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- PDB-2wzk: Structure of the Cul5 N-terminal domain at 2.05A resolution. -

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Basic information

Entry
Database: PDB / ID: 2wzk
TitleStructure of the Cul5 N-terminal domain at 2.05A resolution.
ComponentsCULLIN-5
KeywordsPROTEIN BINDING / UBL CONJUGATION PATHWAY / HIV / PHOSPHOPROTEIN / ISOPEPTIDE BOND
Function / homology
Function and homology information


radial glia guided migration of Purkinje cell / cerebral cortex radially oriented cell migration / Downregulation of ERBB2 signaling / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / cullin-RING ubiquitin ligase complex / Cul5-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / site of DNA damage ...radial glia guided migration of Purkinje cell / cerebral cortex radially oriented cell migration / Downregulation of ERBB2 signaling / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / cullin-RING ubiquitin ligase complex / Cul5-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / site of DNA damage / regulation of cytosolic calcium ion concentration / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Cullin Repeats / 5 helical Cullin repeat like / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Cullin / Cullin, N-terminal ...Cullin Repeats / 5 helical Cullin repeat like / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsMuniz, J.R.C. / Ayinampudi, V. / Zhang, Y. / Babon, J.J. / Chaikuad, A. / Krojer, T. / Pike, A.C.W. / Vollmar, M. / von Delft, F. / Arrowsmith, C.H. ...Muniz, J.R.C. / Ayinampudi, V. / Zhang, Y. / Babon, J.J. / Chaikuad, A. / Krojer, T. / Pike, A.C.W. / Vollmar, M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Bullock, A.N.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Molecular Architecture of the Ankyrin Socs Box Family of Cul5-Dependent E3 Ubiquitin Ligases
Authors: Muniz, J.R.C. / Guo, K. / Kershaw, N.J. / Ayinampudi, V. / von Delft, F. / Babon, J.J. / Bullock, A.N.
History
DepositionNov 30, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Structure summary / Version format compliance
Revision 1.2Jul 3, 2013Group: Atomic model / Database references ...Atomic model / Database references / Other / Source and taxonomy / Structure summary
Revision 1.3Jul 10, 2013Group: Database references
Revision 1.4Aug 28, 2013Group: Database references
Revision 1.5Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CULLIN-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8366
Polymers45,5261
Non-polymers3105
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.180, 64.500, 197.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CULLIN-5 / / CUL-5


Mass: 45525.980 Da / Num. of mol.: 1 / Fragment: N-TERMINAL, RESIDUES 1-386 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q9D5V5
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, VAL 341 TO ARG ENGINEERED RESIDUE IN CHAIN A, LEU 345 TO ASP

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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: 2.12 Å3/Da / Density % sol: 41.96 % / Description: NONE
Crystal growDetails: 20% JEFFAMINE ED 2001 PH 7.0, 0.1M HEPES PH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97960, 0.98000
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.981
ReflectionResolution: 2.05→33.69 Å / Num. obs: 25439 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 28.98 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 7.4
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER-TNT2.8.0refinement
iMOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.05→33.69 Å / Cor.coef. Fo:Fc: 0.9402 / Cor.coef. Fo:Fc free: 0.9244 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 1280 5.07 %RANDOM
Rwork0.1883 ---
obs0.1901 25227 --
Displacement parametersBiso mean: 35.42 Å2
Baniso -1Baniso -2Baniso -3
1--1.5956 Å20 Å20 Å2
2---4.2876 Å20 Å2
3---5.8832 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.05→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 20 365 3325
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083033HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.944092HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1086SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes88HARMONIC2
X-RAY DIFFRACTIONt_gen_planes429HARMONIC5
X-RAY DIFFRACTIONt_it3033HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.09
X-RAY DIFFRACTIONt_other_torsion17.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion400SEMIHARMONIC5
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_contact3905SEMIHARMONIC4
LS refinement shellResolution: 2.05→2.13 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2598 133 4.74 %
Rwork0.2156 2672 -
all0.2177 2805 -
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)
10.0068-1.7271.41520.00980.53860.71770.02330.0490.0515-0.16070.02350.05610.0340.0115-0.0467-0.13890.0904-0.00430.3229-0.061-0.1703-2.521216.0024105.13
20.53080.1082-0.44880.86610.3882.9850.07070.1969-0.0002-0.0487-0.04680.0576-0.3609-0.2952-0.0239-0.13470.0793-0.00250.07820.0014-0.1177-7.380921.4183122.72
30.07960.16621.64771.57551.01111.1981-0.0103-0.0332-0.05570.020.0025-0.0405-0.0280.05090.0079-0.00320.0299-0.06070.17730.02690.0231.995511.3088130.118
41.1396-0.3005-1.53380.96081.72766.37460.219-0.03680.0555-0.0417-0.0983-0.1348-0.26150.3408-0.1207-0.0422-0.02670.02630.00350.0219-0.0825-5.847427.2189144.933
50.8361-0.3865-1.11991.19420.52785.4855-0.085-0.1206-0.1391-0.066-0.09380.0724-0.1238-0.19990.1788-0.0577-0.09940.00720.07680.0058-0.1133-15.846925.2856165.919
60.8647-0.12460.13570.9832-1.95855.03210.1668-0.11860.06730.06740.0073-0.10910.5234-0.2436-0.17410.0401-0.1453-0.02270.12920.0228-0.1358-13.32417.7993174.889
70.01450.0393-0.38181.8205-1.20242.7597-0.1606-0.0530.05570.03280.12180.0829-0.40220.0870.0389-0.1137-0.0612-0.05210.13770.0437-0.1335-17.66064.3703197.421
81.8849-0.0034-2.0762.8009-2.17972.1884-0.2292-0.11990.0079-0.58040.44290.03710.24590.0013-0.2137-0.0839-0.1722-0.07370.09860.0542-0.1251-15.54712.4024193.244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 12:18)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 19:119)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 120:133)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 134:210)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 211:252)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 253:301)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 302:348)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 349:388)

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