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(-) Description

Title :  THE MCL-1 BH3 HELIX IS AN EXCLUSIVE MCL-1 INHIBITOR AND APOPTOSIS SENSITIZER
 
Authors :  M. Stewart, E. Fire, A. E. Keating, L. D. Walensky
Date :  14 Apr 10  (Deposition) - 23 Jun 10  (Release) - 04 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mcl-1, Mcl-1 Sahb D, Staple, Sahb, Bcl-2 Family, Apoptosis, Anti- Apoptotic, Apoptosis-Apoptosis Regulator Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. L. Stewart, E. Fire, A. E. Keating, L. D. Walensky
The Mcl-1 Bh3 Helix Is An Exclusive Mcl-1 Inhibitor And Apoptosis Sensitizer.
Nat. Chem. Biol. V. 6 595 2010
PubMed-ID: 20562877  |  Reference-DOI: 10.1038/NCHEMBIO.391

(-) Compounds

Molecule 1 - INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL- 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentMCL-1, RESIDUES 172-327
    GeneBCL2L3, MCL-1, MCL1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBCL-2-RELATED PROTEIN EAT/MCL1, MCL1/EAT, BCL-2-LIKE PROTEIN 3, BCL2-L-3
 
Molecule 2 - INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL- 1
    ChainsB
    EngineeredYES
    FragmentMCL-1, RESIDUES 208-228
    SynonymBCL-2-RELATED PROTEIN EAT/MCL1, MCL1/EAT, BCL-2-LIKE PROTEIN 3, BCL2-L-3
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MK82Mod. Amino Acid2-METHYL-L-NORLEUCINE

(-) Sites  (0, 0)

(no "Site" information available for 3MK8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MK8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MK8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 4)

Asymmetric/Biological Unit (3, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024022A227VMCL1_HUMANPolymorphism11580946B
A
A23
227
V
2UniProtVAR_024021E173DMCL1_HUMANPolymorphism2737820AE173D
3UniProtVAR_054157M231LMCL1_HUMANPolymorphism140449444AM231L

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

(-) PROSITE Motifs  (4, 6)

Asymmetric/Biological Unit (4, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BH3PS01259 Apoptosis regulator, Bcl-2 family BH3 motif signature.MCL1_HUMAN209-223
 
  2A:209-223
B:5-19
2BCL2_FAMILYPS50062 BCL2-like apoptosis inhibitors family profile.MCL1_HUMAN213-314
 
  2A:213-314
B:9-23
3BH1PS01080 Apoptosis regulator, Bcl-2 family BH1 motif signature.MCL1_HUMAN253-272  1A:253-272
4BH2PS01258 Apoptosis regulator, Bcl-2 family BH2 motif signature.MCL1_HUMAN305-316  1A:305-316

(-) Exons   (3, 4)

Asymmetric/Biological Unit (3, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003690261aENSE00001152267chr1:150552066-150551319748MCL1_HUMAN1-2302302A:172-230 (gaps)
B:5-23
59
19
1.2bENST000003690262bENSE00000959746chr1:150550967-150550720248MCL1_HUMAN230-312831A:230-312
-
83
-
1.3dENST000003690263dENSE00001696123chr1:150549967-1505470322936MCL1_HUMAN313-350381A:313-320
-
8
-

