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- PDB-6hrl: Crystal structure of the Kelch domain of human KLHL17 -

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Basic information

Entry
Database: PDB / ID: 6hrl
TitleCrystal structure of the Kelch domain of human KLHL17
ComponentsKelch-like protein 17
KeywordsLIGASE / Kelch domain / Cullin 3 E3 ligase substrate adaptor / Actinfilin / Homo sapiens / ubiquitination
Function / homology
Function and homology information


POZ domain binding / regulation protein catabolic process at postsynapse / dendrite cytoplasm / actin filament binding / actin cytoskeleton / actin cytoskeleton organization / molecular adaptor activity / postsynaptic density / protein ubiquitination / neuronal cell body ...POZ domain binding / regulation protein catabolic process at postsynapse / dendrite cytoplasm / actin filament binding / actin cytoskeleton / actin cytoskeleton organization / molecular adaptor activity / postsynaptic density / protein ubiquitination / neuronal cell body / glutamatergic synapse / extracellular space
Similarity search - Function
Kelch-type beta propeller / Galactose oxidase/kelch, beta-propeller / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch motif / Kelch / Kelch repeat type 1 / Kelch-type beta propeller ...Kelch-type beta propeller / Galactose oxidase/kelch, beta-propeller / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch motif / Kelch / Kelch repeat type 1 / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / 6 Propeller / Neuraminidase / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Mainly Beta
Similarity search - Domain/homology
Kelch-like protein 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChen, Z. / Williams, E. / Sorrell, F.J. / Newman, J.A. / Shrestha, L. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, F. / Edwards, C.H. / Bountra, C. / Bullock, A.N.
CitationJournal: To Be Published
Title: Crystal structure of the Kelch domain of human KLHL17
Authors: Chen, Z. / Williams, E. / Sorrell, F.J. / Newman, J.A. / Shrestha, L. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, F. / Edwards, C.H. / Bountra, C. / Bullock, A.N.
History
DepositionSep 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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: Kelch-like protein 17
B: Kelch-like protein 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,26626
Polymers60,9542
Non-polymers1,31324
Water3,513195
1
A: Kelch-like protein 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,21416
Polymers30,4771
Non-polymers73715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kelch-like protein 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,05310
Polymers30,4771
Non-polymers5769
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.353, 118.774, 124.991
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 340 through 388 or (resid 390...
21(chain C and (resid 340 through 367 or (resid 368...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 340 through 388 or (resid 390...A340 - 388
121(chain A and (resid 340 through 388 or (resid 390...A390
131(chain A and (resid 340 through 388 or (resid 390...A337 - 623
141(chain A and (resid 340 through 388 or (resid 390...A337 - 623
151(chain A and (resid 340 through 388 or (resid 390...A337 - 623
161(chain A and (resid 340 through 388 or (resid 390...A337 - 623
171(chain A and (resid 340 through 388 or (resid 390...A337 - 623
181(chain A and (resid 340 through 388 or (resid 390...A337 - 623
191(chain A and (resid 340 through 388 or (resid 390...A337 - 623
211(chain C and (resid 340 through 367 or (resid 368...C340 - 367
221(chain C and (resid 340 through 367 or (resid 368...C368
231(chain C and (resid 340 through 367 or (resid 368...C1 - 8
241(chain C and (resid 340 through 367 or (resid 368...C1 - 8
251(chain C and (resid 340 through 367 or (resid 368...C1 - 8
261(chain C and (resid 340 through 367 or (resid 368...C1 - 8

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Kelch-like protein 17 / Actinfilin


Mass: 30476.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHL17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6TDP4

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Non-polymers , 5 types, 219 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 4.1 Å3/Da / Density % sol: 70.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.26M ammonium sulfate, 0.2M lithium sulfate, 0.1M tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→62.495 Å / Num. obs: 31573 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 39.22 Å2 / Rmerge(I) obs: 0.188 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.6-2.6750.809199.4
11.63-62.485.20.067199.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
xia2data scaling
PDB_EXTRACT3.24data extraction
PHENIX1.13_2998model building
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NKP

