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- PDB-6gy5: Crystal structure of the kelch domain of human KLHL20 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6gy5
TitleCrystal structure of the kelch domain of human KLHL20 in complex with DAPK1 peptide
Components
  • Death-associated protein kinase 1
  • Kelch-like protein 20
KeywordsLIGASE / Complex / E3 ligase / substrate / Ubiquitination / Kelch domain / Death Domain
Function / homology
Function and homology information


type II interferon binding / protein K33-linked ubiquitination / response to interferon-alpha / Golgi to endosome transport / cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand ...type II interferon binding / protein K33-linked ubiquitination / response to interferon-alpha / Golgi to endosome transport / cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / regulation of NMDA receptor activity / syntaxin-1 binding / calcium/calmodulin-dependent protein kinase activity / Cul3-RING ubiquitin ligase complex / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / cytoskeleton organization / regulation of autophagy / apoptotic signaling pathway / trans-Golgi network / PML body / cellular response to type II interferon / ubiquitin-protein transferase activity / protein transport / Antigen processing: Ubiquitination & Proteasome degradation / actin cytoskeleton / Neddylation / actin binding / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein autophosphorylation / postsynaptic density / negative regulation of translation / non-specific serine/threonine protein kinase / calmodulin binding / protein kinase activity / protein ubiquitination / intracellular signal transduction / positive regulation of apoptotic process / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / dendrite / GTP binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Death-associated protein kinase 1 / Kelch-type beta propeller / Roc domain profile. / Roc domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Death domain profile. ...Death-associated protein kinase 1 / Kelch-type beta propeller / Roc domain profile. / Roc domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Death domain profile. / Kelch repeat type 1 / Kelch motif / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / 6 Propeller / Neuraminidase / SKP1/BTB/POZ domain superfamily / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Death-associated protein kinase 1 / Kelch-like protein 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.086 Å
AuthorsChen, Z. / Hozjan, V. / Strain-Damerell, C. / Williams, E. / Wang, D. / Cooper, C.D.O. / Sanvitale, C.E. / Fairhead, M. / Carpenter, E.P. / Pike, A.C.W. ...Chen, Z. / Hozjan, V. / Strain-Damerell, C. / Williams, E. / Wang, D. / Cooper, C.D.O. / Sanvitale, C.E. / Fairhead, M. / Carpenter, E.P. / Pike, A.C.W. / Krojer, T. / Srikannathasan, V. / Sorrell, F. / Johansson, C. / Mathea, S. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustH9R00050 United Kingdom
CitationJournal: Structure / Year: 2019
Title: Structural Basis for Recruitment of DAPK1 to the KLHL20 E3 Ligase.
Authors: Chen, Z. / Picaud, S. / Filippakopoulos, P. / D'Angiolella, V. / Bullock, A.N.
History
DepositionJun 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kelch-like protein 20
U: Death-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,27526
Polymers34,3592
Non-polymers91624
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-114 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.459, 47.361, 151.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AU

#1: Protein Kelch-like protein 20 / Kelch-like ECT2-interacting protein / Kelch-like protein X


Mass: 33155.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHL20, KLEIP, KLHLX / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRARE / References: UniProt: Q9Y2M5
#2: Protein/peptide Death-associated protein kinase 1


Mass: 1203.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P53355*PLUS

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Non-polymers , 4 types, 429 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.2 Å3/Da / Density % sol: 44.21 % / Description: Prisms
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 2M Sodium Chloride, 0.1M Acetate pH 4.5

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.06→29.65 Å / Num. obs: 130575 / % possible obs: 97.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 9.65 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.045 / Rrim(I) all: 0.085 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.06-1.092.20.4481.474880.7060.4270.6277.3
4.74-29.655.90.06626.116990.9950.040.07799.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.32data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vpj

