITIIGGGFLGSELACALGRKARALGTEVIQLFPEKENMGKILPEYLSNWTMEKVRREGVKVMPNAIVQSVGVSSGKLLIKLKDGRKVETDHIVAAVGLEPNVELAKTGGLEIDSDFGGFRVNAELQARSNIWVAGDAACFYDIKLGRRRVEHHDHAVVSGRLAGENMTGAAKPYWHQSMFWSDLGPDVGYEAIGLVDSSLPTVGVFAKATAQDNPKSATEQSGTGIRSDYGKGVIFYLRDKVVVGIVLWNIFNRMPIARKIIKDGEQHEDLNEVAKLFNIHE 612
                                   135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525    || 563       573       583       593       603         
                                                                                                                                                                                                                                                                                                                                                                                                                                              530|                                                     
                                                                                                                                                                                                                                                                                                                                                                                                                                               559                                                     

Chain B from PDB  Type:PROTEIN  Length:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee..hhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhh....hhhhhheee.....eee....hhhhh............eeeeee...eeeee....eeee....eeeeeeeee...eee..hhhhhhhhhhhhhheee..hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhhhh..eee....eeeeeee..eeeeee....eeee.eeee...eee...hhhhhh.........ee.....eee..eee....eeeee...eeee..hhhhhhhhhhhhhhhhh..........eeeee.....eeeeee.......eeeeee......hhhhhhhhhh.........eeeeeeee..eeeeeeee....hhhhhhhhhhhh....hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fs9 B 126 DKAPSHVPFLLIGGGTAAFAAARSIRARDPGARVLIVSEDPELPYMRPPLSKELWFSDDPNVTKTLRFKQWNGKERSIYFQPPSFYVSAQDLPHIENGGVAVLTGKKVVQLDVRDNMVKLNDGSQITYEKCLIATGGTPRSLSAIDRAGAEVKSRTTLFRKIGDFRSLEKISREVKSITIIGGGFLGSELACALGRKARALGTEVIQLFPEKENMGKILPEYLSNWTMEKVRREGVKVMPNAIVQSVGVSSGKLLIKLKDGRKVETDHIVAAVGLEPNVELAKTGGLEIDSDFGGFRVNAELQARSNIWVAGDAACFYDIKLGRRRVEHHDHAVVSGRLAGENMTGAAKPYWHQSMFWSDLGPDVGYEAIGLVDSSLPTVGVFAKATAQDNPKSATEQSGTGIRSEDYGKGVIFYLRDKVVVGIVLWNIFNRMPIARKIIKDGEQHEDLNEVAKLFNIHEDLVPR 617
                                   135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525    || 562       572       582       592       602       612     
                                                                                                                                                                                                                                                                                                                                                                                                                                              530|                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                               558                                                           

   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 5FS9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FS9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FS9)

(-) Gene Ontology  (39, 39)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        AIFM1_HUMAN | O958311m6i 4bur 4bv6 4fdc 4lii 5fmh 5fs6 5fs7 5fs8 5kvh 5kvi

(-) Related Entries Specified in the PDB File

5fs6 CRYSTAL STRUCTURE OF THE V243L MUTANT OF HUMAN APOPTOSIS INDUCING FACTOR
5fs7 CRYSTAL STRUCTURE OF THE G262S MUTANT OF HUMAN APOPTOSIS INDUCING FACTOR
5fs8 CRYSTAL STRUCTURE OF THE G308E MUTANT OF HUMAN APOPTOSIS INDUCING FACTOR