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- PDB-4wmt: STRUCTURE OF MBP-MCL1 BOUND TO ligand 1 AT 2.35A -

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Basic information

Entry
Database: PDB / ID: 4wmt
TitleSTRUCTURE OF MBP-MCL1 BOUND TO ligand 1 AT 2.35A
ComponentsMBP-MCL1 chimera protein
KeywordsAPOPTOSIS / protein-protein interaction
Function / homology
Function and homology information


positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / detection of maltose stimulus / maltose transport complex / carbohydrate transport / BH3 domain binding / negative regulation of anoikis ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / detection of maltose stimulus / maltose transport complex / carbohydrate transport / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / extrinsic apoptotic signaling pathway in absence of ligand / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to cytokine / negative regulation of autophagy / ATP-binding cassette (ABC) transporter complex / release of cytochrome c from mitochondria / cell chemotaxis / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / positive regulation of neuron apoptotic process / outer membrane-bounded periplasmic space / channel activity / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / mitochondrial outer membrane / periplasmic space / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Chem-865 / FORMIC ACID / Maltose/maltodextrin-binding periplasmic protein / Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsClifton, M.C. / Dranow, D.M.
CitationJournal: Plos One / Year: 2015
Title: A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1.
Authors: Clifton, M.C. / Dranow, D.M. / Leed, A. / Fulroth, B. / Fairman, J.W. / Abendroth, J. / Atkins, K.A. / Wallace, E. / Fan, D. / Xu, G. / Ni, Z.J. / Daniels, D. / Van Drie, J. / Wei, G. / ...Authors: Clifton, M.C. / Dranow, D.M. / Leed, A. / Fulroth, B. / Fairman, J.W. / Abendroth, J. / Atkins, K.A. / Wallace, E. / Fan, D. / Xu, G. / Ni, Z.J. / Daniels, D. / Van Drie, J. / Wei, G. / Burgin, A.B. / Golub, T.R. / Hubbard, B.K. / Serrano-Wu, M.H.
History
DepositionOct 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_oper_list / pdbx_validate_close_contact / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MBP-MCL1 chimera protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,85015
Polymers57,3111
Non-polymers1,53914
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.970, 136.300, 38.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein MBP-MCL1 chimera protein


Mass: 57310.883 Da / Num. of mol.: 1
Fragment: UNP P0AEX9 residues 27-392,UNP Q07820 residues 174-321
Mutation: K194A, K197A, R201A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: malE, b4034, JW3994, MCL1, BCL2L3 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: Q07820
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 287 molecules

#3: Chemical ChemComp-865 / 7-[2-(1H-imidazol-1-yl)-4-methylpyridin-3-yl]-3-[3-(naphthalen-1-yloxy)propyl]-1-[2-oxo-2-(piperazin-1-yl)ethyl]-1H-indole-2-carboxylic acid


Mass: 628.720 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H36N6O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10 MG/ML MBP-MCL1, 200MM MG FORMATE, 20% PEG3350, 1MM MALTOSE, 2MM ligand

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 22069 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 32.63 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.114 / Χ2: 0.943 / Net I/σ(I): 14.77 / Num. measured all: 152847
Reflection shellResolution: 2.35→2.41 Å / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 4.8 / Num. measured obs: 1749 / Num. possible: 307 / Num. unique obs: 296 / Rrim(I) all: 0.042 / Rejects: 0 / % possible all: 84.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OQ6; 4MBP

4oq6

4mbp


Resolution: 2.35→41.29 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 1127 5.11 %
Rwork0.167 --
obs0.169 22069 98.2 %
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.94 Å2 / Biso mean: 29.77 Å2 / Biso min: 11.64 Å2
Refinement stepCycle: final / Resolution: 2.35→41.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3918 0 107 274 4299
Biso mean--40.79 34.39 -
Num. residues----513
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)
12.33480.82070.02070.87950.20560.7393-0.08920.13470.0276-0.03480.09710.0053-0.03490.0833-0.00930.181-0.0131-0.01690.14510.01250.1055-10.086419.162-16.7799
24.64081.5249-1.22982.9024-0.24581.9670.0305-0.1990.231-0.0016-0.12050.1312-0.1647-0.02610.04370.24140.01840.01410.102-0.0190.2285-25.295530.7085-8.6304
31.55410.2156-1.13622.96540.05833.01790.0383-0.10410.01440.2383-0.1-0.1292-0.07510.21660.07240.1428-0.0151-0.03750.170.02430.2157-16.256554.8167-6.8145
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth seq-ID
1X-RAY DIFFRACTION10
2X-RAY DIFFRACTION20
3X-RAY DIFFRACTION30

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