2vpj


Resolution: 1.086→29.65 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.86
RfactorNum. reflection% reflection
Rfree0.1724 6234 5.07 %
Rwork0.1534 --
obs0.1543 122958 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.83 Å2
Refinement stepCycle: LAST / Resolution: 1.086→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 0 51 405 2686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012443
X-RAY DIFFRACTIONf_angle_d1.3333346
X-RAY DIFFRACTIONf_dihedral_angle_d10.824902
X-RAY DIFFRACTIONf_chiral_restr0.08369
X-RAY DIFFRACTIONf_plane_restr0.007440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0863-1.09870.23871820.23753453X-RAY DIFFRACTION89
1.0987-1.11160.21682030.2183592X-RAY DIFFRACTION94
1.1116-1.12510.19831970.20933702X-RAY DIFFRACTION95
1.1251-1.13940.21222110.20193822X-RAY DIFFRACTION99
1.1394-1.15440.21722380.19353889X-RAY DIFFRACTION100
1.1544-1.17020.17261990.18363822X-RAY DIFFRACTION100
1.1702-1.18690.18482160.17853899X-RAY DIFFRACTION100
1.1869-1.20460.16661750.17293866X-RAY DIFFRACTION100
1.2046-1.22350.20242250.17313905X-RAY DIFFRACTION100
1.2235-1.24350.19332060.17543893X-RAY DIFFRACTION100
1.2435-1.2650.18511800.17423900X-RAY DIFFRACTION100
1.265-1.2880.18372300.17333843X-RAY DIFFRACTION100
1.288-1.31270.18571660.173928X-RAY DIFFRACTION100
1.3127-1.33950.18572090.16893899X-RAY DIFFRACTION100
1.3395-1.36870.18252100.17243883X-RAY DIFFRACTION100
1.3687-1.40050.1542110.16433915X-RAY DIFFRACTION100
1.4005-1.43550.16981890.16453928X-RAY DIFFRACTION100
1.4355-1.47430.19672130.15773883X-RAY DIFFRACTION100
1.4743-1.51770.17412160.15933923X-RAY DIFFRACTION100
1.5177-1.56670.15811970.15183920X-RAY DIFFRACTION100
1.5667-1.62270.15362120.14893922X-RAY DIFFRACTION100
1.6227-1.68770.17681920.1463958X-RAY DIFFRACTION100
1.6877-1.76450.16062150.15013905X-RAY DIFFRACTION100
1.7645-1.85750.15842090.14623924X-RAY DIFFRACTION100
1.8575-1.97390.15772240.1473947X-RAY DIFFRACTION100
1.9739-2.12630.15692140.13963960X-RAY DIFFRACTION100
2.1263-2.34030.16781980.14013987X-RAY DIFFRACTION100
2.3403-2.67890.16712210.15464001X-RAY DIFFRACTION100
2.6789-3.3750.17542420.14284038X-RAY DIFFRACTION100
3.375-45.25430.16922340.1354217X-RAY DIFFRACTION100
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)
13.34032.64181.18924.45380.11582.7795-0.01640.01720.00020.12760.01350.0142-0.2305-0.0728-0.00790.1120.02220.0050.0522-0.0070.04748.21757.3261-14.0206
28.92090.60245.49893.66640.20276.0201-0.1441-0.54760.32820.63550.0485-0.4155-0.39120.18750.09680.2756-0.0138-0.05850.1715-0.04650.146515.498714.4068-7.5782
31.93411.19710.36383.4730.23651.4986-0.00920.0310.14990.01750.01430.0277-0.2238-0.0377-0.00420.10050.01260.00420.05210.00840.052710.21889.8788-23.9927
41.4841-0.3357-0.22562.2024-0.8211.26510.01490.0688-0.0174-0.0876-0.010.0983-0.0331-0.0732-0.0050.08660.00440.00340.0862-0.00540.055912.6161-2.0953-29.5275
50.49570.3527-0.44872.0019-1.80873.97290.04710.1057-0.0157-0.2338-0.0944-0.1445-0.05640.21770.05190.08960.00660.00410.0840.00940.074718.81543.3945-36.0553
61.62190.6779-0.9111.3901-0.54962.6675-0.04820.0135-0.1267-0.0824-0.0014-0.06610.14360.05640.04750.05950.01190.00090.0516-0.0010.06220.6201-11.5765-25.8813
73.12320.13470.04981.456-0.08061.1958-0.0067-0.01620.02360.0216-0.0317-0.11-0.00940.09690.03220.05940.00680.00210.07550.01640.055121.7846-9.8455-13.9569
87.44670.3586-3.04210.4416-0.3162.3765-0.084-0.0693-0.20220.04440.0017-0.0420.06590.05980.06640.05660.0032-0.00520.04270.01120.055620.7653-13.8536-10.8661
92.77070.6725-1.52112.6042-2.37782.89620.0896-0.18230.18040.2773-0.1154-0.076-0.27120.1020.01580.1138-0.0056-0.0120.0742-0.01350.065817.9619-0.7578-6.7042
106.1444-1.9142.11141.9051-1.02112.0017-0.1995-0.27110.3040.22760.0074-0.1056-0.2019-0.01020.18720.13190.00880.00210.1132-0.00420.05615.6684-1.0869-1.7012
114.3505-0.0695-0.1991.94080.78363.0165-0.0038-0.06660.37540.20890.00820.0061-0.3167-0.0417-0.01450.15140.009-0.01010.05020.00690.091311.80957.6262-10.8844
122.87561.4590.615.9427-1.31042.01230.0826-0.1868-0.07010.25090.0430.2412-0.2863-0.4387-0.12960.06320.02260.01340.15760.01650.0992-1.2222-8.1102-16.4731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 317 through 334 )
2X-RAY DIFFRACTION2chain 'A' and (resid 335 through 348 )
3X-RAY DIFFRACTION3chain 'A' and (resid 349 through 393 )
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 429 )
5X-RAY DIFFRACTION5chain 'A' and (resid 430 through 442 )
6X-RAY DIFFRACTION6chain 'A' and (resid 443 through 489 )
7X-RAY DIFFRACTION7chain 'A' and (resid 490 through 512 )
8X-RAY DIFFRACTION8chain 'A' and (resid 513 through 537 )
9X-RAY DIFFRACTION9chain 'A' and (resid 538 through 559 )
10X-RAY DIFFRACTION10chain 'A' and (resid 560 through 584 )
11X-RAY DIFFRACTION11chain 'A' and (resid 585 through 601 )
12X-RAY DIFFRACTION12chain 'U' and (resid 1334 through 1344 )

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