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- PDB-4wmx: The structure of MBP-MCL1 bound to ligand 6 at 2.0A -

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Basic information

Entry
Database: PDB / ID: 4wmx
TitleThe structure of MBP-MCL1 bound to ligand 6 at 2.0A
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 / carbohydrate transmembrane transporter activity / protein transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to cytokine / extrinsic apoptotic signaling pathway in absence of ligand / ATP-binding cassette (ABC) transporter complex / negative regulation of autophagy / 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 / cytoplasm / cytosol
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 / 4-ethenyl-2-[(phenylsulfonyl)amino]benzoic acid / 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 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 1.1May 13, 2015Group: Structure summary
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn / struct_conn_type / 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_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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

Downloads & links

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Assembly

Deposited unit
A: MBP-MCL1 chimera protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,44114
Polymers57,3111
Non-polymers1,13013
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.560, 135.870, 37.800
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, 379 molecules

#3: Chemical ChemComp-3R7 / 4-ethenyl-2-[(phenylsulfonyl)amino]benzoic acid


Mass: 303.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13NO4S
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.22 Å3/Da / Density % sol: 44.48 % / Description: Rods
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 6, CRYOPROTECTANT 20% ETHYLENE GLYCOL, PH 7.0

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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: Aug 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 34824 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 23 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.09 / Χ2: 0.881 / Net I/σ(I): 20.58 / Num. measured all: 297756
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.050.7940.5793.211669254322050.63986.7
2.05-2.110.8390.4744.2214850252224180.51795.9
2.11-2.170.9270.3726.0718923239123900.398100
2.17-2.240.9550.3187.6421578239523940.337100
2.24-2.310.9650.2768.7820655227422740.292100
2.31-2.390.9730.22510.5120632226322630.239100
2.39-2.480.9780.20711.419261212321230.22100
2.48-2.580.9850.17812.8418935206920690.189100
2.58-2.70.9910.13915.8218421201220120.147100
2.7-2.830.9930.12116.9217347189418940.129100
2.83-2.980.9940.10418.7616755182018200.11100
2.98-3.160.9960.08422.4416024174117410.089100
3.16-3.380.9980.06629.7614822161316130.07100
3.38-3.650.9990.0541.1113941152915290.053100
3.65-40.9990.04249.1712702140714070.045100
4-4.470.9990.03754.6611576128112800.03999.9
4.47-5.160.9990.03456.3510504115911590.037100
5.16-6.320.9990.03746.9688249909900.039100
6.32-8.940.9990.02954.5467397767760.031100
8.940.9990.02266.1635984734670.02398.7

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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→46.327 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2167 2056 5.9 %
Rwork0.1717 32768 -
obs0.1744 34824 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.6 Å2 / Biso mean: 26.1347 Å2 / Biso min: 11.81 Å2
Refinement stepCycle: final / Resolution: 2→46.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3926 0 75 367 4368
Biso mean--32.65 31.48 -
Num. residues----516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074103
X-RAY DIFFRACTIONf_angle_d0.9725576
X-RAY DIFFRACTIONf_chiral_restr0.038625
X-RAY DIFFRACTIONf_plane_restr0.005721
X-RAY DIFFRACTIONf_dihedral_angle_d12.5391459
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.04640.26711190.20391852197186
2.0464-2.09760.28361190.20692091221095
2.0976-2.15430.24571280.193721552283100
2.1543-2.21770.24981560.182721742330100
2.2177-2.28930.2471340.181421532287100
2.2893-2.37110.2371220.178222192341100
2.3711-2.46610.24981350.172621832318100
2.4661-2.57830.1891310.179321932324100
2.5783-2.71420.22281330.174222282361100
2.7142-2.88420.23851490.175221852334100
2.8842-3.10690.211350.176522232358100
3.1069-3.41950.21651500.176522142364100
3.4195-3.9140.22261480.159922252373100
3.914-4.93040.16731470.149722662413100
4.9304-46.33940.1981500.166624072557100
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)
11.7137-0.90150.10040.7501-0.04780.3464-0.0948-0.1133-0.09040.08560.08270.1145-0.0212-0.06380.01190.18380.00940.02880.1499-0.00020.136311.0947156.371752.0369
20.2285-0.6148-0.35762.22980.90630.5646-0.1101-0.06150.05940.29880.0612-0.2330.0909-0.00430.04870.20440.0068-0.02190.20620.00210.214623.484188.366451.6779
32.1767-1.355-0.1223.51150.25841.13090.06030.0895-0.085-0.3408-0.0520.24290.0299-0.08750.00550.2129-0.0027-0.03920.18470.02120.145914.1816190.783243.2388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -196 through 160 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 161 through 223 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 224 through 321 )A0

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