5nkp


Resolution: 2.6→62.495 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.72
RfactorNum. reflection% reflection
Rfree0.2686 1448 4.72 %
Rwork0.2272 --
obs0.2292 30692 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.4 Å2 / Biso mean: 46.994 Å2 / Biso min: 23.82 Å2
Refinement stepCycle: final / Resolution: 2.6→62.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4255 0 65 195 4515
Biso mean--97.57 41.69 -
Num. residues----574
Refine LS restraints NCSNumber: 2498 / Rms: 5.973 / Type: TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6003-2.69320.47731280.42792689281790
2.6932-2.80110.43531210.39572810293194
2.8011-2.92860.42241380.33812865300397
2.9286-3.08290.38771730.31462861303497
3.0829-3.27610.33111690.27982872304198
3.2761-3.5290.27961250.24282976310199
3.529-3.88410.24061420.19862949309199
3.8841-4.4460.17431560.14923011316799
4.446-5.6010.18461350.144730643199100
5.601-62.51350.23611610.20623147330899
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)
12.90531.9604-2.3666.7981-6.06185.65930.19440.10890.21920.29070.0340.2017-0.75050.0777-0.26710.28950.00260.00960.29610.04750.350714.199152.656757.1787
23.86341.09351.07089.1323.82836.8405-0.2661-0.7624-0.06270.7199-0.2391-0.1041-0.002-0.61460.52720.35470.033-0.03010.34630.00550.32888.651452.97666.6008
31.59370.30190.05922.41041.06591.2451-0.04620.3630.0474-0.20450.1044-0.1172-0.14330.194-0.06040.2666-0.0282-0.00520.40490.02710.298422.970738.696352.4532
43.3102-1.05510.8554.55460.47690.771-0.00690.07060.037-0.17930.10160.50370.0414-0.3596-0.0750.2686-0.03270.00310.46960.00920.31454.485232.704949.6495
56.91072.0397-0.17316.89460.15364.2251-0.1270.02310.21790.016-0.03980.0251-0.1753-0.16120.21540.26710.0437-0.0350.43180.0120.34423.418742.723256.2281
64.95322.70280.60193.25391.23091.6634-0.04810.39320.632-0.00320.16860.283-0.2958-0.3473-0.0920.28860.05450.02220.32440.00840.34484.546547.329458.0378
70.55310.8397-0.14.0214-5.04478.4641-0.1724-0.3375-0.6375-0.043-0.3903-0.35690.12460.60440.59060.27610.0149-0.06270.38380.03420.454413.069662.148425.0843
82.0572-7.5391-3.95366.96866.06739.0145-0.1941-0.14650.10560.55860.3-0.0591-0.2849-0.6067-0.07960.51710.08880.04530.60710.09230.45713.388365.903336.3768
92.5005-0.95981.86473.3379-0.26815.8036-0.072-0.3231-0.45560.05780.0293-0.15781.02240.3504-0.0020.45390.06510.00140.37480.05730.45038.979252.235924.8748
103.28030.2479-0.72223.5093-0.44483.68860.0337-0.3974-0.55760.16370.00610.3710.2511-0.3586-0.08240.4425-0.1024-0.05470.52080.11190.4466-2.268552.402920.1067
112.4318-0.3055-0.8053.3923-0.20713.2773-0.0236-0.1875-0.62830.04570.09040.41320.8034-0.579-0.07780.4288-0.1311-0.06620.43090.07920.466-7.773757.494416.114
126.6717-1.2304-0.57566.97840.61217.73470.0071-0.2644-0.00490.24450.06520.299-0.0909-0.4496-0.07480.2407-0.0321-0.04250.310.01430.2524-6.480373.85420.249
134.5744-2.5555-2.04178.00554.53444.6336-0.2441-0.89150.06890.50860.1577-0.09040.4750.07490.05850.29220.0629-0.05310.45850.03710.33083.418373.240326.8301
145.6235-3.3231.10525.22041.32561.996-0.4065-0.9504-0.06210.64170.42580.0033-0.13970.34350.030.3737-0.0152-0.01260.28380.03110.25755.871176.849227.3434
152.2889-0.69212.74812.5990.63125.08640.1292-0.2299-0.34940.18840.24020.3310.02920.1352-0.28280.3150.0236-0.01690.33880.05650.391510.625264.764129.9021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 339 through 358 )A339 - 358
2X-RAY DIFFRACTION2chain 'A' and (resid 359 through 372 )A359 - 372
3X-RAY DIFFRACTION3chain 'A' and (resid 373 through 513 )A373 - 513
4X-RAY DIFFRACTION4chain 'A' and (resid 514 through 560 )A514 - 560
5X-RAY DIFFRACTION5chain 'A' and (resid 561 through 582 )A561 - 582
6X-RAY DIFFRACTION6chain 'A' and (resid 583 through 625 )A583 - 625
7X-RAY DIFFRACTION7chain 'C' and (resid 340 through 358 )C340 - 358
8X-RAY DIFFRACTION8chain 'C' and (resid 359 through 372 )C359 - 372
9X-RAY DIFFRACTION9chain 'C' and (resid 373 through 419 )C373 - 419
10X-RAY DIFFRACTION10chain 'C' and (resid 420 through 441 )C420 - 441
11X-RAY DIFFRACTION11chain 'C' and (resid 442 through 513 )C442 - 513
12X-RAY DIFFRACTION12chain 'C' and (resid 514 through 560 )C514 - 560
13X-RAY DIFFRACTION13chain 'C' and (resid 561 through 582 )C561 - 582
14X-RAY DIFFRACTION14chain 'C' and (resid 583 through 607 )C583 - 607
15X-RAY DIFFRACTION15chain 'C' and (resid 608 through 625 )C608 - 625

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