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- PDB-6v7o: Structural Elucidation of Peptide Binding to KLHL-12, a Substrate... -

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Basic information

Entry
Database: PDB / ID: 6v7o
TitleStructural Elucidation of Peptide Binding to KLHL-12, a Substrate Specific Adapter Protein in a Cul3-Ring E3 Ligase Complex
Components
  • Dvl3-peptide
  • Kelch-like protein 12
KeywordsLIGASE / E3 ligase / KLHL-12 / Ubiquitination
Function / homology
Function and homology information


Negative regulation of TCF-dependent signaling by DVL-interacting proteins / neural crest formation / positive regulation of neuron projection arborization / non-canonical Wnt signaling pathway / neural crest cell development / COPII vesicle coating / COPII vesicle coat / WNT5:FZD7-mediated leishmania damping / frizzled binding / PCP/CE pathway ...Negative regulation of TCF-dependent signaling by DVL-interacting proteins / neural crest formation / positive regulation of neuron projection arborization / non-canonical Wnt signaling pathway / neural crest cell development / COPII vesicle coating / COPII vesicle coat / WNT5:FZD7-mediated leishmania damping / frizzled binding / PCP/CE pathway / WNT mediated activation of DVL / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Wnt signaling pathway, planar cell polarity pathway / Cul3-RING ubiquitin ligase complex / COPII-coated ER to Golgi transport vesicle / protein monoubiquitination / endoplasmic reticulum to Golgi vesicle-mediated transport / canonical Wnt signaling pathway / ubiquitin-like ligase-substrate adaptor activity / positive regulation of GTPase activity / TCF dependent signaling in response to WNT / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / Degradation of DVL / RHO GTPases Activate Formins / beta-catenin binding / small GTPase binding / centriolar satellite / Wnt signaling pathway / regulation of protein localization / protease binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / intracellular signal transduction / response to xenobiotic stimulus / signaling receptor binding / intracellular membrane-bounded organelle / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Dishevelled-3 / Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain ...Dishevelled-3 / Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Kelch-type beta propeller / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / 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 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Kelch-like protein 12 / Segment polarity protein dishevelled homolog DVL-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhao, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Biochemistry / Year: 2020
Title: Structural Elucidation of Peptide Binding to KLHL-12, a Substrate Specific Adapter Protein in a Cul3-Ring E3 Ligase Complex.
Authors: Zhao, B. / Payne, W.G. / Sai, J. / Lu, Z. / Olejniczak, E.T. / Fesik, S.W.
History
DepositionDec 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kelch-like protein 12
B: Kelch-like protein 12
C: Dvl3-peptide
D: Dvl3-peptide


Theoretical massNumber of molelcules
Total (without water)67,7144
Polymers67,7144
Non-polymers00
Water00
1
A: Kelch-like protein 12
C: Dvl3-peptide


Theoretical massNumber of molelcules
Total (without water)33,8572
Polymers33,8572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-7 kcal/mol
Surface area11060 Å2
MethodPISA
2
B: Kelch-like protein 12
D: Dvl3-peptide


Theoretical massNumber of molelcules
Total (without water)33,8572
Polymers33,8572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-8 kcal/mol
Surface area11070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.679, 105.124, 63.148
Angle α, β, γ (deg.)90.000, 90.180, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 279 through 292 or (resid 293...
21(chain B and (resid 279 through 304 or (resid 305...
12(chain C and resid 679 through 684)
22(chain D and (resid 679 through 681 or (resid 682...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAGLNGLN(chain A and (resid 279 through 292 or (resid 293...AA279 - 29213 - 26
121GLNGLNGLNGLN(chain A and (resid 279 through 292 or (resid 293...AA29327
131ALAALAGLUGLU(chain A and (resid 279 through 292 or (resid 293...AA279 - 56713 - 301
141ALAALAGLUGLU(chain A and (resid 279 through 292 or (resid 293...AA279 - 56713 - 301
151ALAALAGLUGLU(chain A and (resid 279 through 292 or (resid 293...AA279 - 56713 - 301
161ALAALAGLUGLU(chain A and (resid 279 through 292 or (resid 293...AA279 - 56713 - 301
211ALAALAPROPRO(chain B and (resid 279 through 304 or (resid 305...BB279 - 30413 - 38
221LYSLYSLYSLYS(chain B and (resid 279 through 304 or (resid 305...BB30539
231ALAALAGLUGLU(chain B and (resid 279 through 304 or (resid 305...BB279 - 56713 - 301
241ALAALAGLUGLU(chain B and (resid 279 through 304 or (resid 305...BB279 - 56713 - 301
251ALAALAGLUGLU(chain B and (resid 279 through 304 or (resid 305...BB279 - 56713 - 301
261ALAALAGLUGLU(chain B and (resid 279 through 304 or (resid 305...BB279 - 56713 - 301
112PROPROGLYGLY(chain C and resid 679 through 684)CC679 - 6841 - 6
212PROPROALAALA(chain D and (resid 679 through 681 or (resid 682...DD679 - 6811 - 3
222PROPROPROPRO(chain D and (resid 679 through 681 or (resid 682...DD6824
232PROPROGLYGLY(chain D and (resid 679 through 681 or (resid 682...DD679 - 6841 - 6
242PROPROGLYGLY(chain D and (resid 679 through 681 or (resid 682...DD679 - 6841 - 6
252PROPROGLYGLY(chain D and (resid 679 through 681 or (resid 682...DD679 - 6841 - 6

