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- PDB-2kbw: Solution Structure of human Mcl-1 complexed with human Bid_BH3 peptide -

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Basic information

Entry
Database: PDB / ID: 2kbw
TitleSolution Structure of human Mcl-1 complexed with human Bid_BH3 peptide
Components
  • BH3-interacting domain death agonist
  • Induced myeloid leukemia cell differentiation protein Mcl-1
KeywordsAPOPTOSIS / Mcl-1 / Bid_BH3 / complex / Alternative splicing / Cytoplasm / Developmental protein / Differentiation / Membrane / Mitochondrion / Nucleus / Phosphoprotein / Polymorphism / Transmembrane / Ubl conjugation
Function / homology
Function and homology information


cysteine-type endopeptidase regulator activity involved in apoptotic process / mitochondrial outer membrane permeabilization / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of fibroblast apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / cell fate determination / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage ...cysteine-type endopeptidase regulator activity involved in apoptotic process / mitochondrial outer membrane permeabilization / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of fibroblast apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / cell fate determination / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / regulation of epithelial cell proliferation / cellular homeostasis / death receptor binding / establishment of protein localization to membrane / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of mitochondrial membrane potential / mitochondrial fusion / Bcl-2 family protein complex / protein targeting to mitochondrion / mitochondrial ATP synthesis coupled electron transport / apoptotic mitochondrial changes / hepatocyte apoptotic process / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / regulation of G1/S transition of mitotic cell cycle / BH3 domain binding / regulation of T cell proliferation / negative regulation of anoikis / extrinsic apoptotic signaling pathway via death domain receptors / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / signal transduction in response to DNA damage / Activation of BAD and translocation to mitochondria / extrinsic apoptotic signaling pathway in absence of ligand / supramolecular fiber organization / positive regulation of intrinsic apoptotic signaling pathway / response to cytokine / negative regulation of autophagy / release of cytochrome c from mitochondria / positive regulation of protein-containing complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / positive regulation of neuron apoptotic process / channel activity / protein-containing complex assembly / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / ubiquitin protein ligase binding / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
BH3-interacting domain death agonist / BH3 interacting domain (BID) / Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site ...BH3-interacting domain death agonist / BH3 interacting domain (BID) / Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BH3-interacting domain death agonist / Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsLiu, Q. / Moldoveanu, T. / Sprules, T. / Matta-Camacho, E. / Mansur-Azzam, N. / Gehring, K.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Apoptotic regulation by MCL-1 through heterodimerization.
Authors: Liu, Q. / Moldoveanu, T. / Sprules, T. / Matta-Camacho, E. / Mansur-Azzam, N. / Gehring, K.
History
DepositionDec 9, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: BH3-interacting domain death agonist


Theoretical massNumber of molelcules
Total (without water)22,4492
Polymers22,4492
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Induced myeloid leukemia cell differentiation protein Mcl-1 / Bcl-2-related protein EAT/mcl1 / mcl1/EAT


Mass: 18716.164 Da / Num. of mol.: 1 / Fragment: residues 167-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCL1, Myeloid Cell Leukemia 1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q07820
#2: Protein/peptide BH3-interacting domain death agonist / p22 BID / BID / BH3-interacting domain death agonist p15 / p15 BID / BH3-interacting domain death ...p22 BID / BID / BH3-interacting domain death agonist p15 / p15 BID / BH3-interacting domain death agonist p13 / p13 BID / BH3-interacting domain death agonist p11 / p11 BID


Mass: 3733.175 Da / Num. of mol.: 1 / Fragment: BH3 motif, residues 76-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BID / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P55957

