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- PDB-6iwb: Crystal structure of a computationally designed protein (LD3) in ... -

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Basic information

Entry
Database: PDB / ID: 6iwb
TitleCrystal structure of a computationally designed protein (LD3) in complex with BCL-2
Components
  • Apolipoprotein E
  • Apoptosis regulator Bcl-2,Apoptosis regulator Bcl-2
KeywordsAPOPTOSIS
Function / homology
Function and homology information


BCL-2 complex / BAD-BCL-2 complex / channel inhibitor activity / lipid transport involved in lipid storage / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / triglyceride-rich lipoprotein particle clearance / discoidal high-density lipoprotein particle ...BCL-2 complex / BAD-BCL-2 complex / channel inhibitor activity / lipid transport involved in lipid storage / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / triglyceride-rich lipoprotein particle clearance / discoidal high-density lipoprotein particle / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / chylomicron remnant clearance / chylomicron remnant / lipoprotein particle / negative regulation of cholesterol biosynthetic process / regulation of amyloid-beta clearance / intermediate-density lipoprotein particle / NMDA glutamate receptor clustering / very-low-density lipoprotein particle remodeling / Chylomicron clearance / acylglycerol homeostasis / The NLRP1 inflammasome / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron remodeling / positive regulation of low-density lipoprotein particle receptor catabolic process / very-low-density lipoprotein particle clearance / cellular response to lipoprotein particle stimulus / Chylomicron assembly / lipoprotein biosynthetic process / response to caloric restriction / high-density lipoprotein particle clearance / chylomicron / phospholipid efflux / very-low-density lipoprotein particle receptor binding / regulation of protein metabolic process / high-density lipoprotein particle remodeling / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of amyloid-beta clearance / triglyceride metabolic process / reverse cholesterol transport / very-low-density lipoprotein particle / regulation of amyloid fibril formation / positive regulation of cholesterol metabolic process / high-density lipoprotein particle assembly / low-density lipoprotein particle / host-mediated activation of viral process / multivesicular body, internal vesicle / melanosome organization / high-density lipoprotein particle / cholesterol transfer activity / hair follicle morphogenesis / regulation of viral genome replication / pigmentation / endoplasmic reticulum calcium ion homeostasis / amyloid precursor protein metabolic process / protein import / low-density lipoprotein particle remodeling / negative regulation of amyloid fibril formation / negative regulation of protein metabolic process / regulation of behavioral fear response / Regulation of MITF-M-dependent genes involved in apoptosis / heparan sulfate proteoglycan binding / regulation of mitochondrial membrane permeability / B cell proliferation / negative regulation of endothelial cell migration / positive regulation of membrane protein ectodomain proteolysis / regulation of Cdc42 protein signal transduction / regulation of amyloid precursor protein catabolic process / cholesterol efflux / HDL remodeling / response to iron ion / regulation of axon extension / negative regulation of mitochondrial depolarization / regulation of cholesterol metabolic process / NFE2L2 regulating tumorigenic genes / pore complex / triglyceride homeostasis / Scavenging by Class A Receptors / low-density lipoprotein particle receptor binding / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of amyloid fibril formation / virion assembly / regulation of innate immune response / positive regulation of dendritic spine development / negative regulation of endothelial cell proliferation / antioxidant activity / synaptic transmission, cholinergic / negative regulation of intrinsic apoptotic signaling pathway / humoral immune response / lipid carrier activity / positive regulation of lipoprotein transport / negative regulation of platelet-derived growth factor receptor signaling pathway / regulation of calcium ion transport / locomotory exploration behavior / negative regulation of amyloid-beta formation / negative regulation of apoptotic signaling pathway / lipoprotein particle binding / negative regulation of blood vessel endothelial cell migration
Similarity search - Function
Apolipoprotein / Apoptosis regulator, Bcl-2 / Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain / 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 ...Apolipoprotein / Apoptosis regulator, Bcl-2 / Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain / 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-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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Apolipoprotein E / Apoptosis regulator Bcl-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKim, S. / Kwak, M.J. / Oh, B.-H. / Correia, B.E. / Gainza, P.
CitationJournal: Nat.Biotechnol. / Year: 2020
Title: A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy.
Authors: Giordano-Attianese, G. / Gainza, P. / Gray-Gaillard, E. / Cribioli, E. / Shui, S. / Kim, S. / Kwak, M.J. / Vollers, S. / Corria Osorio, A.J. / Reichenbach, P. / Bonet, J. / Oh, B.H. / ...Authors: Giordano-Attianese, G. / Gainza, P. / Gray-Gaillard, E. / Cribioli, E. / Shui, S. / Kim, S. / Kwak, M.J. / Vollers, S. / Corria Osorio, A.J. / Reichenbach, P. / Bonet, J. / Oh, B.H. / Irving, M. / Coukos, G. / Correia, B.E.
History
DepositionDec 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Apolipoprotein E
B: Apoptosis regulator Bcl-2,Apoptosis regulator Bcl-2
C: Apolipoprotein E
D: Apoptosis regulator Bcl-2,Apoptosis regulator Bcl-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5966
Polymers74,4034
Non-polymers1922
Water1629
1
A: Apolipoprotein E
B: Apoptosis regulator Bcl-2,Apoptosis regulator Bcl-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3944
Polymers37,2022
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-20 kcal/mol
Surface area13740 Å2
MethodPISA
2
C: Apolipoprotein E
D: Apoptosis regulator Bcl-2,Apoptosis regulator Bcl-2


