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- PDB-3fsh: Crystal structure of the ubiquitin conjugating enzyme Ube2g2 boun... -

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Basic information

Entry
Database: PDB / ID: 3fsh
TitleCrystal structure of the ubiquitin conjugating enzyme Ube2g2 bound to the G2BR domain of ubiquitin ligase gp78
Components
  • Autocrine motility factor receptor, isoform 2
  • Ubiquitin-conjugating enzyme E2 G2
KeywordsLIGASE / PROTEIN-PEPTIDE COMPLEX / Ubl conjugation pathway / Alternative splicing / Endoplasmic reticulum / Membrane / Metal-binding / Phosphoprotein / Polymorphism / Receptor / Transmembrane / Zinc / Zinc-finger
Function / homology
Function and homology information


protein catabolic process => GO:0030163 / negative regulation of retrograde protein transport, ER to cytosol / regulation of SREBP signaling pathway / positive regulation of plant-type hypersensitive response / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / RING-type E3 ubiquitin transferase (cysteine targeting) / : / protein K27-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / Derlin-1 retrotranslocation complex ...protein catabolic process => GO:0030163 / negative regulation of retrograde protein transport, ER to cytosol / regulation of SREBP signaling pathway / positive regulation of plant-type hypersensitive response / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / RING-type E3 ubiquitin transferase (cysteine targeting) / : / protein K27-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / Derlin-1 retrotranslocation complex / BAT3 complex binding / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / ubiquitin-specific protease binding / non-canonical NF-kappaB signal transduction / ubiquitin conjugating enzyme activity / cellular response to interferon-beta / protein autoubiquitination / protein K48-linked ubiquitination / ERAD pathway / ubiquitin ligase complex / endoplasmic reticulum unfolded protein response / ER Quality Control Compartment (ERQC) / 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 / signaling receptor activity / protein-folding chaperone binding / growth cone / ubiquitin-dependent protein catabolic process / learning or memory / neuronal cell body / dendrite / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / signal transduction / protein-containing complex / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane / 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 / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsTu, D. / Brunger, A.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Mechanistic insights into active site-associated polyubiquitination by the ubiquitin-conjugating enzyme Ube2g2.
Authors: Li, W. / Tu, D. / Li, L. / Wollert, T. / Ghirlando, R. / Brunger, A.T. / Ye, Y.
History
DepositionJan 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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: Ubiquitin-conjugating enzyme E2 G2
B: Ubiquitin-conjugating enzyme E2 G2
C: Autocrine motility factor receptor, isoform 2


Theoretical massNumber of molelcules
Total (without water)41,1823
Polymers41,1823
Non-polymers00
Water72140
1
A: Ubiquitin-conjugating enzyme E2 G2


Theoretical massNumber of molelcules
Total (without water)18,8651
Polymers18,8651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin-conjugating enzyme E2 G2
C: Autocrine motility factor receptor, isoform 2


Theoretical massNumber of molelcules
Total (without water)22,3182
Polymers22,3182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-12 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.719, 105.719, 142.855
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 G2 / Ubiquitin-protein ligase G2 / Ubiquitin carrier protein G2


Mass: 18864.537 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ube2g2 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60605, ubiquitin-protein ligase
#2: Protein/peptide Autocrine motility factor receptor, isoform 2 / AMF receptor / isoform 2 / gp78 / RING finger protein 45


Mass: 3452.988 Da / Num. of mol.: 1 / Fragment: G2BR / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
References: UniProt: Q9UKV5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 4.84 Å3/Da / Density % sol: 74.6 %
Crystal growpH: 7.7
Details: 2.8M SODIUM FORMATE, 0.1M TRIS PH 7.7, 5MM DTT, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 27, 2007
RadiationMonochromator: FLAT MIRROR(VERTICAL FOCUSING), SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.76→50 Å / Num. obs: 21654 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 53.1 Å2 / Rsym value: 0.105 / Net I/σ(I): 19.4
Reflection shellResolution: 2.76→2.86 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.65 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CYX

2cyx


Resolution: 2.76→50 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2034 9.5 %RANDOM
Rwork0.216 ---
obs0.216 20376 94.9 %-
Displacement parametersBiso mean: 61.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 0 40 2862
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.61
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.76→2.86 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3719 164 7.8 %
Rwork0.3622 1533 -
obs--80.65 %

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