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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


chylomicron remnant / lipid transport involved in lipid storage / triglyceride-rich lipoprotein particle clearance / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / positive regulation of heparan sulfate proteoglycan binding / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / discoidal high-density lipoprotein particle ...chylomicron remnant / lipid transport involved in lipid storage / triglyceride-rich lipoprotein particle clearance / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / positive regulation of heparan sulfate proteoglycan binding / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / discoidal high-density lipoprotein particle / negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / chylomicron remnant clearance / BAD-BCL-2 complex / lipoprotein particle / intermediate-density lipoprotein particle / maintenance of location in cell / very-low-density lipoprotein particle clearance / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / very-low-density lipoprotein particle remodeling / positive regulation of melanocyte differentiation / regulation of amyloid-beta clearance / response to caloric restriction / Chylomicron clearance / myeloid cell apoptotic process / negative regulation of triglyceride metabolic process / NMDA glutamate receptor clustering / chylomicron / phosphatidylcholine-sterol O-acyltransferase activator activity / Chylomicron remodeling / osteoblast proliferation / positive regulation of phospholipid efflux / cochlear nucleus development / lipid transporter activity / Chylomicron assembly / mesenchymal cell development / positive regulation of cholesterol metabolic process / positive regulation of low-density lipoprotein particle receptor catabolic process / retinal cell programmed cell death / regulation of behavioral fear response / positive regulation of neuron maturation / high-density lipoprotein particle remodeling / phospholipid efflux / high-density lipoprotein particle clearance / multivesicular body, internal vesicle / lipoprotein catabolic process / very-low-density lipoprotein particle receptor binding / negative regulation of osteoblast proliferation / regulation of amyloid fibril formation / AMPA glutamate receptor clustering / regulation of protein metabolic process / low-density lipoprotein particle / cholesterol transfer activity / gland morphogenesis / renal system process / reverse cholesterol transport / positive regulation by host of viral process / high-density lipoprotein particle assembly / very-low-density lipoprotein particle / positive regulation of amyloid-beta clearance / T cell apoptotic process / lipoprotein biosynthetic process / regulation of cell-matrix adhesion / melanosome organization / positive regulation of CoA-transferase activity / stem cell development / negative regulation of calcium ion transport into cytosol / protein import / melanocyte differentiation / ear development / The NLRP1 inflammasome / dendritic cell apoptotic process / lymphoid progenitor cell differentiation / negative regulation of blood coagulation / low-density lipoprotein particle remodeling / high-density lipoprotein particle / negative regulation of myeloid cell apoptotic process / negative regulation of amyloid fibril formation / negative regulation of epithelial cell apoptotic process / regulation of nitrogen utilization / negative regulation of cholesterol biosynthetic process / triglyceride homeostasis / amyloid precursor protein metabolic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / regulation of Cdc42 protein signal transduction / heparan sulfate proteoglycan binding / B cell apoptotic process / glomerulus development / regulation of amyloid precursor protein catabolic process / negative regulation of T cell apoptotic process / negative regulation of dendritic cell apoptotic process / oocyte development / neuron maturation / positive regulation of multicellular organism growth / cholesterol catabolic process
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 / Apoptosis regulator, Bcl-2 family BH4 motif profile. ...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 (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 / 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 / Sulfate


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