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- PDB-4g3o: Crystal structure of the CUE domain of the E3 ubiquitin ligase AM... -

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Basic information

Entry
Database: PDB / ID: 4g3o
TitleCrystal structure of the CUE domain of the E3 ubiquitin ligase AMFR (gp78)
ComponentsE3 ubiquitin-protein ligase AMFR
KeywordsLIGASE / all-helical structure / BAG6
Function / homology
Function and homology information


regulation of SREBP signaling pathway / positive regulation of plant-type hypersensitive response / RING-type E3 ubiquitin transferase (cysteine targeting) / protein K27-linked ubiquitination / Derlin-1 retrotranslocation complex / BAT3 complex binding / ubiquitin-ubiquitin ligase activity / ubiquitin-specific protease binding / non-canonical NF-kappaB signal transduction / protein autoubiquitination ...regulation of SREBP signaling pathway / positive regulation of plant-type hypersensitive response / RING-type E3 ubiquitin transferase (cysteine targeting) / protein K27-linked ubiquitination / Derlin-1 retrotranslocation complex / BAT3 complex binding / ubiquitin-ubiquitin ligase activity / ubiquitin-specific protease binding / non-canonical NF-kappaB signal transduction / protein autoubiquitination / protein K48-linked ubiquitination / ERAD pathway / ubiquitin ligase complex / endoplasmic reticulum unfolded protein response / ER Quality Control Compartment (ERQC) / 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 / 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-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Ring finger ...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-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
E3 ubiquitin-protein ligase AMFR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKozlov, G. / LePage, K. / Gehring, K.
CitationJournal: To be Published
Title: Crystal structure of the CUE domain of the E3 ubiquitin ligase AMFR (gp78)
Authors: Kozlov, G. / LePage, K. / Gehring, K.
History
DepositionJul 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 AMFR


Theoretical massNumber of molelcules
Total (without water)6,6581
Polymers6,6581
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.396, 55.396, 30.993
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein E3 ubiquitin-protein ligase AMFR / Autocrine motility factor receptor / isoform 2 / AMF receptor / isoform 2 / RING finger protein 45 / gp78


Mass: 6657.504 Da / Num. of mol.: 1 / Fragment: CUE domain (unp residues 456-498)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMFR, RNF45 / Plasmid: pET42a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9UKV5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.056 M sodium phosphate, 1.344 M potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9183 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 10, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9183 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 6932 / Num. obs: 6929 / % possible obs: 0.9996 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.1 % / Rsym value: 0.075 / Net I/σ(I): 55.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 11 % / Mean I/σ(I) obs: 8.1 / Num. unique all: 503 / Rsym value: 0.44 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ejs

2ejs


Resolution: 1.6→48 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.361 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.081 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18626 339 4.7 %RANDOM
Rwork0.15872 ---
all0.161 6932 --
obs0.16001 6929 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.977 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0.21 Å20 Å2
2---0.43 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms432 0 0 53 485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022439
X-RAY DIFFRACTIONr_angle_refined_deg1.091.957595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.72552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19725.225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9031577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.325153
X-RAY DIFFRACTIONr_chiral_restr0.0790.267
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02341
X-RAY DIFFRACTIONr_nbd_refined0.1960.2211
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2308
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.233
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.210
X-RAY DIFFRACTIONr_mcbond_it0.6621.5271
X-RAY DIFFRACTIONr_mcangle_it1.0352427
X-RAY DIFFRACTIONr_scbond_it1.8373183
X-RAY DIFFRACTIONr_scangle_it2.9714.5168
LS refinement shellResolution: 1.602→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.172 30 -
Rwork0.158 503 -
obs--100 %
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)
11.6699-0.74520.77666.6507-4.39695.8780.021-0.01910.16320.01790.15360.2375-0.3169-0.3591-0.17460.04490.0040.01590.0396-0.02250.0321-21.443127.63590.1639
22.40380.27611.76362.4805-0.51793.23810.0502-0.174-0.16340.1268-0.0039-0.02280.0948-0.1085-0.04630.0363-0.01840.00260.04710.00060.0385-13.541517.78312.8629
30.7526-0.85050.21476.3757-2.25381.3333-0.01230.1036-0.0707-0.1480.06920.08710.1133-0.0477-0.05690.0524-0.0226-0.00620.0382-0.00620.035-20.17314.8658-3.9113
418.49994.7836-9.12098.2746-0.049311.3515-0.08180.24760.6158-0.65260.2913-0.6344-0.35090.2214-0.20950.0379-0.00970.0485-0.0302-0.01710.1051-13.77188.4935-3.5707
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A446 - 465
2X-RAY DIFFRACTION2A466 - 481
3X-RAY DIFFRACTION3A482 - 493
4X-RAY DIFFRACTION4A494 - 498

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