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- PDB-2xn4: Crystal structure of the kelch domain of human KLHL2 (Mayven) -

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Basic information

Entry
Database: PDB / ID: 2xn4
TitleCrystal structure of the kelch domain of human KLHL2 (Mayven)
ComponentsKELCH-LIKE PROTEIN 2
KeywordsSTRUCTURAL PROTEIN / CYTOSKELETON
Function / homology
Function and homology information


Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / ruffle / Antigen processing: Ubiquitination & Proteasome degradation / lamellipodium / actin cytoskeleton / Neddylation / actin binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination ...Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / ruffle / Antigen processing: Ubiquitination & Proteasome degradation / lamellipodium / actin cytoskeleton / Neddylation / actin binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Kelch-like protein 2 , BTB/POZ domain / Kelch-type 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-like protein 2 , BTB/POZ domain / Kelch-type 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 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsCanning, P. / Hozjan, V. / Cooper, C.D.O. / Ayinampudi, V. / Vollmar, M. / Pike, A.C.W. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. ...Canning, P. / Hozjan, V. / Cooper, C.D.O. / Ayinampudi, V. / Vollmar, M. / Pike, A.C.W. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N.
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
DepositionJul 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references / Structure summary / Version format compliance
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 / _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 2
B: KELCH-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,40712
Polymers65,6612
Non-polymers74610
Water9,674537
1
A: KELCH-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2046
Polymers32,8301
Non-polymers3735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: KELCH-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2046
Polymers32,8301
Non-polymers3735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.994, 46.005, 71.762
Angle α, β, γ (deg.)86.68, 82.75, 68.48
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 5 / Auth seq-ID: 306 - 591 / Label seq-ID: 15 - 300

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.36691, -0.93026, -0.00029), (-0.93026, 0.36691, 0.00088), (-0.00071, 0.00059, -1)
Vector: 14.58385, 9.96143, 3.81407)

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Components

#1: Protein KELCH-LIKE PROTEIN 2 / ACTIN-BINDING PROTEIN MAYVEN


Mass: 32830.262 Da / Num. of mol.: 2 / Fragment: KELCH DOMAIN, RESIDUES 294-591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: O95198
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.14 Å3/Da / Density % sol: 42.59 % / Description: NONE
Crystal growDetails: 0.2M (NH4)2SO4, 0.1M MES PH 6.5, 30% PEG 5000 MME, 0.2M NASCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: May 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→19.83 Å / Num. obs: 34329 / % possible obs: 92.5 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.9
Reflection shellResolution: 1.99→2.09 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.3 / % possible all: 67.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ADE

3ade


Resolution: 1.99→19.82 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.286 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22155 1698 4.9 %RANDOM
Rwork0.1693 ---
obs0.17195 32617 92.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.168 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.99→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4310 0 40 537 4887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214435
X-RAY DIFFRACTIONr_bond_other_d0.0020.022914
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.9426023
X-RAY DIFFRACTIONr_angle_other_deg1.68737037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3775572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9222.737190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83515681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0641540
X-RAY DIFFRACTIONr_chiral_restr0.0970.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02959
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5531.52811
X-RAY DIFFRACTIONr_mcbond_other0.1221.51197
X-RAY DIFFRACTIONr_mcangle_it1.09524501
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.92431624
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9534.51521
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1674medium positional0.050.5
2B1674medium positional0.050.5
1A1929loose positional0.195
2B1929loose positional0.195
1A1674medium thermal0.262
2B1674medium thermal0.262
1A1929loose thermal0.3710
2B1929loose thermal0.3710
LS refinement shellResolution: 1.993→2.044 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 65 -
Rwork0.19 1456 -
obs--57.05 %
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)
11.2483-0.1139-0.48710.0138-0.43593.69190.06430.09260.07160.0289-0.00470.0026-0.1458-0.1581-0.05960.08210.0059-0.0090.07940.01850.05360.791.35-15.245
20.5029-0.0704-0.07090.6755-0.05020.446-0.01420.011-0.0325-0.03050.01280.02570.0461-0.02040.00140.07010.0002-0.00440.0577-0.00350.04863.371-16.8-9.149
315.06520.6624-6.639456.9121-7.01733.0608-0.62240.1282-0.7436-1.75180.3374-1.77410.2171-0.01720.2850.0562-0.00570.0490.0495-0.02180.048419.791-18.599-22.586
40.9922-0.3503-0.33920.3653-0.0721.4067-0.02160.0450.0824-0.03090.0166-0.0296-0.0536-0.02230.0050.0933-0.0251-0.00680.06520.00470.056510.806-3.53-17.93
50.00910.324-0.36871.99740.38223.57410.05860.03830.02780.20530.02520.1091-0.0835-0.0746-0.08390.07850.01980.03220.0692-0.02080.077713.019.67719.149
60.5903-0.183-0.07060.7406-0.07160.53530.0042-0.0280.0109-0.0013-0.0087-0.039-0.00410.06480.00450.0540-0.00580.0671-0.00090.049729.3431.78612.16
76.5443-0.55023.49030.7273-1.56083.8573-0.0666-0.3456-0.1445-0.03980.0385-0.03690.0554-0.16910.02810.05220.0352-0.00870.07530.00340.022625.279-13.53123.401
80.5905-0.19770.13091.2581-0.51261.3120.0198-0.09180.03730.05280.0310.0553-0.0593-0.1433-0.05080.0434-0.00420.00240.1162-0.0070.040614.121-1.97721.955
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A306 - 332
2X-RAY DIFFRACTION2A333 - 521
3X-RAY DIFFRACTION3A522 - 527
4X-RAY DIFFRACTION4A528 - 591
5X-RAY DIFFRACTION5B306 - 332
6X-RAY DIFFRACTION6B333 - 507
7X-RAY DIFFRACTION7B508 - 524
8X-RAY DIFFRACTION8B525 - 591

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