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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN APOPTOSIS-INDUCING FACTOR WITH W196A MUTATION
 
Authors :  C. A. Brosey, J. Nix, T. Ellenberger, J. A. Tainer
Date :  14 Jul 16  (Deposition) - 16 Nov 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Flavoprotein, Mitochondria, Cell Death (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. A. Brosey, C. Ho, W. Z. Long, S. Singh, K. Burnett, G. L. Hura, J. C. Nix G. R. Bowman, T. Ellenberger, J. A. Tainer
Defining Nadh-Driven Allostery Regulating Apoptosis-Inducin Factor.
Structure V. 24 2067 2016
PubMed-ID: 27818101  |  Reference-DOI: 10.1016/J.STR.2016.09.012

(-) Compounds

Molecule 1 - APOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL
    Chains: A, B
    EC Number: 1.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24B
    Expression System Strain: ROSETTA2 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AIFM1, AIF, PDCD8
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: EXPRESSED AS AIF(78-613). RESIDUES L614-Q619 REMAIN FROM PRESCISSION PROTEASE CLEAVAGE.
    Synonym: PROGRAMMED CELL DEATH PROTEIN 8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
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:232 , VAL A:233 , ALA A:259 , THR A:260 , GLY A:261 , PHE A:284 , ARG A:285 , 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:818 , HOH A:849 , HOH A:852 , HOH A:854 , HOH A:867 , HOH A:882 , HOH A:885 , HOH A:892 , HOH A:904 , HOH A:913binding site for residue FAD A 701
2AC2SOFTWARETYR A:347 , TRP A:351 , PHE A:508 , TYR A:560binding site for residue GOL A 702
3AC3SOFTWAREGLY B:138 , GLY B:139 , GLY B:140 , THR B:141 , ALA B:142 , VAL B:162 , GLU B:164 , 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 , PHE B:284 , ARG B:285 , LEU B:311 , GLU B:314 , 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:805 , HOH B:818 , HOH B:821 , HOH B:822 , HOH B:830 , HOH B:836 , HOH B:841 , HOH B:871 , HOH B:957binding site for residue FAD B 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KVH)

(-) Sequences/Alignments

Asymmetric/Biological 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:438
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeee..hhhhhhhhhhhhhhh...eeeeee........hhhhhh........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..hhhhhhhhhhhhhhhh...........eeeee.....eeeeee.......eeeeee...eeeeeeee..eeeeeeee....hhhhhhhhhhhh....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5kvh A 126 DKAPSHVPFLLIGGGTAAFAAARSIRARDPGARVLIVSEDPELPYMRPPLSKELWFSDDPNVTKTLRFKQANGKERSIYFQPPSFYVSAQDLPHIENGGVAVLTGKKVVQLDVRDNMVKLNDGSQITYEKCLIATGGTPRSLSAIDRAGAEVKSRTTLFRKIGDFRSLEKISREVKSITIIGGGFLGSELACALGRKARALGTEVIQLFPEKGNMGKILPEYLSNWTMEKVRREGVKVMPNAIVQSVGVSSGKLLIKLKDGRKVETDHIVAAVGLEPNVELAKTGGLEIDSDFGGFRVNAELQARSNIWVAGDAACFYDIKLGRRRVEHHDHAVVSGRLAGENMTGAAKPYWHQSMFWSDLGPDVGYEAIGLVDSSLPTVGVFAKYGKGVIFYLRDKVVVGIVLWNIFNRMPIARKIIKDGEQHEDLNEVAKLFNIHE 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    || 564       574       584       594       604        
                                                                                                                                                                                                                                                                                                                                                                                                                          510|                                                    
                                                                                                                                                                                                                                                                                                                                                                                                                           560                                                    


Chain B from PDB  Type:PROTEIN  Length:438
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               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..hhhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhhhh..eee....eeeeeee..eeeeee....eeee.eeee...eee...hhhhhh.........ee.....eee..eee....eeeee...eee...hhhhhhhhhhhhhhhh...........eeeee.....eeeeee.......eeeeee...eeeeeeee..eeeeeeee....hhhhhhhhhhhh....hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5kvh B 126 DKAPSHVPFLLIGGGTAAFAAARSIRARDPGARVLIVSEDPELPYMRPPLSKELWFSDDPNVTKTLRFKQANGKERSIYFQPPSFYVSAQDLPHIENGGVAVLTGKKVVQLDVRDNMVKLNDGSQITYEKCLIATGGTPRSLSAIDRAGAEVKSRTTLFRKIGDFRSLEKISREVKSITIIGGGFLGSELACALGRKARALGTEVIQLFPEKGNMGKILPEYLSNWTMEKVRREGVKVMPNAIVQSVGVSSGKLLIKLKDGRKVETDHIVAAVGLEPNVELAKTGGLEIDSDFGGFRVNAELQARSNIWVAGDAACFYDIKLGRRRVEHHDHAVVSGRLAGENMTGAAKPYWHQSMFWSDLGPDVGYEAIGLVDSSLPTVGVFAKYGKGVIFYLRDKVVVGIVLWNIFNRMPIARKIIKDGEQHEDLNEVAKLFNIHE 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    || 564       574       584       594       604        
                                                                                                                                                                                                                                                                                                                                                                                                                          510|                                                    
                                                                                                                                                                                                                                                                                                                                                                                                                           560
   Legend:   → Mismatch (orange background)
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  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 5KVH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (39, 39)

Asymmetric/Biological 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 | O95831: 1m6i 4bur 4bv6 4fdc 4lii 5fmh 5fs6 5fs7 5fs8 5fs9 5kvi

(-) Related Entries Specified in the PDB File

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