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- PDB-6stj: Selective Affimers Recognize BCL-2 Family Proteins Through Non-Ca... -

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Basic information

Entry
Database: PDB / ID: 6stj
TitleSelective Affimers Recognize BCL-2 Family Proteins Through Non-Canonical Structural Motifs
Components
  • Cystatin domain-containing protein
  • Induced myeloid leukemia cell differentiation protein Mcl-1
KeywordsPROTEIN BINDING / Affimer
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 / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine / negative regulation of autophagy / release of cytochrome c from mitochondria / 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 / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / mitochondrial outer membrane / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsHobor, F. / Miles, J.A. / Trinh, C.H. / Taylor, J. / Tiede, C. / Rowell, P.R. / Jackson, B. / Nadat, F. / Kyle, H.F. / Wicky, B.I.M. ...Hobor, F. / Miles, J.A. / Trinh, C.H. / Taylor, J. / Tiede, C. / Rowell, P.R. / Jackson, B. / Nadat, F. / Kyle, H.F. / Wicky, B.I.M. / Clarke, J. / Tomlinson, D.C. / Wilson, A.J. / Edwards, T.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/N013573/1 United Kingdom
CitationJournal: Chembiochem / Year: 2021
Title: Selective Affimers Recognise the BCL-2 Family Proteins BCL-x L and MCL-1 through Noncanonical Structural Motifs*.
Authors: Miles, J.A. / Hobor, F. / Trinh, C.H. / Taylor, J. / Tiede, C. / Rowell, P.R. / Jackson, B.R. / Nadat, F.A. / Ramsahye, P. / Kyle, H.F. / Wicky, B.I.M. / Clarke, J. / Tomlinson, D.C. / ...Authors: Miles, J.A. / Hobor, F. / Trinh, C.H. / Taylor, J. / Tiede, C. / Rowell, P.R. / Jackson, B.R. / Nadat, F.A. / Ramsahye, P. / Kyle, H.F. / Wicky, B.I.M. / Clarke, J. / Tomlinson, D.C. / Wilson, A.J. / Edwards, T.A.
History
DepositionSep 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 11, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.3Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Induced myeloid leukemia cell differentiation protein Mcl-1
C: Induced myeloid leukemia cell differentiation protein Mcl-1
D: Induced myeloid leukemia cell differentiation protein Mcl-1
E: Cystatin domain-containing protein
F: Cystatin domain-containing protein
G: Cystatin domain-containing protein
H: Cystatin domain-containing protein


Theoretical massNumber of molelcules
Total (without water)114,9278
Polymers114,9278
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-41 kcal/mol
Surface area44930 Å2
Unit cell
Length a, b, c (Å)92.142, 107.498, 226.154
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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: 17765.219 Da / Num. of mol.: 4
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
Cystatin domain-containing protein


Mass: 10966.528 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEG MME 2K, 0.2M ammonium sulfate, 0.1M sodium acetate pH4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.2→113.1 Å / Num. obs: 57159 / % possible obs: 99.4 % / Redundancy: 11.8 % / CC1/2: 0.988 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.5
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.644 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2578 / CC1/2: 0.681 / Rpim(I) all: 0.591 / % possible all: 91.4

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Processing

Software
NameVersionClassification
xia2data reduction
Aimlessdata scaling
REFMAC5.8.0253refinement
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5FC4, 4N6T

5fc4

4n6t


Resolution: 2.2→113.08 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.92 / SU B: 20.404 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.311 / ESU R Free: 0.238
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2895 2850 5 %RANDOM
Rwork0.2569 ---
obs0.2585 54259 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 167.55 Å2 / Biso mean: 61.212 Å2 / Biso min: 31.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--0.07 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 2.2→113.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7257 0 0 51 7308
Biso mean---48.29 -
Num. residues----875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0137408
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177001
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.6389966
X-RAY DIFFRACTIONr_angle_other_deg1.1321.58516174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9025861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09322.051434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.695151393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0661556
X-RAY DIFFRACTIONr_chiral_restr0.0540.2910
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021678
LS refinement shellResolution: 2.2→2.254 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.385 189 -
Rwork0.374 3720 -
obs--93.56 %
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)
13.49372.0691-0.75284.70060.45243.5789-0.13540.09460.09970.22990.01340.0595-0.2052-0.12260.1220.3318-0.0683-0.00590.1332-0.01350.0106-16.539-6.215-14.718
23.80752.27021.28755.3748-0.61813.7554-0.04220.1473-0.10430.1726-0.0115-0.04430.17430.20430.05380.3159-0.0529-0.00520.12580.02630.012518.786.085-14.731
39.13155.06714.51187.10634.91528.9016-0.17120.61430.3135-0.09630.3262-0.5143-0.0090.7045-0.1550.6858-0.0856-0.02850.6191-0.16250.3758-2.331-31.371-40.957
49.33514.3115-1.26995.7792-2.85666.3433-0.01140.695-0.4347-0.35440.24610.12050.298-0.3995-0.23470.5677-0.1362-0.06280.51660.17090.23545.01329.173-42.105
55.20150.40895.45631.910.44666.54120.01120.37320.0316-0.23790.0341-0.1433-0.27310.0912-0.04530.3706-0.08990.04270.40210.12990.1072-16.774-1.405-41.224
64.96280.4323-5.34472.1356-0.27276.42530.02890.2642-0.0939-0.33360.02640.05970.31090.055-0.05530.4547-0.0261-0.08480.4569-0.12810.086919.0931.202-41.079
74.270.7341-1.31475.1386-3.16327.6050.29330.0173-0.303-0.0897-0.0566-0.57010.10710.6831-0.23670.3793-0.0446-0.16140.3044-0.14070.3737-0.348-28.585-14.634
82.83730.88410.96664.76123.23387.67220.1412-0.05970.232-0.01620.13740.6173-0.1272-0.6369-0.27860.3343-0.02640.13430.34920.19970.37292.28228.41-15.183
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A172 - 322
2X-RAY DIFFRACTION2B172 - 322
3X-RAY DIFFRACTION3C176 - 320
4X-RAY DIFFRACTION4D172 - 320
5X-RAY DIFFRACTION5E3 - 91
6X-RAY DIFFRACTION6F2 - 91
7X-RAY DIFFRACTION7G4 - 91
8X-RAY DIFFRACTION8H4 - 91

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