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- PDB-5vx2: Mcl-1 in complex with Bim-h3Pc-RT -

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Basic information

Entry
Database: PDB / ID: 5vx2
TitleMcl-1 in complex with Bim-h3Pc-RT
Components
  • Bcl-2-like protein 11
  • Induced myeloid leukemia cell differentiation protein Mcl-1 homolog,Induced myeloid leukemia cell differentiation protein Mcl-1 chimera
KeywordsAPOPTOSIS / Bcl-2 Family / Pro-surivial
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Activation of BIM and translocation to mitochondria / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Activation of BIM and translocation to mitochondria / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / ear development / 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 / meiosis I / regulation of organ growth / positive regulation of T cell apoptotic process / tube formation / mammary gland development / cellular homeostasis / myeloid cell homeostasis / mitochondrial fusion / Bcl-2 family protein complex / cellular response to glucocorticoid stimulus / NRAGE signals death through JNK / thymocyte apoptotic process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / BH3 domain binding / T cell homeostasis / B cell homeostasis / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of intrinsic apoptotic signaling pathway / spleen development / positive regulation of cell cycle / response to cytokine / extrinsic apoptotic signaling pathway in absence of ligand / FLT3 Signaling / endomembrane system / negative regulation of autophagy / response to endoplasmic reticulum stress / thymus development / release of cytochrome c from mitochondria / cell-matrix adhesion / post-embryonic development / kidney development / positive regulation of protein-containing complex assembly / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / channel activity / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / regulation of apoptotic process / microtubule binding / in utero embryonic development / mitochondrial outer membrane / cell differentiation / positive regulation of apoptotic process / mitochondrial matrix / protein heterodimerization activity / apoptotic process / DNA damage response / protein kinase binding / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site ...Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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
Bcl-2-like protein 11 / Induced myeloid leukemia cell differentiation protein Mcl-1 homolog / Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 Å
AuthorsCowan, A.D. / Brouwer, J.M. / Colman, P.M. / Czabotar, P.E.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1079706 Australia
National Health and Medical Research Council (NHMRC, Australia)1058331 Australia
National Health and Medical Research Council (NHMRC, Australia)1113133 Australia
CitationJournal: Mol. Cell / Year: 2017
Title: Conversion of Bim-BH3 from Activator to Inhibitor of Bak through Structure-Based Design.
Authors: Brouwer, J.M. / Lan, P. / Cowan, A.D. / Bernardini, J.P. / Birkinshaw, R.W. / van Delft, M.F. / Sleebs, B.E. / Robin, A.Y. / Wardak, A. / Tan, I.K. / Reljic, B. / Lee, E.F. / Fairlie, W.D. / ...Authors: Brouwer, J.M. / Lan, P. / Cowan, A.D. / Bernardini, J.P. / Birkinshaw, R.W. / van Delft, M.F. / Sleebs, B.E. / Robin, A.Y. / Wardak, A. / Tan, I.K. / Reljic, B. / Lee, E.F. / Fairlie, W.D. / Call, M.J. / Smith, B.J. / Dewson, G. / Lessene, G. / Colman, P.M. / Czabotar, P.E.
History
DepositionMay 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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 homolog,Induced myeloid leukemia cell differentiation protein Mcl-1 chimera
B: Bcl-2-like protein 11
C: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog,Induced myeloid leukemia cell differentiation protein Mcl-1 chimera
D: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1257
Polymers42,9384
Non-polymers1863
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.031, 66.157, 76.673
Angle α, β, γ (deg.)90.00, 105.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 18227.592 Da / Num. of mol.: 2
Fragment: UNP P97287 residues 152-189, UNP Q07820 residues 209-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Mcl1, MCL1, BCL2L3 / Production host: Escherichia coli (E. coli) / References: UniProt: P97287, UniProt: Q07820
#2: Protein/peptide Bcl-2-like protein 11 / Bcl2-L-11 / Bcl2-interacting mediator of cell death


Mass: 3241.641 Da / Num. of mol.: 2 / Fragment: UNP residues 141-166 / Mutation: W147R, Y163T / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 281 K / Method: vapor diffusion
Details: 20 % PEG 3000, 100 mM trisodium citrate buffered with citric acid pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.851→32.25 Å / Num. obs: 34486 / % possible obs: 99 % / Redundancy: 3.7 % / Net I/σ(I): 15.79

