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Basic information

Entry
Database: PDB / ID: 8iqm
TitleStructural basis of the specificity and interaction mechanism of Bmf binding to pro-survival proteins
Components
  • Bcl2 modifying factor
  • Induced myeloid leukemia cell differentiation protein Mcl-1
KeywordsAPOPTOSIS / Complex
Function / homology
Function and homology information


positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / anoikis / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / anoikis / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein transmembrane transporter activity / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / response to cytokine / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / Signaling by ALK fusions and activated point mutants / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Bcl-2-modifying factor / Bcl-2-modifying factor, apoptosis / Apoptosis regulator, Mcl-1 / 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 (B-Cell lymphoma); contains BH1, BH2 regions ...Bcl-2-modifying factor / Bcl-2-modifying factor, apoptosis / Apoptosis regulator, Mcl-1 / 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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Bcl2 modifying factor / Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.967 Å
AuthorsWang, H. / Guo, M. / Wei, H. / Chen, Y.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81570537 China
National Natural Science Foundation of China (NSFC)81974074 China
National Natural Science Foundation of China (NSFC)82172654 China
National Natural Science Foundation of China (NSFC)82273496 China
National Natural Science Foundation of China (NSFC)31900880 China
CitationJournal: Comput Struct Biotechnol J / Year: 2023
Title: Structural basis of the specificity and interaction mechanism of Bmf binding to pro-survival Bcl-2 family proteins.
Authors: Wang, H. / Guo, M. / Wei, H. / Chen, Y.
History
DepositionMar 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Bcl2 modifying factor


Theoretical massNumber of molelcules
Total (without water)20,4602
Polymers20,4602
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-15 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.465, 56.294, 62.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Induced myeloid leukemia cell differentiation protein Mcl-1 / Bcl-2-like protein 3 / Bcl2-L-3 / Bcl-2-related protein EAT/mcl1 / mcl1/EAT


Mass: 17922.344 Da / Num. of mol.: 1 / Fragment: UNP residues 171-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCL1, BCL2L3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07820
#2: Protein/peptide Bcl2 modifying factor


Mass: 2537.958 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMF / Production host: Escherichia coli (E. coli) / References: UniProt: H0WYH6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M potassium thiocyanate, 20% polyethylene glycol monomethyl ether 2,000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.967→31.34 Å / Num. obs: 21592 / % possible obs: 98.02 % / Redundancy: 8.5 % / Biso Wilson estimate: 34.88 Å2 / CC1/2: 0.996 / Net I/σ(I): 2.77
Reflection shellResolution: 1.967→2.037 Å / Num. unique obs: 1172 / CC1/2: 0.851

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Processing

Software
NameVersionClassification
PHENIX1.9-1692refinement
autoPROCdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.967→31.337 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 2159 10.01 %
Rwork0.1961 --
obs0.1999 21592 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.967→31.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1291 0 0 40 1331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021351
X-RAY DIFFRACTIONf_angle_d0.5211827
X-RAY DIFFRACTIONf_dihedral_angle_d13.078491
X-RAY DIFFRACTIONf_chiral_restr0.019211
X-RAY DIFFRACTIONf_plane_restr0.002235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.967-2.01250.34021460.29161340X-RAY DIFFRACTION100
2.0125-2.06280.29231510.29191321X-RAY DIFFRACTION100
2.0628-2.11850.30771450.30091268X-RAY DIFFRACTION98
2.1185-2.18090.26531470.23561360X-RAY DIFFRACTION100
2.1809-2.25120.27231220.24141089X-RAY DIFFRACTION91
2.2512-2.33170.26961270.21861156X-RAY DIFFRACTION95
2.3317-2.4250.27671490.21541319X-RAY DIFFRACTION100
2.425-2.53530.2711430.21841330X-RAY DIFFRACTION100
2.5353-2.66890.22171480.22171328X-RAY DIFFRACTION100
2.6689-2.8360.26081480.20651309X-RAY DIFFRACTION100
2.836-3.05480.28231470.21621329X-RAY DIFFRACTION100
3.0548-3.36190.24671510.20481322X-RAY DIFFRACTION100
3.3619-3.84770.20661460.17871317X-RAY DIFFRACTION99
3.8477-4.84480.1751480.15161319X-RAY DIFFRACTION100
4.8448-31.3370.22211440.17031323X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.90411.5425-1.21093.81530.46458.3185-0.421-0.1128-0.6186-0.0966-0.01361.6819-0.1454-1.0030.1610.2353-0.00080.00180.2879-0.00160.435135.92270.924267.7981
24.86792.2045-0.69793.7699-0.65084.669-0.09580.5262-0.8546-0.3475-0.21361.16860.6223-0.510.2110.3872-0.089-0.02670.3111-0.15420.592438.837-6.75260.9381
33.8768-0.3173-4.71412.56912.08298.6493-0.5124-1.5771-0.69580.72860.70340.24370.73550.7243-0.08340.4840.34660.08190.8060.09940.381954.2534-8.104376.0915
43.6473-1.7836-3.87615.88941.3264.0454-0.1957-1.82250.70680.71250.03490.4254-1.29340.8065-0.05840.37090.00830.07320.784-0.09540.408850.95054.497476.5747
54.8408-2.9575-1.66815.2780.2447.3604-0.1796-0.6197-0.1370.29440.21150.1186-0.0690.7321-0.02230.19510.03690.01060.2724-0.01150.227949.207-1.598467.952
67.5529-1.529-1.60763.817-3.246.6136-0.4851-1.0625-0.2561.26890.66690.2681-0.6124-0.1072-0.26750.41520.08290.06430.35540.02570.239141.68431.59575.333
77.7291-1.9139-2.6929.5653-0.16485.91970.54271.090.4391-1.0927-0.24680.1865-0.938-0.4407-0.24580.41840.0515-0.00040.3890.07550.284443.02826.361555.8882
86.87010.31791.17967.57181.35713.9506-0.0960.51290.3913-0.39550.61510.13640.24862.062-0.5350.25820.00230.02070.62510.04340.29158.2743-1.824661.1028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 171 through 191 )
2X-RAY DIFFRACTION2chain 'A' and (resid 192 through 223 )
3X-RAY DIFFRACTION3chain 'A' and (resid 224 through 239 )
4X-RAY DIFFRACTION4chain 'A' and (resid 240 through 254 )
5X-RAY DIFFRACTION5chain 'A' and (resid 255 through 280 )
6X-RAY DIFFRACTION6chain 'A' and (resid 281 through 301 )
7X-RAY DIFFRACTION7chain 'A' and (resid 302 through 321 )
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 50 )

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