(-) 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:141
 aligned with MCL1_HUMAN | Q07820 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:149
                                   181       191       201       211       221       231       241       251       261       271       281       291       301       311         
           MCL1_HUMAN   172 DELYRQSLEIISRYLREQATGAKDTKPMGRSGATSRKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFH 320
               SCOP domains d3mk8a_ A: automated m        atches                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....--------..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -D---------------------------------------------------------L----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------BH3            -----------------------------BH1  PDB: A:253-272 --------------------------------BH2         ---- PROSITE (1)
                PROSITE (2) -----------------------------------------BCL2_FAMILY  PDB: A:213-314 UniProt: 213-314                                                          ------ PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: A:172-230 (gaps) UniProt: 1-230            ----------------------------------------------------------------------------------1.3d     Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.2b  PDB: A:230-312 UniProt: 230-312                                         -------- Transcript 1 (2)
                 3mk8 A 172 DELYRQSLEIISRYLREQATGA--------SGATSRKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFH 320
                                   181       191 |       -|      211       221       231       241       251       261       271       281       291       301       311         
                                               193      202                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:19
 aligned with MCL1_HUMAN | Q07820 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:19
                                   218         
           MCL1_HUMAN   209 ALETLRRVGDGVQRNHETA 227
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
           Pfam domains (1) ----Bcl-2-3mk8B01   Pfam domains (1)
           Pfam domains (2) ----Bcl-2-3mk8B02   Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------V SAPs(SNPs)
                PROSITE (1) BH3  PDB: B:5-1---- PROSITE (1)
                PROSITE (2) ----BCL2_FAMILY     PROSITE (2)
           Transcript 1 (1) Exon 1.1a           Transcript 1 (1)
           Transcript 1 (2) ------------------- Transcript 1 (2)
                 3mk8 B   5 ALETLRRVGDGVlRNHlTA  23
                                    14  |   |  
                                       17-MK8  
                                           21-MK8

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MK8)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MCL1_HUMAN | Q07820)
molecular function
    GO:0051434    BH3 domain binding    Interacting selectively and non-covalently with the BH3 domain of a protein of the Bcl-2 family. The BH3 domain is a potent death domain and has an important role in protein-protein interactions and in cell death.
    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:0015266    protein channel activity    Enables the energy-independent facilitated diffusion, mediated by passage of proteins through a transmembrane aqueous pore or channel.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0008637    apoptotic mitochondrial changes    The morphological and physiological alterations undergone by mitochondria during apoptosis.
    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:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0001709    cell fate determination    A process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment.
    GO:0019725    cellular homeostasis    Any process involved in the maintenance of an internal steady state at the level of the cell.
    GO:0097192    extrinsic apoptotic signaling pathway in absence of ligand    A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with withdrawal of a ligand from a cell surface receptor, and ends when the execution phase of apoptosis is triggered.
    GO:0008630    intrinsic apoptotic signaling pathway in response to DNA damage    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:2000811    negative regulation of anoikis    Any process that stops, prevents or reduces the frequency, rate or extent of anoikis.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:2001240    negative regulation of extrinsic apoptotic signaling pathway in absence of ligand    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand.
    GO:2001243    negative regulation of intrinsic apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway.
    GO:1903378    positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of oxidative stress-induced neuron intrinsic apoptotic signaling pathway.
    GO:0071806    protein transmembrane transport    The directed movement of a protein across a membrane by means of some agent such as a transporter or pore.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:2001020    regulation of response to DNA damage stimulus    Any process that modulates the frequency, rate or extent of response to DNA damage stimulus.
    GO:0034097    response to cytokine    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 cytokine stimulus.
cellular component
    GO:0097136    Bcl-2 family protein complex    A protein complex that consists of members of the Bcl-2 family of anti- and proapoptotic regulators. Bcl-2 proteins respond to cues from various forms of intracellular stress, such as DNA damage or cytokine deprivation, and interact with opposing family members to determine whether or not the caspase proteolytic cascade should be unleashed.
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer 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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MCL1_HUMAN | Q078202kbw 2mhs 2nl9 2nla 2pqk 3d7v 3io9 3kj0 3kj1 3kj2 3kz0 3pk1 3twu 3wix 3wiy 4bpi 4bpj 4hw2 4hw3 4hw4 4oq5 4oq6 4wgi 4wmr 4wms 4wmt 4wmu 4wmv 4wmw 4wmx 4zbf 4zbi 5c3f 5c6h 5fc4 5fdo 5fdr 5iez 5if4 5jsb 5ku9 5lof 5mes 5mev 5uum 5vkc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3MK8)