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata processing
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.851→32.25 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.58
RfactorNum. reflection% reflection
Rfree0.2104 1998 5.8 %
Rwork0.1693 --
obs0.1717 34460 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.851→32.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2827 0 12 211 3050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062959
X-RAY DIFFRACTIONf_angle_d0.7613985
X-RAY DIFFRACTIONf_dihedral_angle_d16.9141798
X-RAY DIFFRACTIONf_chiral_restr0.046431
X-RAY DIFFRACTIONf_plane_restr0.014526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.851-1.89730.36541380.3212227X-RAY DIFFRACTION96
1.8973-1.94860.27291450.26312308X-RAY DIFFRACTION100
1.9486-2.00590.28621470.23352342X-RAY DIFFRACTION100
2.0059-2.07060.28191400.20812298X-RAY DIFFRACTION100
2.0706-2.14460.23771440.19182302X-RAY DIFFRACTION100
2.1446-2.23050.23981470.17752338X-RAY DIFFRACTION100
2.2305-2.3320.22591390.17562321X-RAY DIFFRACTION100
2.332-2.45490.23941440.18422335X-RAY DIFFRACTION100
2.4549-2.60860.21831420.18232336X-RAY DIFFRACTION100
2.6086-2.80990.23781470.18372326X-RAY DIFFRACTION100
2.8099-3.09250.22141390.18512331X-RAY DIFFRACTION100
3.0925-3.53950.20121410.16262335X-RAY DIFFRACTION100
3.5395-4.45750.18421490.13572337X-RAY DIFFRACTION100
4.4575-32.3160.171360.14972326X-RAY DIFFRACTION96
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.0412-5.0899-4.1796.245.08484.2437-0.4094-0.2204-0.03140.62230.3624-0.09990.56880.17160.13120.32890.01060.01910.29130.02160.2294-5.9556-13.863131.3235
22.4158-1.75612.00462.2214-3.00594.25370.15630.509-0.3328-0.1243-0.1185-0.58650.530.1679-0.10870.58620.01720.02570.4738-0.06220.4335-2.9763-12.829939.5648
34.5982-2.91092.22057.1366-2.37857.7405-0.3733-0.37990.09420.44170.2225-0.1303-0.78480.06530.16670.2618-0.04970.00820.2783-0.02770.2086-5.9016-0.982426.0395
42.393-0.4093-1.73386.5410.89418.01180.0558-0.3234-0.4490.3718-0.13751.1410.4522-0.6140.08280.4602-0.12970.06020.39490.02720.4411-14.7529-11.002916.1346
56.9759-1.0278-3.70093.79031.30996.85480.0722-0.0730.4033-0.12580.2412-0.0067-0.38370.1087-0.30260.2705-0.0528-0.01980.1920.0230.2163-7.4067-5.255422.4915
65.1867-5.3187-4.99155.58694.67057.2704-0.2924-0.1166-1.09370.0002-0.11970.84190.2122-0.43340.4070.3666-0.03430.01290.35590.00760.382-12.5904-14.285625.1817
75.77081.45730.28587.9330.54827.8426-0.2785-0.2950.0005-0.06740.1839-1.11510.10860.98870.07680.1817-0.0357-0.00120.3793-0.05330.39547.5458-11.429823.1779
89.5355-1.06010.96283.13260.56213.7171-0.3210.21670.2585-0.50970.2566-0.2823-0.63690.35640.20570.3851-0.10810.03240.2779-0.00060.26-3.9245-1.063813.2024
92.98331.77762.35964.10915.0676.4803-0.20250.31060.0539-1.04190.5653-0.3212-0.77730.4098-0.34770.5309-0.04640.09260.36430.01230.26980.333828.75196.7023
106.95-0.31381.53352.8134-2.22317.09320.1662-0.94171.10381.40670.19370.4232-0.10490.0111-0.23070.78160.03170.16720.6199-0.19170.41835.860826.44070.0458
117.83582.678-1.18946.07750.31524.5422-0.31350.3677-0.4339-0.45210.2707-0.47780.35720.44720.10370.32610.07940.03590.30640.0020.2113-1.512116.178711.2026
123.75651.0832-1.0453.11883.21017.4673-0.13130.23710.1793-0.43470.02790.1632-0.311-0.26980.14040.32330.046-0.00280.18160.0510.2369-10.018922.847614.6561
138.25895.29355.64048.39395.05114.269-0.20880.1380.7263-0.7634-0.29950.3823-0.8781-0.67930.49970.48870.06630.04310.3654-0.0030.3292-8.723929.44758.93
147.0381-4.027-4.58017.36593.18037.41160.1597-0.022-0.0355-0.05740.3827-0.9753-0.23921.3876-0.46420.24780.079-0.02950.5161-0.13560.39477.763727.013920.4625
158.4319-0.09451.92386.58620.01828.43760.0714-0.3397-0.20950.23850.08380.09050.6836-0.0043-0.12210.3820.10130.02030.17540.01890.1805-8.100416.399523.4705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 172 through 191 )
2X-RAY DIFFRACTION2chain 'A' and (resid 192 through 204 )
3X-RAY DIFFRACTION3chain 'A' and (resid 205 through 235 )
4X-RAY DIFFRACTION4chain 'A' and (resid 236 through 256 )
5X-RAY DIFFRACTION5chain 'A' and (resid 257 through 280 )
6X-RAY DIFFRACTION6chain 'A' and (resid 281 through 301 )
7X-RAY DIFFRACTION7chain 'A' and (resid 302 through 322 )
8X-RAY DIFFRACTION8chain 'B' and (resid 53 through 75 )
9X-RAY DIFFRACTION9chain 'C' and (resid 172 through 191 )
10X-RAY DIFFRACTION10chain 'C' and (resid 192 through 202 )
11X-RAY DIFFRACTION11chain 'C' and (resid 203 through 235 )
12X-RAY DIFFRACTION12chain 'C' and (resid 236 through 280 )
13X-RAY DIFFRACTION13chain 'C' and (resid 281 through 301 )
14X-RAY DIFFRACTION14chain 'C' and (resid 302 through 321 )
15X-RAY DIFFRACTION15chain 'D' and (resid 51 through 75 )

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