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- PDB-4lad: Crystal Structure of the Ube2g2:RING-G2BR complex -

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Basic information

Entry
Database: PDB / ID: 4lad
TitleCrystal Structure of the Ube2g2:RING-G2BR complex
Components
  • E3 ubiquitin-protein ligase AMFR
  • Ubiquitin-conjugating enzyme E2 G2
KeywordsLIGASE/LIGASE / E2:E3 complex / LIGASE-LIGASE complex
Function / homology
Function and homology information


regulation of SREBP signaling pathway / negative regulation of retrograde protein transport, ER to cytosol / RING-type E3 ubiquitin transferase (cysteine targeting) / endoplasmic reticulum mannose trimming / protein K27-linked ubiquitination / endoplasmic reticulum quality control compartment / BAT3 complex binding / Derlin-1 retrotranslocation complex / non-canonical NF-kappaB signal transduction / ubiquitin-ubiquitin ligase activity ...regulation of SREBP signaling pathway / negative regulation of retrograde protein transport, ER to cytosol / RING-type E3 ubiquitin transferase (cysteine targeting) / endoplasmic reticulum mannose trimming / protein K27-linked ubiquitination / endoplasmic reticulum quality control compartment / BAT3 complex binding / Derlin-1 retrotranslocation complex / non-canonical NF-kappaB signal transduction / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / ubiquitin-specific protease binding / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / protein K48-linked ubiquitination / endoplasmic reticulum unfolded protein response / cellular response to interferon-beta / protein autoubiquitination / ERAD pathway / lipid droplet / ER Quality Control Compartment (ERQC) / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / signaling receptor activity / protein-folding chaperone binding / growth cone / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / learning or memory / neuronal cell body / dendrite / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / signal transduction / protein-containing complex / zinc ion binding / ATP binding / identical protein binding / 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 ...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. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Herpes Virus-1 / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
OXALATE ION / 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: 2.3 Å
AuthorsLiang, Y.-H. / Li, J. / Das, R. / Byrd, R.A. / Ji, X.
CitationJournal: Embo J. / Year: 2013
Title: Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine.
Authors: Das, R. / Liang, Y.H. / Mariano, J. / Li, J. / Huang, T. / King, A. / Tarasov, S.G. / Weissman, A.M. / Ji, X. / Byrd, R.A.
History
DepositionJun 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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: E3 ubiquitin-protein ligase AMFR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3606
Polymers34,0532
Non-polymers3074
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-36 kcal/mol
Surface area13370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.246, 58.246, 158.431
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 18582.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2G2, Ubiquitin-conjugating enzyme E2G2 isoform 1 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(star) / References: UniProt: P60604, ubiquitin-protein ligase
#2: Protein E3 ubiquitin-protein ligase AMFR / Autocrine motility factor receptor / AMF receptor / RING finger protein 45 / gp78


Mass: 15471.062 Da / Num. of mol.: 1
Fragment: RING region (UNP residues 313-393) and G2BR region (UNP residues 574-600)
Mutation: 40 a.a. insertion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMFR, Autocrine motility factor receptor, RNF45 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(star)
References: UniProt: Q9UKV5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1.97 Å3/Da / Density % sol: 37.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG-3350, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 12528 / Num. obs: 12528 / % possible obs: 96.9 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.044 / Χ2: 1.071 / Net I/σ(I): 18.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.3-2.384.70.3962.611321.05490.3
2.38-2.485.50.2994.710831.03686.2
2.48-2.597.60.3136.612231.01197
2.59-2.738.90.2319.612540.94399.9
2.73-2.99.40.14718.312651.049100
2.9-3.129.50.08530.312731.056100
3.12-3.449.30.06235.913011.06799.8
3.44-3.938.90.04637.612911.0699.8
3.93-4.9590.0357.813141.15999.2
4.95-408.40.02754.213921.2396

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H8K

3h8k


Resolution: 2.3→39.123 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.7449 / SU ML: 0.41 / σ(F): 1.35 / Phase error: 30.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1000 8.01 %RANDOM
Rwork0.2259 ---
obs0.2302 12488 96.97 %-
all-12488 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.368 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 108.62 Å2 / Biso mean: 61.0837 Å2 / Biso min: 35.14 Å2
Baniso -1Baniso -2Baniso -3
1-7.245 Å20 Å2-0 Å2
2--7.245 Å20 Å2
3----14.49 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1783 0 14 39 1836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091843
X-RAY DIFFRACTIONf_angle_d1.222489
X-RAY DIFFRACTIONf_chiral_restr0.083262
X-RAY DIFFRACTIONf_plane_restr0.006326
X-RAY DIFFRACTIONf_dihedral_angle_d19.349703
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.41840.37461260.300414451571157188
2.4184-2.56980.36141340.28715301664166493
2.5698-2.76820.39041450.2832167118161816100
2.7682-3.04670.33131430.2701165317961796100
3.0467-3.48730.27721460.2426167618221822100
3.4873-4.39270.26581490.1849170818571857100
4.3927-39.12910.21861570.190518051962196298

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