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- PDB-6st2: Selective Affimers Recognize BCL-2 Family Proteins Through Non-Ca... -

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Basic information

Entry
Database: PDB / ID: 6st2
TitleSelective Affimers Recognize BCL-2 Family Proteins Through Non-Canonical Structural Motifs
Components
  • Affimer AF6
  • Bcl-2-like protein 1
KeywordsPROTEIN BINDING / Affimer
Function / homology
Function and homology information


apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / negative regulation of dendritic cell apoptotic process ...apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / negative regulation of dendritic cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / regulation of mitochondrial membrane permeability / negative regulation of protein localization to plasma membrane / regulation of growth / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / response to cycloheximide / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / BH3 domain binding / germ cell development / apoptotic mitochondrial changes / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / endocytosis / RAS processing / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / spermatogenesis / nuclear membrane / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / defense response to virus / in utero embryonic development / mitochondrial outer membrane / negative regulation of neuron apoptotic process / mitochondrial inner membrane / mitochondrial matrix / protein heterodimerization activity / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. ...Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / 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
Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 9, 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: Bcl-2-like protein 1
B: Bcl-2-like protein 1
C: Affimer AF6
D: Affimer AF6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6305
Polymers56,5334
Non-polymers961
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-61 kcal/mol
Surface area24050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.891, 71.891, 204.057
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Bcl-2-like protein 1 / Bcl2-L-1 / Apoptosis regulator Bcl-X


Mass: 17506.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Production host: Escherichia coli (E. coli) / References: UniProt: Q07817
#2: Protein Affimer AF6


Mass: 10760.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 8000, 0.2M magnesium chloride and 0.1M Tris pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.79→102.1 Å / Num. obs: 51639 / % possible obs: 100 % / Redundancy: 13.9 % / Biso Wilson estimate: 35 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.031 / Rrim(I) all: 0.085 / Net I/σ(I): 13.8
Reflection shellResolution: 1.79→1.84 Å / Redundancy: 14.2 % / Rmerge(I) obs: 4.694 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3727 / CC1/2: 0.53 / Rpim(I) all: 1.835 / Rrim(I) all: 5.044 / % possible all: 100

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Processing

Software
NameVersionClassification
xia2data reduction
Aimlessdata scaling
REFMAC5.8.0253refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R2D, 4N6T

1r2d

4n6t


Resolution: 1.79→71.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.941 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.123
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 2531 4.9 %RANDOM
Rwork0.2142 ---
obs0.2156 49022 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.48 Å2 / Biso mean: 50.222 Å2 / Biso min: 24.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.85 Å2
Refinement stepCycle: final / Resolution: 1.79→71.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 5 94 3861
Biso mean--69.54 46.09 -
Num. residues----459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133850
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173499
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.6365188
X-RAY DIFFRACTIONr_angle_other_deg1.3021.5798103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1165455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76522.931232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86515679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6181524
X-RAY DIFFRACTIONr_chiral_restr0.0650.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02883
LS refinement shellResolution: 1.79→1.84 Å / Rfactor Rfree error: 0
Num. reflection% reflection
Rfree196 -
Rwork3509 -
obs-99.2 %
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)
11.7868-0.0839-0.09442.77760.8582.8326-0.0026-0.28340.20840.21890.0728-0.1786-0.15280.2873-0.07020.0379-0.0056-0.01090.1448-0.02330.0373-21.467.72466.233
21.62180.035-0.19173.19920.55962.31290.0073-0.0053-0.3234-0.1524-0.02060.02250.33570.09090.01330.0680.0208-0.00860.053-0.0090.0667-24.545-11.3541-10.6336
34.96441.30262.96310.35380.73962.0343-0.1124-0.00760.31430.0019-0.02340.0545-0.09560.09160.13580.2371-0.0287-0.07510.0963-0.02580.2328-55.1445-8.6672-32.1558
44.3371-0.7426-4.08990.73420.40954.5797-0.0546-0.37030.16990.18360.14220.16970.10060.1554-0.08760.25790.06660.05160.1969-0.03480.1381-44.92247.467535.7832
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 999
2X-RAY DIFFRACTION2B0 - 999
3X-RAY DIFFRACTION3C0 - 999
4X-RAY DIFFRACTION4D0 - 999

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