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- PDB-3icu: Protease-associated domain of the E3 ligase grail -

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Basic information

Entry
Database: PDB / ID: 3icu
TitleProtease-associated domain of the E3 ligase grail
ComponentsE3 ubiquitin-protein ligase RNF128
KeywordsLIGASE / E3 LIGASE / ENERGY / PA DOMAIN / TRANSMEMBRANE / PROTEIN TURNOVER / UBL CONJUGATION PATHWAY / GLYCOPROTEIN / STRUCTURAL GENOMICS CONSORTIUM / SGC / Membrane / Metal-binding / Zinc-finger
Function / homology
Function and homology information


negative regulation of cytokine production => GO:0001818 / positive regulation of protein catabolic process in the vacuole / protein localization to lysosome / protein deubiquitination / RING-type E3 ubiquitin transferase / regulation of protein stability / ubiquitin protein ligase activity / Ovarian tumor domain proteases / late endosome / ubiquitin-dependent protein catabolic process ...negative regulation of cytokine production => GO:0001818 / positive regulation of protein catabolic process in the vacuole / protein localization to lysosome / protein deubiquitination / RING-type E3 ubiquitin transferase / regulation of protein stability / ubiquitin protein ligase activity / Ovarian tumor domain proteases / late endosome / ubiquitin-dependent protein catabolic process / membrane => GO:0016020 / cytoskeleton / Ub-specific processing proteases / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ring finger domain / Glucose Oxidase; domain 1 - #30 / PA domain / PA domain / Glucose Oxidase; domain 1 / Ring finger / Zinc finger RING-type profile. / 3-Layer(bba) Sandwich / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF128
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWalker, J.R. / Yermekbayeva, L. / Seitova, A. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: PA Domain of the E3 Ligase Grail
Authors: Walker, J.R. / Yermekbayeva, L. / Seitova, A. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionJul 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF128
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2732
Polymers21,0521
Non-polymers2211
Water2,558142
1
A: E3 ubiquitin-protein ligase RNF128
hetero molecules

A: E3 ubiquitin-protein ligase RNF128
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5464
Polymers42,1032
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2490 Å2
ΔGint-10 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.795, 65.795, 136.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-383-

HOH

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Components

#1: Protein E3 ubiquitin-protein ligase RNF128 / RING finger protein 128 / Gene related to energy in lymphocytes protein


Mass: 21051.746 Da / Num. of mol.: 1 / Fragment: UNP residues 38-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRAIL, RNF128 / Plasmid: PFHMSP-LIC-N / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: Q8TEB7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 3.58 Å3/Da / Density % sol: 65.35 %
Crystal growTemperature: 290.9 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 3350, 0.2 M NaH2PO4. PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290.9K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 25, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 18428 / Num. obs: 18428 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.6 % / Rsym value: 0.101 / Net I/σ(I): 30.7647
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 3.633 / Num. unique all: 1804 / Rsym value: 0.748 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EK8, 1XF1

2ek8

1xf1


Resolution: 2.1→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.377 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 927 5.1 %RANDOM
Rwork0.19461 ---
obs0.19576 17299 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.997 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2--0.75 Å20 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 14 142 1442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221372
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.941884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1955176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.43224.25954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76215198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.775156
X-RAY DIFFRACTIONr_chiral_restr0.0930.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211064
X-RAY DIFFRACTIONr_mcbond_it0.7011.5864
X-RAY DIFFRACTIONr_mcangle_it1.28721403
X-RAY DIFFRACTIONr_scbond_it2.0843508
X-RAY DIFFRACTIONr_scangle_it3.3654.5480
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 79 -
Rwork0.288 1239 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 32.9688 Å / Origin y: 14.9519 Å / Origin z: 16.7889 Å
111213212223313233
T0.0194 Å2-0.0058 Å2-0.0064 Å2-0.0242 Å20.0058 Å2--0.021 Å2
L2.5537 °2-0.9746 °22.2448 °2-0.7617 °2-1.1661 °2--3.7254 °2
S0.071 Å °-0.0418 Å °-0.0214 Å °-0.0699 Å °-0.0398 Å °-0.0192 Å °0.1301 Å °0.0561 Å °-0.0313 Å °

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