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(-) Description

Title :  REFINED CRYSTAL STRUCTURE OF THE HUMAN APOPTOSIS INDUCING FACTOR
 
Authors :  M. Martinez-Julvez, B. Herguedas, J. A. Hermoso, P. Ferreira, R. Villa M. Medina
Date :  25 Jun 13  (Deposition) - 17 Sep 14  (Release) - 17 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Apoptosis, Nuclear Chromatinolysis, Dna Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Ferreira, R. Villanueva, M. Martinez-Julvez, B. Herguedas, C. Marcuello, P. Fernandez-Silva, L. Cabon, J. A. Hermoso, A. Lostao, S. A. Susin, M. Medina
Structural Insights Into The Coenzyme Mediated Monomer- Dimer Transition Of The Pro-Apoptotic Apoptosis Inducing Factor.
Biochemistry V. 53 4204 2014
PubMed-ID: 24914854  |  Reference-DOI: 10.1021/BI500343R

(-) Compounds

Molecule 1 - APOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL
    ChainsA
    EC Number1.-.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 121-613
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROGRAMMED CELL DEATH PROTEIN 8

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
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: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:2011 , HOH A:2012 , HOH A:2014 , HOH A:2094 , HOH A:2095 , HOH A:2232 , HOH A:2287BINDING SITE FOR RESIDUE FAD A1449
2AC2SOFTWAREPHE A:310 , ILE A:343 , HIS A:454 , PHE A:482 , HOH A:2227 , HOH A:2228 , HOH A:2231BINDING SITE FOR RESIDUE GOL A1611

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BV6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BV6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (14, 14)

Asymmetric/Biological Unit (14, 14)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_072791V243LAIFM1_HUMANDisease  ---AV243L
02UniProtVAR_076211T260AAIFM1_HUMANDisease (DFNX5)863225432AT260A
03UniProtVAR_067334G308EAIFM1_HUMANDisease (COXPD6)  ---AG308E
04UniProtVAR_076212L344FAIFM1_HUMANUnclassified (DFNX5)184474885AL344F
05UniProtVAR_076213G360RAIFM1_HUMANUnclassified (DFNX5)724160026AG360R
06UniProtVAR_076214R422QAIFM1_HUMANDisease (DFNX5)724160021AR422Q
07UniProtVAR_076215R422WAIFM1_HUMANDisease (DFNX5)724160020AR422W
08UniProtVAR_076216R430CAIFM1_HUMANUnclassified (DFNX5)  ---AR430C
09UniProtVAR_076217R451QAIFM1_HUMANDisease (DFNX5)863225431AR451Q
10UniProtVAR_076218A472VAIFM1_HUMANUnclassified (DFNX5)  ---AA472V
11UniProtVAR_076219P475LAIFM1_HUMANUnclassified (DFNX5)724160022AP475L
12UniProtVAR_069468E493VAIFM1_HUMANDisease (COWCK)281864468AE493V
13UniProtVAR_076220V498MAIFM1_HUMANUnclassified (DFNX5)724160023AV498M
14UniProtVAR_076221I591MAIFM1_HUMANUnclassified (DFNX5)  ---AI591M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BV6)

(-) Exons   (13, 13)

Asymmetric/Biological Unit (13, 13)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002872951aENSE00002159904X:129299861-129299525337AIFM1_HUMAN1-36360--
1.2ENST000002872952ENSE00001027915X:129290577-129290435143AIFM1_HUMAN36-83480--
1.4ENST000002872954ENSE00001027918X:129283543-129283444100AIFM1_HUMAN84-117340--
1.5bENST000002872955bENSE00001027925X:129281851-129281727125AIFM1_HUMAN117-158421A:127-15832
1.6bENST000002872956bENSE00001027914X:129281598-129281468131AIFM1_HUMAN159-202441A:159-20244
1.7ENST000002872957ENSE00001027922X:129279544-12927945491AIFM1_HUMAN202-232311A:202-23231
1.8ENST000002872958ENSE00001027917X:129274592-12927450885AIFM1_HUMAN233-261291A:233-26129
1.9ENST000002872959ENSE00001027923X:129273846-12927377077AIFM1_HUMAN261-286261A:261-28626
1.10ENST0000028729510ENSE00001027927X:129272676-129272568109AIFM1_HUMAN287-323371A:287-32337
1.11cENST0000028729511cENSE00001670915X:129271160-129271053108AIFM1_HUMAN323-359371A:323-35937
1.12bENST0000028729512bENSE00001691451X:129270706-12927061889AIFM1_HUMAN359-388301A:359-38830
1.13ENST0000028729513ENSE00001768965X:129270160-129270020141AIFM1_HUMAN389-435471A:389-43547
1.14ENST0000028729514ENSE00001641738X:129267430-129267288143AIFM1_HUMAN436-483481A:436-48348
1.15ENST0000028729515ENSE00001692207X:129265774-129265650125AIFM1_HUMAN483-525431A:483-52543
1.16ENST0000028729516ENSE00001635661X:129264141-129263945197AIFM1_HUMAN525-590661A:525-590 (gaps)66
1.17aENST0000028729517aENSE00002157720X:129263603-129263345259AIFM1_HUMAN591-613231A:591-61020

(-) 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:471
 aligned with AIFM1_HUMAN | O95831 from UniProtKB/Swiss-Prot  Length:613

