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(-) Description

Title :  CRYSTAL STRUCTURE OF THE V243L MUTANT OF HUMAN APOPTOSIS INDUCING FACTOR
 
Authors :  I. Sevrioukova
Date :  30 Dec 15  (Deposition) - 11 May 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase, Mitochondria, Flavoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. 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
    Chains: A, B
    EC Number: 1.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PKK233-3
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, RESIDUES 103-613
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: RESIDUES 522-558 IN CHAIN A AND 523-558 IN CHAIN B ARE DISORDERED. BOTH CHAINS HAVE ADDITIONAL C-TERMINAL RESIDUES L614-V615-P616-R617, PART OF THE THROMBIN CLEAVAGE SITE. RESIDUES 614-617 ARE DISORDERED IN CHAIN B.
    Synonym: PROGRAMMED 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
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) 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 , ASP A:165 , ARG A:172 , PRO A:173 , SER A:176 , LYS A:177 , LYS A:232 , VAL A:233 , ALA A:259 , THR A:260 , GLY A:261 , PHE A:284 , ARG A:285 , LYS A:286 , LEU A:311 , 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:2008 , HOH A:2009 , HOH A:2013 , HOH A:2015 , HOH A:2137 , HOH A:2138 , HOH A:2214 , HOH A:2215 , HOH A:2299 , HOH A:2362BINDING SITE FOR RESIDUE FAD A1000
2AC2SOFTWAREGLY 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 , LYS B:232 , VAL B:233 , ALA B:259 , THR B:260 , GLY B:261 , ARG B:285 , LYS B:286 , 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:2009 , HOH B:2012 , HOH B:2013 , HOH B:2014 , HOH B:2044 , HOH B:2145 , HOH B:2146 , HOH B:2184 , HOH B:2291 , HOH B:2342 , TRS B:7000BINDING SITE FOR RESIDUE FAD B1000
3AC3SOFTWAREGLU B:164 , LYS B:232 , THR B:263 , ASN B:403 , GLU B:405 , FAD B:1000 , HOH B:2149 , HOH B:2286 , HOH B:2445BINDING SITE FOR RESIDUE TRS B7000
4AC4SOFTWARETHR B:328 , GLU B:329 , VAL B:330 , GLY B:360 , THR B:470 , HOH B:2025 , HOH B:2236 , HOH B:2446BINDING SITE FOR RESIDUE TRS B7001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FS6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FS6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FS6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FS6)

(-) Exons   (0, 0)

(no "Exon" information available for 5FS6)

(-) 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:454
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee..hhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhh...hhhhhheee.....eee....hhhhh............eeeeee...eeeeehhh.eeee....eeeeeeeee...eee..hhhhhhhhhhhhhhee...hhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhhhh..eee....eeeeeee..eeeeee....eeee.eeee...eee...hhhhhh.........ee.....eee..eee....eeeee...eeee..hhhhhhhhhhhhhhhh...........eeeee.....eeeeee.......eeeeee...............eeeeeeee..eeeeeeee....hhhhhhhhhhhh....hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fs6 A 127 KAPSHVPFLLIGGGTAAFAAARSIRARDPGARVLIVSEDPELPYMRPPLSKELWFSDDPNVTKTLRFKQWNGKERSIYFQPPSFYVSAQDLPHIENGGVAVLTGKKVVQLDVRDNMLKLNDGSQITYEKCLIATGGTPRSLSAIDRAGAEVKSRTTLFRKIGDFRSLEKISREVKSITIIGGGFLGSELACALGRKARALGTEVIQLFPEKGNMGKILPEYLSNWTMEKVRREGVKVMPNAIVQSVGVSSGKLLIKLKDGRKVETDHIVAAVGLEPNVELAKTGGLEIDSDFGGFRVNAELQARSNIWVAGDAACFYDIKLGRRRVEHHDHAVVSGRLAGENMTGAAKPYWHQSMFWSDLGPDVGYEAIGLVDSSLPTVGVFAKATAQDNPKSATDYGKGVIFYLRDKVVVGIVLWNIFNRMPIARKIIKDGEQHEDLNEVAKLFNIHEDLVPR 617
                                   136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516    || 563       573       583       593       603       613    
                                                                                                                                                                                                                                                                                                                                                                                                                                    521|                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                                     559                                                          


Chain B from PDB  Type:PROTEIN  Length:451
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               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..hhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhhhh..eee....eeeeee....eeeee....eeee.eeee...eee...hhhhhh.........ee.....eee..eee....eeeee...eeee..hhhhhhhhhhhhhhhh...........eeeee.....eeeeee.......eeeeee........hhhhh...eeeeeeee..eeeeeeee....hhhhhhhhhhhh....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fs6 B 126 DKAPSHVPFLLIGGGTAAFAAARSIRARDPGARVLIVSEDPELPYMRPPLSKELWFSDDPNVTKTLRFKQWNGKERSIYFQPPSFYVSAQDLPHIENGGVAVLTGKKVVQLDVRDNMLKLNDGSQITYEKCLIATGGTPRSLSAIDRAGAEVKSRTTLFRKIGDFRSLEKISREVKSITIIGGGFLGSELACALGRKARALGTEVIQLFPEKGNMGKILPEYLSNWTMEKVRREGVKVMPNAIVQSVGVSSGKLLIKLKDGRKVETDHIVAAVGLEPNVELAKTGGLEIDSDFGGFRVNAELQARSNIWVAGDAACFYDIKLGRRRVEHHDHAVVSGRLAGENMTGAAKPYWHQSMFWSDLGPDVGYEAIGLVDSSLPTVGVFAKATAQDNPKSATEDYGKGVIFYLRDKVVVGIVLWNIFNRMPIARKIIKDGEQHEDLNEVAKLFNIHE 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      |561       571       581       591       601       611 
                                                                                                                                                                                                                                                                                                                                                                                                                                      522|                                                     
                                                                                                                                                                                                                                                                                                                                                                                                                                       559
   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 5FS6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FS6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FS6)

(-) Gene Ontology  (39, 39)

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  5fs6
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  AIFM1_HUMAN | O95831
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 Related Entries

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

UniProtKB/Swiss-Prot
        AIFM1_HUMAN | O95831: 1m6i 4bur 4bv6 4fdc 4lii 5fmh 5fs7 5fs8 5fs9 5kvh 5kvi

(-) Related Entries Specified in the PDB File

5fs7 CRYSTAL STRUCTURE OF THE G262S MUTANT OF HUMAN APOPTOSIS INDUCING FACTOR
5fs8 CRYSTAL STRUCTURE OF THE G308E MUTANT OF HUMAN APOPTOSIS INDUCING FACTOR
5fs9 CRYSTAL STRUCTURE OF THE G338E MUTANT OF HUMAN APOPTOSIS INDUCING FACTOR