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- PDB-4apf: Crystal structure of the human KLHL11-Cul3 complex at 3.1A resolution -

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Basic information

Entry
Database: PDB / ID: 4apf
TitleCrystal structure of the human KLHL11-Cul3 complex at 3.1A resolution
Components
  • CULLIN 3
  • KELCH-LIKE PROTEIN 11
KeywordsCELL CYCLE / UBIQUITINATION / E3 LIGASE
Function / homology
Function and homology information


liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / polar microtubule / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating / stem cell division ...liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / polar microtubule / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating / stem cell division / RHOBTB3 ATPase cycle / embryonic cleavage / cell projection organization / positive regulation of mitotic metaphase/anaphase transition / Notch binding / RHOBTB1 GTPase cycle / fibroblast apoptotic process / negative regulation of Rho protein signal transduction / negative regulation of type I interferon production / ubiquitin ligase complex scaffold activity / mitotic metaphase chromosome alignment / Cul3-RING ubiquitin ligase complex / stress fiber assembly / positive regulation of cytokinesis / protein monoubiquitination / sperm flagellum / protein autoubiquitination / RHOBTB2 GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / protein K48-linked ubiquitination / gastrulation / positive regulation of TORC1 signaling / cyclin binding / intrinsic apoptotic signaling pathway / positive regulation of protein ubiquitination / integrin-mediated signaling pathway / Degradation of DVL / cellular response to amino acid stimulus / Hedgehog 'on' state / protein destabilization / mitotic spindle / Wnt signaling pathway / spindle pole / G1/S transition of mitotic cell cycle / Regulation of RAS by GAPs / protein polyubiquitination / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / cell migration / Neddylation / gene expression / ubiquitin-dependent protein catabolic process / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / protein ubiquitination / inflammatory response / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / Golgi apparatus / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #420 / Cullin Repeats / 5 helical Cullin repeat like / BTB/Kelch-associated / BTB And C-terminal Kelch / Cullin protein neddylation domain / BTB And C-terminal Kelch / Cullin, conserved site / Cullin family signature. / Cullin ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #420 / Cullin Repeats / 5 helical Cullin repeat like / BTB/Kelch-associated / BTB And C-terminal Kelch / Cullin protein neddylation domain / BTB And C-terminal Kelch / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Kelch / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Kelch repeat type 1 / Kelch motif / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cullin-3 / Kelch-like protein 11
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.1 Å
AuthorsCanning, P. / Cooper, C.D.O. / Krojer, T. / Vollmar, M. / Ugochukwu, E. / Muniz, J.R.C. / Ayinampudi, V. / Savitsky, P. / Arrowsmith, C.H. / Edwards, A.M. ...Canning, P. / Cooper, C.D.O. / Krojer, T. / Vollmar, M. / Ugochukwu, E. / Muniz, J.R.C. / Ayinampudi, V. / Savitsky, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Bullock, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Basis for Cul3 Assembly with the Btb-Kelch Family of E3 Ubiquitin Ligases.
Authors: Canning, P. / Cooper, C.D.O. / Krojer, T. / Murray, J.W. / Pike, A.C.W. / Chaikuad, A. / Keates, T. / Thangaratnarajah, C. / Hojzan, V. / Marsden, B.D. / Gileadi, O. / Knapp, S. / von Delft, F. / Bullock, A.N.
History
DepositionApr 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references / Refinement description / Structure summary
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KELCH-LIKE PROTEIN 11
B: CULLIN 3


Theoretical massNumber of molelcules
Total (without water)80,2502
Polymers80,2502
Non-polymers00
Water18010
1
A: KELCH-LIKE PROTEIN 11
B: CULLIN 3

A: KELCH-LIKE PROTEIN 11
B: CULLIN 3


Theoretical massNumber of molelcules
Total (without water)160,5004
Polymers160,5004
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7540 Å2
ΔGint-45.5 kcal/mol
Surface area55360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)238.640, 41.440, 147.780
Angle α, β, γ (deg.)90.00, 110.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein KELCH-LIKE PROTEIN 11


Mass: 34526.215 Da / Num. of mol.: 1 / Fragment: BTB DOMAIN, BACK DOMAIN, RESIDUES 67-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): R3 PRARE2 / References: UniProt: Q9NVR0
#2: Protein CULLIN 3 / CUL-3


Mass: 45723.953 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 23-388 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): R3 / References: UniProt: Q13618
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, ILE 342 TO ARG ENGINEERED RESIDUE IN CHAIN B, LEU 346 TO ASP
Sequence detailsI342R AND L346D ARE MUTATIONS ENGINEERED AS PART OF THE SPLIT-N-EXPRESS EXPRESSION STRATEGY.

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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: 4.28 Å3/Da / Density % sol: 71.27 % / Description: STATISTICS DERIVED FROM THE NATIVE DATASET.
Crystal growDetails: 0.12 M K CITRATE; 17% PEG 3350; 10% ETHYLENE GLYCOL; PH 6.5 BIS TRIS PROPANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9681
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9681 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 25043 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 127.51 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.8
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / % possible all: 96.8

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 3.1→35.88 Å / Cor.coef. Fo:Fc: 0.9483 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.509 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.489 / SU Rfree Blow DPI: 0.29 / SU Rfree Cruickshank DPI: 0.297
Details: NUMBER OF LIBRARIES USED : 8 REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOM HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 1282 5.12 %RANDOM
Rwork0.193 ---
obs0.1945 25015 98.33 %-
Displacement parametersBiso mean: 115.67 Å2
Baniso -1Baniso -2Baniso -3
1--2.8811 Å20 Å22.9461 Å2
2--0.7034 Å20 Å2
3---2.1777 Å2
Refine analyzeLuzzati coordinate error obs: 0.756 Å
Refinement stepCycle: LAST / Resolution: 3.1→35.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4626 0 0 10 4636
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014716HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.076389HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2192SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes106HARMONIC2
X-RAY DIFFRACTIONt_gen_planes709HARMONIC5
X-RAY DIFFRACTIONt_it4716HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion3.06
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion627SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5668SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.23 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2995 138 5.06 %
Rwork0.241 2589 -
all0.2437 2727 -
obs--98.33 %
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)
12.7871-1.534-3.89231.79782.19329.1204-0.05070.532-0.0851-0.8023-0.06180.15750.4028-0.84970.1125-0.1069-0.27020.0573-0.20040.0169-0.30555.9293-11.7473-30.5535
23.1515-0.99152.53451.1521-1.49573.719-0.0875-0.16970.12570.00260.0078-0.17940.07520.40160.0797-0.29780.04430.126-0.1216-0.131-0.096942.8931-9.91.1496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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