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- PDB-3olm: Structure and Function of a Ubiquitin Binding Site within the Cat... -

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Basic information

Entry
Database: PDB / ID: 3olm
TitleStructure and Function of a Ubiquitin Binding Site within the Catalytic Domain of a HECT Ubiquitin Ligase
Components
  • E3 ubiquitin-protein ligase RSP5
  • Ubiquitin
KeywordsLIGASE / ubiquitin E3 ligase
Function / homology
Function and homology information


regulation of dolichol biosynthetic process / RSP5-BUL ubiquitin ligase complex / regulation of ribosomal large subunit export from nucleus / regulation of tRNA processing / regulation of tRNA export from nucleus / regulation of ubiquinone biosynthetic process / regulation of phosphate metabolic process / regulation of ergosterol biosynthetic process / RHOQ GTPase cycle / Josephin domain DUBs ...regulation of dolichol biosynthetic process / RSP5-BUL ubiquitin ligase complex / regulation of ribosomal large subunit export from nucleus / regulation of tRNA processing / regulation of tRNA export from nucleus / regulation of ubiquinone biosynthetic process / regulation of phosphate metabolic process / regulation of ergosterol biosynthetic process / RHOQ GTPase cycle / Josephin domain DUBs / RHOU GTPase cycle / RAS processing / positive regulation of ubiquitin-dependent endocytosis / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / Pexophagy / regulation of multivesicular body size / Interleukin-1 signaling / Aggrephagy / ribophagy / ubiquitin-dependent endocytosis / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of mRNA export from nucleus / mitochondria-associated ubiquitin-dependent protein catabolic process / Metalloprotease DUBs / regulation of rRNA processing / Endosomal Sorting Complex Required For Transport (ESCRT) / actin cortical patch / cellular bud tip / late endosome to vacuole transport via multivesicular body sorting pathway / E3 ubiquitin ligases ubiquitinate target proteins / nonfunctional rRNA decay / Translesion Synthesis by POLH / positive regulation of fatty acid biosynthetic process / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / regulation of nitrogen utilization / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HECT-type E3 ubiquitin transferase / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / poly(A)+ mRNA export from nucleus / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Formation of TC-NER Pre-Incision Complex / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / positive regulation of endocytosis / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein K63-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / Dual incision in TC-NER / Ub-specific processing proteases / cytosolic ribosome / ubiquitin ligase complex / mitochondrion organization / phosphatidylinositol binding / ubiquitin binding / regulation of actin cytoskeleton organization / positive regulation of receptor-mediated endocytosis / modification-dependent protein catabolic process / ubiquitin-protein transferase activity / protein tag activity / regulation of protein localization / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / chromatin organization / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endosome membrane / protein ubiquitination / ubiquitin protein ligase binding / Golgi apparatus / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / E3 ubiquitin-protein ligase, SMURF1 type / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) ...Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / E3 ubiquitin-protein ligase, SMURF1 type / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / C2 domain / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / C2 domain superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin / E3 ubiquitin-protein ligase RSP5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.495 Å
AuthorsKim, H.C. / Steffen, A. / Chen, J. / Huibregtse, J.M.
CitationJournal: Embo Rep. / Year: 2011
Title: Structure and function of a HECT domain ubiquitin-binding site.
Authors: Kim, H.C. / Steffen, A.M. / Oldham, M.L. / Chen, J. / Huibregtse, J.M.
History
DepositionAug 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Sep 6, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RSP5
D: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)59,2082
Polymers59,2082
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-12 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.570, 50.331, 79.684
Angle α, β, γ (deg.)90.00, 116.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein E3 ubiquitin-protein ligase RSP5 / Reverses SPT-phenotype protein 5


Mass: 50366.660 Da / Num. of mol.: 1 / Fragment: WW3 and HECT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RSP5, MDP1, NPI1, YER125W, SYGP-ORF41 / Production host: Escherichia coli (E. coli)
References: UniProt: P39940, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Ubiquitin


Mass: 8841.026 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBI4, SCD2, YLL039C / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG63
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 13.5% PEG 4000, 0.2M magnesium chloride, 0.1M Tris-HCl pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03326 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 28, 2009
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03326 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 14422 / % possible obs: 75.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 38.76 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 33.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ND7

1nd7


Resolution: 2.495→42.085 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 31.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2716 718 4.98 %RANDOM
Rwork0.22 ---
obs0.2227 14421 71.26 %-
all-14421 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.734 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.7464 Å20 Å22.6181 Å2
2---1.6535 Å2-0 Å2
3---3.3999 Å2
Refinement stepCycle: LAST / Resolution: 2.495→42.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4023 0 0 51 4074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024112
X-RAY DIFFRACTIONf_angle_d0.4885554
X-RAY DIFFRACTIONf_dihedral_angle_d14.9031539
X-RAY DIFFRACTIONf_chiral_restr0.038595
X-RAY DIFFRACTIONf_plane_restr0.001725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4949-2.68750.3195620.299988X-RAY DIFFRACTION26
2.6875-2.95790.3698970.28851957X-RAY DIFFRACTION51
2.9579-3.38580.33531460.25643036X-RAY DIFFRACTION79
3.3858-4.26510.2631950.2083800X-RAY DIFFRACTION99
4.2651-42.09070.23932180.19463922X-RAY DIFFRACTION100
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)
1-0.0002-0.00130.01070.00490.0034-0.0097-0.03390.03680.00890.0066-0.00060.01270.0410.1157-0.0345-0.0571-0.0518-0.0447-0.4545-0.03720.0156-55.92137.2548-37.5414
20.09820.03190.01350.0462-0.02810.05960.1457-0.0446-0.1411-0.1492-0.05190.34230.0445-0.050900.2820.00090.06620.5015-0.07070.9746-36.61198.0638-19.2273
30.40290.11630.21310.49520.16680.6013-0.0326-0.4409-0.09070.19220.01470.143-0.2087-0.203-0.20420.15440.04280.12320.43470.19860.1239-29.683916.8019-9.0273
40.4014-0.26810.17530.2098-0.06510.0514-0.1181-0.2712-0.19140.03570.07360.16820.0065-0.06950.3555-0.57920.239-0.0783-0.32820.3056-0.0943-10.986712.3634-18.2854
50.193-0.74010.00881.196-0.446-0.1043-0.116-0.08930.12990.3370.1923-0.2538-0.15060.05780.20930.04350.1377-0.1689-0.5517-0.00670.0643-47.055528.4026-28.3862
60.02950.010.0060.111-0.01970.0381-0.0464-0.31720.26620.5109-0.0248-0.3521-0.25480.152-0.00030.3788-0.01610.0441.299-0.45460.7157-16.472735.98522.8035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 385:427)
2X-RAY DIFFRACTION2(chain A and resid 428:469)
3X-RAY DIFFRACTION3(chain A and resid 470:552)
4X-RAY DIFFRACTION4(chain A and resid 553:689)
5X-RAY DIFFRACTION5(chain A and resid 690:804)
6X-RAY DIFFRACTION6(chain D and resid 1:74)

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