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- PDB-4ap2: Crystal structure of the human KLHL11-Cul3 complex at 2.8A resolution -

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Basic information

Entry
Database: PDB / ID: 4ap2
TitleCrystal structure of the human KLHL11-Cul3 complex at 2.8A resolution
Components
  • CULLIN-3
  • KELCH-LIKE PROTEIN 11
KeywordsCELL CYCLE / UBIQUITINATION / E3 LIGASE
Function / homology
Function and homology information


positive regulation of mitotic cell cycle phase transition / POZ domain binding / negative regulation of Rho protein signal transduction / embryonic cleavage / polar microtubule / anaphase-promoting complex-dependent catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / COPII vesicle coat assembly / cell projection organization ...positive regulation of mitotic cell cycle phase transition / POZ domain binding / negative regulation of Rho protein signal transduction / embryonic cleavage / polar microtubule / anaphase-promoting complex-dependent catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / COPII vesicle coat assembly / cell projection organization / RHOBTB3 ATPase cycle / stem cell division / positive regulation of mitotic metaphase/anaphase transition / Notch binding / stress fiber assembly / RHOBTB1 GTPase cycle / Cul3-RING ubiquitin ligase complex / negative regulation of type I interferon production / positive regulation of cytokinesis / ubiquitin ligase complex scaffold activity / protein monoubiquitination / mitotic metaphase chromosome alignment / endoplasmic reticulum to Golgi vesicle-mediated transport / RHOBTB2 GTPase cycle / sperm flagellum / protein autoubiquitination / ubiquitin-like ligase-substrate adaptor activity / kidney development / intrinsic apoptotic signaling pathway / protein K48-linked ubiquitination / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / gene expression / integrin-mediated signaling pathway / cellular response to amino acid stimulus / cyclin binding / positive regulation of protein ubiquitination / G1/S transition of mitotic cell cycle / protein destabilization / Degradation of DVL / Hedgehog 'on' state / mitotic spindle / SPOP-mediated proteasomal degradation of PD-L1(CD274) / spindle pole / protein polyubiquitination / microtubule cytoskeleton / Regulation of RAS by GAPs / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / cell migration / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / postsynapse / protein ubiquitination / inflammatory response / ubiquitin protein ligase binding / centrosome / positive regulation of cell population proliferation / glutamatergic synapse / Golgi apparatus / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Calicin, beta-propeller domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #420 / Cullin Repeats / 5 helical Cullin repeat like / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Kelch ...Calicin, beta-propeller domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #420 / Cullin Repeats / 5 helical Cullin repeat like / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Kelch / Kelch repeat type 1 / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin alpha solenoid domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / 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
IODIDE ION / Cullin-3 / Kelch-like protein 11
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCanning, P. / Cooper, C.D.O. / Krojer, T. / Filippakopoulos, P. / Ayinampudi, V. / 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
DepositionMar 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references / 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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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 11
B: CULLIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1318
Polymers82,7202
Non-polymers4116
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-22 kcal/mol
Surface area30170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.536, 40.162, 234.758
Angle α, β, γ (deg.)90.00, 107.36, 90.00
Int Tables number5
Space group name H-MI121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein KELCH-LIKE PROTEIN 11


Mass: 34526.215 Da / Num. of mol.: 1 / Fragment: BTB AND 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: 48193.871 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-388 / 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

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Non-polymers , 4 types, 213 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.02 Å3/Da / Density % sol: 69.41 % / Description: NONE
Crystal growDetails: 25% PEG3350, 0.15M NAI, 8% ETHGLY

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.8→48.97 Å / Num. obs: 33319 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9 % / Biso Wilson estimate: 93.33 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 9.2 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→46.94 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.9052 / SU R Cruickshank DPI: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.356 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.254
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 1686 5.06 %RANDOM
Rwork0.2043 ---
obs0.2059 33317 99.98 %-
Displacement parametersBiso mean: 89.67 Å2
Baniso -1Baniso -2Baniso -3
1-6.4057 Å20 Å26.7222 Å2
2--12.2887 Å20 Å2
3----18.6944 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 2.8→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4747 0 18 207 4972
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084880HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.896625HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2245SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes108HARMONIC2
X-RAY DIFFRACTIONt_gen_planes729HARMONIC5
X-RAY DIFFRACTIONt_it4880HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.91
X-RAY DIFFRACTIONt_other_torsion2.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion652SEMIHARMONIC5
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_contact5809SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.89 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2817 137 4.75 %
Rwork0.2409 2747 -
all0.2429 2884 -
obs--99.98 %
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)
17.0631-0.4817-0.05891.51680.21060.5569-0.01230.5211-0.5773-0.30450.1573-0.692-0.05720.1701-0.145-0.3204-0.04880.0511-0.1854-0.1746-0.056130.1464-12.1662-5.0667
21.08010.5257-1.18580.9686-0.80752.01320.09050.0926-0.05190.1821-0.00660.0444-0.1361-0.1443-0.0839-0.10650.0242-0.092-0.14850.0075-0.112912.6733-10.087140.4148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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