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
1322D 1H-15N HSQC
1422D 1H-15N HSQC
1522D 1H-15N HSQC
1633D CBCA(CO)NH
1733D HNCO
1833D HNCA
1933D HN(CA)CB
11033D 1H-15N NOESY
11132D 1H-15N HSQC
11253D CBCA(CO)NH
11353D HN(CA)CB
11453D HNCO
11553D HNCA
11653D 1H-15N NOESY
11752D 1H-15N HSQC
11842D 1H-13C HSQC
11943D (H)CCH-COSY
12043D 1H-13C NOESY
12162D 1H-13C HSQC
12263D (H)CCH-COSY
12363D 1H-13C NOESY
12443D CCH-TOCSY
12543D 1H-15N NOESY N15C13 filtered
12643D 1H-13C NOESY N15C13 filtered
12763D 1H-15N NOESY N15C13 filtered
12863D 1H-13C NOESY N15C13 filtered
12913D 1H-15N heteronuclear NOESY
13023D 1H-15N heteronuclear NOESY
1311IPAP-HSQC
1327IPAP-HSQC
1332IPAP-HSQC
1348IPAP-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-95% 15N] Mcl-1-1, 0.5 mM Bid_BH3-2, 20 mM HEPES-3, 1 mM DTT-4, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM Mcl-1-5, 0.5 mM [U-95% 15N] Bid_BH3-6, 20 mM HEPES-7, 1 mM DTT-8, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-95% 13C; U-95% 15N] Mcl-1-9, 0.5 mM Bid_BH3-10, 20 mM HEPES-11, 1 mM DTT-12, 90% H2O/10% D2O90% H2O/10% D2O
40.5 mM [U-95% 13C; U-95% 15N] Mcl-1-13, 0.5 mM Bid_BH3-14, 20 mM HEPES-15, 1 mM DTT-16, 100 % [U-100% 2H] D2O-17, 100% D2O100% D2O
50.5 mM Mcl-1-18, 0.5 mM [U-95% 13C; U-95% 15N] Bid_BH3-19, 20 mM HEPES-20, 1 mM DTT-21, 90% H2O/10% D2O90% H2O/10% D2O
60.5 mM Mcl-1-22, 0.5 mM [U-95% 13C; U-95% 15N] Bid_BH3-23, 20 mM HEPES-24, 1 mM DTT-25, 100 % [U-100% 2H] D2O-26, 100% D2O100% D2O
70.4 mM [U-95% 15N] Mcl-1-27, 0.4 mM Bid_BH3-28, 20 mM HEPES-29, 1 mM DTT-30, 6 mg/mL Pf1 phage-31, 90% H2O/10% D2O90% H2O/10% D2O
80.4 mM Mcl-1-32, 0.4 mM [U-95% 15N] Bid_BH3-33, 20 mM HEPES-34, 1 mM DTT-35, 8 mg/mL Pf1 phage-36, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMcl-1-1[U-95% 15N]1
0.5 mMBid_BH3-21
20 mMHEPES-31
1 mMDTT-41
0.5 mMMcl-1-52
0.5 mMBid_BH3-6[U-95% 15N]2
20 mMHEPES-72
1 mMDTT-82
0.5 mMMcl-1-9[U-95% 13C; U-95% 15N]3
0.5 mMBid_BH3-103
20 mMHEPES-113
1 mMDTT-123
0.5 mMMcl-1-13[U-95% 13C; U-95% 15N]4
0.5 mMBid_BH3-144
20 mMHEPES-154
1 mMDTT-164
100 %D2O-17[U-100% 2H]4
0.5 mMMcl-1-185
0.5 mMBid_BH3-19[U-95% 13C; U-95% 15N]5
20 mMHEPES-205
1 mMDTT-215
0.5 mMMcl-1-226
0.5 mMBid_BH3-23[U-95% 13C; U-95% 15N]6
20 mMHEPES-246
1 mMDTT-256
100 %D2O-26[U-100% 2H]6
0.4 mMMcl-1-27[U-95% 15N]7
0.4 mMBid_BH3-287
20 mMHEPES-297
1 mMDTT-307
6 mg/mLPf1 phage-317
0.4 mMMcl-1-328
0.4 mMBid_BH3-33[U-95% 15N]8
20 mMHEPES-348
1 mMDTT-358
8 mg/mLPf1 phage-368
Sample conditionsIonic strength: 20 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Bruker AvanceBrukerAVANCE6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
VnmrJVariancollection
NMRViewJohnson, One Moon Scientificdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2934 / NOE intraresidue total count: 973 / NOE long range total count: 386 / NOE medium range total count: 631 / NOE sequential total count: 747 / Hydrogen bond constraints total count: 190 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 141 / Protein psi angle constraints total count: 141
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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