[English] 日本語
Yorodumi
- PDB-6hrl: Crystal structure of the Kelch domain of human KLHL17 -

+
Open data


ID or keywords:

Loading...

-
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 / dendrite cytoplasm / brain development / actin filament binding / actin cytoskeleton / actin cytoskeleton organization / molecular adaptor activity / postsynaptic density / protein ubiquitination / neuronal cell body / extracellular space
Similarity search - Function
Kelch-like protein 17/20 / 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 / Kelch repeat type 1 / Kelch motif ...Kelch-like protein 17/20 / 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 / Kelch repeat type 1 / Kelch motif / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more