    Alignment length:484
                                   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       526       536       546       556       566       576       586       596       606    
          AIFM1_HUMAN   127 KAPSHVPFLLIGGGTAAFAAARSIRARDPGARVLIVSEDPELPYMRPPLSKELWFSDDPNVTKTLRFKQWNGKERSIYFQPPSFYVSAQDLPHIENGGVAVLTGKKVVQLDVRDNMVKLNDGSQITYEKCLIATGGTPRSLSAIDRAGAEVKSRTTLFRKIGDFRSLEKISREVKSITIIGGGFLGSELACALGRKARALGTEVIQLFPEKGNMGKILPEYLSNWTMEKVRREGVKVMPNAIVQSVGVSSGKLLIKLKDGRKVETDHIVAAVGLEPNVELAKTGGLEIDSDFGGFRVNAELQARSNIWVAGDAACFYDIKLGRRRVEHHDHAVVSGRLAGENMTGAAKPYWHQSMFWSDLGPDVGYEAIGLVDSSLPTVGVFAKATAQDNPKSATEQSGTGIRSESETESEASEITIPPSTPAVPQAPVQGEDYGKGVIFYLRDKVVVGIVLWNIFNRMPIARKIIKDGEQHEDLNEVAKLFNI 610
               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..hhhhhh.hhhhhhheee..hhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhhhh..eee....eeeeeee..eeeeee....eeee.eeee...eee...hhhhhh.........ee.....eee..eee....eeeee...eee...hhhhhhhhhhhhhhhhh..........eeeeeee..eeeeeee.......eeeeee......hhhhhhhhhh..hhhhhh............-------------...eeeeeeee..eeeeeeee....hhhhhhhhhhhh....hhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------------------------------------------------------------------------L----------------A-----------------------------------------------E-----------------------------------F---------------R-------------------------------------------------------------Q-------C--------------------Q--------------------V--L-----------------V----M--------------------------------------------------------------------------------------------M------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5b  PDB: A:127-158       Exon 1.6b  PDB: A:159-202 UniProt: 159-202  ------------------------------Exon 1.8  PDB: A:233-261     -------------------------Exon 1.10  PDB: A:287-323            -----------------------------------Exon 1.12b  PDB: A:359-388    Exon 1.13  PDB: A:389-435 UniProt: 389-435     Exon 1.14  PDB: A:436-483 UniProt: 436-483      -----------------------------------------Exon 1.16  PDB: A:525-590 (gaps) UniProt: 525-590                 Exon 1.17a           Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------Exon 1.7  PDB: A:202-232       ----------------------------Exon 1.9  PDB: A:261-286  ------------------------------------Exon 1.11c  PDB: A:323-359           ---------------------------------------------------------------------------------------------------------------------------Exon 1.15  PDB: A:483-525 UniProt: 483-525 ------------------------------------------------------------------------------------- Transcript 1 (2)
                 4bv6 A 127 KAPSHVPFLLIGGGTAAFAAARSIRARDPGARVLIVSEDPELPYMRPPLSKELWFSDDPNVTKTLRFKQWNGKERSIYFQPPSFYVSAQDLPHIENGGVAVLTGKKVVQLDVRDNMVKLNDGSQITYEKCLIATGGTPRSLSAIDRAGAEVKSRTTLFRKIGDFRSLEKISREVKSITIIGGGFLGSELACALGRKARALGTEVIQLFPEKGNMGKILPEYLSNWTMEKVRREGVKVMPNAIVQSVGVSSGKLLIKLKDGRKVETDHIVAAVGLEPNVELAKTGGLEIDSDFGGFRVNAELQARSNIWVAGDAACFYDIKLGRRRVEHHDHAVVSGRLAGENMTGAAKPYWHQSMFWSDLGPDVGYEAIGLVDSSLPTVGVFAKATAQDNPKSATEQSGTGIRSESETESEASEITIPP-------------DYGKGVIFYLRDKVVVGIVLWNIFNRMPIARKIIKDGEQHEDLNEVAKLFNI 610
                                   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       526       536        |-         -  |    566       576       586       596       606    
                                                                                                                                                                                                                                                                                                                                                                                                                                                            545           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 4BV6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BV6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BV6)

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AIFM1_HUMAN | O95831)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0071949    FAD binding    Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0016174    NAD(P)H oxidase activity    Catalysis of the reaction: NAD(P)H + H+ + O2 = NAD(P)+ + hydrogen peroxide.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016651    oxidoreductase activity, acting on NAD(P)H    Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
biological process
    GO:0006308    DNA catabolic process    The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:1904045    cellular response to aldosterone    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an aldosterone stimulus.
    GO:0071392    cellular response to estradiol stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0070301    cellular response to hydrogen peroxide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
    GO:0071732    cellular response to nitric oxide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus.
    GO:0090650    cellular response to oxygen-glucose deprivation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of the deprivation of oxygen and glucose.
    GO:0030261    chromosome condensation    The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
    GO:0070059    intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to a stimulus indicating endoplasmic reticulum (ER) stress, and ends when the execution phase of apoptosis is triggered. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
    GO:0032981    mitochondrial respiratory chain complex I assembly    The aggregation, arrangement and bonding together of a set of components to form mitochondrial respiratory chain complex I.
    GO:0051402    neuron apoptotic process    Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
    GO:0030182    neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0010942    positive regulation of cell death    Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:0043525    positive regulation of neuron apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
    GO:1902510    regulation of apoptotic DNA fragmentation    Any process that modulates the frequency, rate or extent of apoptotic DNA fragmentation.
    GO:1902065    response to L-glutamate    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an L-glutamate stimulus.
    GO:0002931    response to ischemia    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a inadequate blood supply.
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AIFM1_HUMAN | O958311m6i 4bur 4fdc 4lii 5fmh 5fs6 5fs7 5fs8 5fs9 5kvh 5kvi

(-) Related Entries Specified in the PDB File

1m6i CRYSTAL STRUCTURE OF APOPTOSIS INDUCING FACTOR (AIF)
4bur CRYSTAL STRUCTURE OF THE REDUCED HUMAN APOPTOSIS INDUCING FACTOR COMPLEXED WITH NAD