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- PDB-3h8k: Crystal structure of Ube2g2 complxed with the G2BR domain of gp78... -

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Basic information

Entry
Database: PDB / ID: 3h8k
TitleCrystal structure of Ube2g2 complxed with the G2BR domain of gp78 at 1.8-A resolution
Components
  • Autocrine motility factor receptor, isoform 2
  • Ubiquitin-conjugating enzyme E2 G2
KeywordsLIGASE / alpha beta / all alpha / Ubl conjugation pathway / Endoplasmic reticulum / Membrane / Metal-binding / Phosphoprotein / Receptor / Transmembrane / Zinc-finger
Function / homology
Function and homology information


negative regulation of retrograde protein transport, ER to cytosol / regulation of SREBP signaling pathway / RING-type E3 ubiquitin transferase (cysteine targeting) / protein K27-linked ubiquitination / BAT3 complex binding / Derlin-1 retrotranslocation complex / ERAD pathway / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / ubiquitin-specific protease binding ...negative regulation of retrograde protein transport, ER to cytosol / regulation of SREBP signaling pathway / RING-type E3 ubiquitin transferase (cysteine targeting) / protein K27-linked ubiquitination / BAT3 complex binding / Derlin-1 retrotranslocation complex / ERAD pathway / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / ubiquitin-specific protease binding / ubiquitin conjugating enzyme activity / non-canonical NF-kappaB signal transduction / protein K48-linked ubiquitination / cellular response to interferon-beta / protein autoubiquitination / ubiquitin ligase complex / : / endoplasmic reticulum unfolded protein response / ER Quality Control Compartment (ERQC) / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / lipid droplet / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ubiquitin binding / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein-macromolecule adaptor activity / Antigen processing: Ubiquitination & Proteasome degradation / signaling receptor activity / growth cone / ubiquitin-dependent protein catabolic process / protein-folding chaperone binding / learning or memory / dendrite / neuronal cell body / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / signal transduction / protein-containing complex / ATP binding / membrane / identical protein binding / metal ion binding / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase AMFR, Ube2g2-binding region / E3 gp78 Ube2g2-binding region (G2BR) / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Ring finger domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site ...E3 ubiquitin-protein ligase AMFR, Ube2g2-binding region / E3 gp78 Ube2g2-binding region (G2BR) / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Ring finger domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 G2 / E3 ubiquitin-protein ligase AMFR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsKalathur, R.C. / Das, R. / Li, J. / Byrd, R.A. / Ji, X.
CitationJournal: Mol.Cell / Year: 2009
Title: Allosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78.
Authors: Das, R. / Mariano, J. / Tsai, Y.C. / Kalathur, R.C. / Kostova, Z. / Li, J. / Tarasov, S.G. / McFeeters, R.L. / Altieri, A.S. / Ji, X. / Byrd, R.A. / Weissman, A.M.
History
DepositionApr 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.6Sep 6, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 G2
B: Autocrine motility factor receptor, isoform 2


Theoretical massNumber of molelcules
Total (without water)22,0032
Polymers22,0032
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-12 kcal/mol
Surface area10300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.92, 60.15, 61.64
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 Ubiquitin-conjugating enzyme E2 G2 / Ubiquitin-protein ligase G2 / Ubiquitin carrier protein G2


Mass: 18451.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2G2 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P60604, ubiquitin-protein ligase
#2: Protein/peptide Autocrine motility factor receptor, isoform 2 / AMF receptor / isoform 2 / gp78 / RING finger protein 45


Mass: 3552.120 Da / Num. of mol.: 1 / Fragment: Residues 573-600 / Mutation: K573W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMFR, RNF45 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9UKV5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.05 Å3/Da / Density % sol: 39.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 3350, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR300 / Detector: CCD / Date: Jul 21, 2008 / Details: mirrors
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 16657 / % possible obs: 95.4 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.078 / Χ2: 1.051 / Net I/σ(I): 22.381
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.74 / Num. unique all: 1272 / Χ2: 0.959 / % possible all: 74.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 48.91 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.05 Å
Translation2.5 Å43.05 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.1phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CYX

2cyx


Resolution: 1.8→43.048 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.809 / SU ML: 0.27 / Isotropic thermal model: Isotropic / Cross valid method: 15822 / σ(F): 0.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1573 9.94 %RANDOM
Rwork0.193 ---
obs0.198 15822 90.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.284 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso max: 97.34 Å2 / Biso mean: 34.205 Å2 / Biso min: 10.88 Å2
Baniso -1Baniso -2Baniso -3
1-10.605 Å2-0 Å2-0 Å2
2---4.214 Å20 Å2
3----6.39 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.8→43.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1543 0 0 163 1706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051623
X-RAY DIFFRACTIONf_angle_d0.9212207
X-RAY DIFFRACTIONf_chiral_restr0.066232
X-RAY DIFFRACTIONf_plane_restr0.005294
X-RAY DIFFRACTIONf_dihedral_angle_d15.157629
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.8640.2751020.2319511053105362
1.864-1.9390.3181290.24311621291129175
1.939-2.0270.3091550.22613371492149287
2.027-2.1340.2411580.20414521610161093
2.134-2.2670.2571590.19514771636163696
2.267-2.4420.251700.20915001670167097
2.442-2.6880.2761670.21215411708170898
2.688-3.0770.2651750.20315601735173599
3.077-3.8760.2381710.181159217631763100
3.876-43.0610.1941870.167167718641864100

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