NCS ensembles :
ID
1
2

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Components

#1: Protein Kelch-like protein 12 / CUL3-interacting protein 1 / DKIR homolog / hDKIR


Mass: 32905.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHL12, C3IP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53G59
#2: Protein/peptide Dvl3-peptide


Mass: 951.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q92997*PLUS

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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: 2.09 Å3/Da / Density % sol: 41.21 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Sodium cacodylate, Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 11458 / % possible obs: 91.4 % / Redundancy: 2.6 % / CC1/2: 0.959 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.095 / Rrim(I) all: 0.167 / Rsym value: 0.136 / Net I/σ(I): 5.15
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 554 / CC1/2: 0.659 / Rpim(I) all: 0.236 / Rrim(I) all: 0.392 / Rsym value: 0.311 / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VPJ

2vpj


Resolution: 2.9→29.368 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 23.6
RfactorNum. reflection% reflection
Rfree0.2542 1150 10.13 %
Rwork0.2071 --
obs0.2119 11347 91.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.27 Å2 / Biso mean: 25.319 Å2 / Biso min: 7.04 Å2
Refinement stepCycle: final / Resolution: 2.9→29.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4297 0 0 0 4297
Num. residues----580
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1700X-RAY DIFFRACTION4.231TORSIONAL
12B1700X-RAY DIFFRACTION4.231TORSIONAL
21C26X-RAY DIFFRACTION4.231TORSIONAL
22D26X-RAY DIFFRACTION4.231TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9001-3.0320.34471390.2792123388
3.032-3.19170.32911380.2511121388
3.1917-3.39140.29051330.2371124089
3.3914-3.65280.29951470.2188126691
3.6528-4.01950.22631420.1937124290
4.0195-4.59920.19191350.1622121787
4.5992-5.78730.20741580.1741138599
5.7873-29.360.22421580.202140199
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)
12.4163-0.5207-0.19910.37610.31470.5740.03250.25850.3105-0.28580.1016-0.2017-0.28890.06040.21240.2422-0.00060.0010.2819-0.13570.2838-20.6615.446828.5037
21.5993-0.4231-0.04810.16570.07041.24650.0217-0.33650.1576-0.21110.23070.1055-0.3987-0.05850.4220.1581-0.0462-0.01790.15710.06820.1313-31.188412.893633.1944
30.15480.17330.20460.67240.7060.7446-0.1587-0.08630.0449-0.1337-0.02980.0517-0.2103-0.05290.07590.04740.057-0.040.314-0.04280.2911-32.711512.74237.9467
40.13170.18330.07750.24710.11840.05080.00360.0678-0.1164-0.00170.0120.0802-0.11610.0235-0.4339-0.0174-0.20310.0544-0.06860.23130.0263-39.36214.792430.5336
50.31810.3871-0.30370.5866-0.08470.75330.0261-0.16890.04540.0926-0.3008-0.04370.06650.0098-1.0493-0.01820.0657-0.14580.2673-0.0033-0.0252-39.7642-0.493829.4878
60.01550.05470.0530.20040.28840.7167-0.2072-0.1285-0.2254-0.0877-0.14220.10510.072-0.4018-0.25980.11840.0274-0.00610.1571-0.02930.1854-38.0818-9.367824.7526
70.61-0.4847-0.02091.2699-0.20140.7797-0.13910.1502-0.3234-0.16380.31450.42920.11710.03990.15250.1146-0.0187-0.05020.11580.03240.0965-25.8068-5.787417.0566
80.17180.23010.0350.33510.06120.0333-0.06690.12870.0279-0.15450.0889-0.0434-0.0250.3062-0.27720.14930.05540.00080.31090.0896-0.0097-20.15244.788819.257
90.25290.1548-0.26040.3618-0.09270.2801-0.07830.1355-0.1956-0.4764-0.0262-0.06290.08910.021-0.29250.33630.0347-0.08560.1332-0.06760.2692-14.92083.786320.5997
100.0354-0.0512-0.16870.93640.80141.1333-0.09990.0468-0.1007-0.242-0.35440.345-0.32-0.2782-0.58670.35240.23320.0950.18040.03040.1873-19.584110.590224.4967