Theoretical massNumber of molelcules
Total (without water)37,2022
Polymers37,2022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-23 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.718, 129.718, 80.291
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Apolipoprotein E / Apo-E


Mass: 17844.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOE / Production host: Escherichia coli (E. coli) / References: UniProt: P02649
#2: Protein Apoptosis regulator Bcl-2,Apoptosis regulator Bcl-2


Mass: 19357.557 Da / Num. of mol.: 2 / Fragment: UNP residues 1-34,UNP residues 92-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P10415
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAuthors state that the L21, E22, S25, S28, I129, A130, Q132, L133 I136 G137, F140 and A154 residues ...Authors state that the L21, E22, S25, S28, I129, A130, Q132, L133 I136 G137, F140 and A154 residues are mutated regions based on the result of computational design.

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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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 17% PEG2000, 0.1M Sodium Succinate (pH 5.5), 0.32M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25890 / % possible obs: 85.6 % / Redundancy: 9.2 % / Biso Wilson estimate: 45.99 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.022 / Rrim(I) all: 0.086 / Χ2: 1.001 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.442.40.2246160.7240.1190.2570.47841.6
2.44-2.492.40.2338450.5010.1290.270.44156.3
2.49-2.532.70.2339830.5450.1260.2680.42165.6
2.53-2.593.10.23810940.6380.1160.2680.46671.7
2.59-2.643.50.24211370.6920.1110.2690.46676.6
2.64-2.74.10.23712060.8940.1030.2610.51379.7
2.7-2.774.80.23512380.8320.0970.2560.53682
2.77-2.854.90.22512350.8850.0890.2440.59883.2
2.85-2.936.60.2213630.9310.0770.2340.62190.4
2.93-3.027.40.21113870.9480.070.2230.67691.9
3.02-3.138.10.19713850.9710.0630.2070.76392
3.13-3.268.90.17614310.980.0540.1850.85694.5
3.26-3.41100.16114580.9970.0480.1680.95696.2
3.41-3.5811.60.13814470.990.0390.1441.18596.7
3.58-3.8113.10.12715050.9950.0330.1311.28497.9
3.81-4.113.90.11414740.9950.0290.1181.38298.5
4.1-4.52140.115140.9960.0250.1031.44998.4
4.52-5.1715.60.08515010.9970.0210.0881.24299
5.17-6.5114.80.07515150.9980.0190.0780.90898.8
6.51-5016.40.042155610.010.0440.73898.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.025 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.71 / Phase error: 31.32
RfactorNum. reflection% reflection
Rfree0.2749 1202 4.99 %
Rwork0.2389 --
obs0.2408 24082 90.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 150.56 Å2 / Biso mean: 63.0333 Å2 / Biso min: 18.8 Å2
Refinement stepCycle: final / Resolution: 2.5→46.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4447 0 10 9 4466
Biso mean--84.55 48.42 -
Num. residues----563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064535
X-RAY DIFFRACTIONf_angle_d0.7686138
X-RAY DIFFRACTIONf_chiral_restr0.05679
X-RAY DIFFRACTIONf_plane_restr0.004794
X-RAY DIFFRACTIONf_dihedral_angle_d19.2692687
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.60020.3529980.28981964206270
2.6002-2.71850.35641180.28932214233279
2.7185-2.86180.39011240.28942331245583
2.8618-3.04110.31761390.28412584272392
3.0411-3.27580.35241410.29382628276994
3.2758-3.60530.32921440.24292723286796
3.6053-4.12670.29911480.23072775292398
4.1267-5.19810.22091430.20992815295899
5.1981-46.03290.20151470.20912846299399

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