110.6877-0.3359-0.09170.4068-0.12030.68410.2680.3709-0.2009-0.0318-0.177-0.02030.1997-0.42760.24920.159-0.06670.09920.3496-0.03910.0587-50.58719.043159.4542
120.92360.4477-0.35480.4516-0.55810.773-0.2884-0.2792-0.2824-0.32150.29620.16320.4-0.164-0.1060.26440.016-0.02990.16870.04630.1449-40.391712.213864.8261
130.1218-0.0079-0.0020.1989-0.04060.00490.00590.26190.0450.0538-0.00720.16010.13430.2369-0.01230.16550.01560.03410.2086-0.00890.1642-36.954715.289269.1823
140.4430.4208-0.03820.5704-0.10760.2708-0.0706-0.33690.08810.0849-0.0613-0.1146-0.10590.1344-0.25650.31250.07260.00720.1664-0.0115-0.0096-33.284324.327562.5047
150.1262-0.02720.03660.35290.04110.09570.0938-0.1369-0.0545-0.08590.0495-0.1071-0.10180.03550.46710.2238-0.03840.18460.2023-0.13030.1478-25.403616.691662.9304
160.2115-0.265-0.13090.3971-0.08460.68320.0203-0.05510.1938-0.2344-0.1999-0.3268-0.18620.2095-0.1690.19960.0560.0240.0594-0.05380.1775-33.618631.904955.7743
170.3436-0.14690.03960.4344-0.00960.17040.21120.24210.1301-0.09680.03980.0592-0.0378-0.00350.34340.07310.0831-0.02430.11670.00160.1755-45.736530.70948.5772
180.14340.0919-0.18180.0543-0.10830.242-0.2083-0.0351-0.00180.10580.04170.25950.1668-0.0376-0.1210.06870.16160.0742-0.0689-0.05820.1357-51.156820.043650.7505
190.01720.01320.02770.3029-0.04230.07750.18170.063-0.0793-0.1243-0.05180.1157-0.1692-0.10450.19170.28350.1775-0.1097-0.0041-0.10830.3468-56.356121.08451.9402
200.41560.354-0.14530.5369-0.76811.6106-0.2089-0.0152-0.2968-0.1964-0.1313-0.07110.54050.1867-0.5245-0.08960.34420.0106-0.0756-0.07750.3058-51.831114.169855.4566
210.00090.0010.00040.0057-0.00160.01260.0128-0.0202-0.0110.08030.02220.09730.0405-0.029-0.00030.69510.0537-0.09880.1810.10530.2681-19.5408-3.784437.4881
220.13260.05950.10960.04660.07850.1333-0.09890.02620.0175-0.01410.0205-0.0247-0.08030.0311-0.0570.38070.0763-0.09530.4625-0.30110.543-51.58929.754867.2942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 279 through 311 )A279 - 311
2X-RAY DIFFRACTION2chain 'A' and (resid 312 through 334 )A312 - 334
3X-RAY DIFFRACTION3chain 'A' and (resid 335 through 362 )A335 - 362
4X-RAY DIFFRACTION4chain 'A' and (resid 363 through 384 )A363 - 384
5X-RAY DIFFRACTION5chain 'A' and (resid 385 through 431 )A385 - 431
6X-RAY DIFFRACTION6chain 'A' and (resid 432 through 455 )A432 - 455
7X-RAY DIFFRACTION7chain 'A' and (resid 456 through 503 )A456 - 503
8X-RAY DIFFRACTION8chain 'A' and (resid 504 through 525 )A504 - 525
9X-RAY DIFFRACTION9chain 'A' and (resid 526 through 545 )A526 - 545
10X-RAY DIFFRACTION10chain 'A' and (resid 546 through 567 )A546 - 567
11X-RAY DIFFRACTION11chain 'B' and (resid 279 through 311 )B279 - 311
12X-RAY DIFFRACTION12chain 'B' and (resid 312 through 334 )B312 - 334
13X-RAY DIFFRACTION13chain 'B' and (resid 335 through 372 )B335 - 372
14X-RAY DIFFRACTION14chain 'B' and (resid 373 through 395 )B373 - 395
15X-RAY DIFFRACTION15chain 'B' and (resid 396 through 408 )B396 - 408
16X-RAY DIFFRACTION16chain 'B' and (resid 409 through 456 )B409 - 456
17X-RAY DIFFRACTION17chain 'B' and (resid 457 through 503 )B457 - 503
18X-RAY DIFFRACTION18chain 'B' and (resid 504 through 525 )B504 - 525
19X-RAY DIFFRACTION19chain 'B' and (resid 526 through 545 )B526 - 545
20X-RAY DIFFRACTION20chain 'B' and (resid 546 through 567 )B546 - 567
21X-RAY DIFFRACTION21chain 'C' and (resid 679 through 685 )C679 - 685
22X-RAY DIFFRACTION22chain 'D' and (resid 679 through 684 )D679 - 684

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