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- PDB-4x57: Structure of an Arabidopsis E2 / Membrane-anchored Ubiquitin-fold... -

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Basic information

Entry
Database: PDB / ID: 4x57
TitleStructure of an Arabidopsis E2 / Membrane-anchored Ubiquitin-fold Protein Complex
Components
  • Membrane-anchored ubiquitin-fold protein 3
  • Ubiquitin-conjugating enzyme E2 8
Keywordsligase/protein binding / Ubiquitin / Ubconjugating (E2) enzymes / Membrane anchored / Ubiquitin-fold protein 3 / MUB3 / E1:E2 Complex / ligase-protein binding complex
Function / homology
Function and homology information


endosperm development / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Membrane-anchored ubiquitin-fold protein / UBL3-like, ubiquitin domain / UBL3-like / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme ...Membrane-anchored ubiquitin-fold protein / UBL3-like, ubiquitin domain / UBL3-like / Ubiquitin-2 like Rad60 SUMO-like / 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 E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 8 / Membrane-anchored ubiquitin-fold protein 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKorolev, S. / Koroleva, O. / Lu, X. / Downes, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM096279 United States
CitationJournal: To Be Published
Title: Structure of an Arabidopsis E2 / Membrane-anchored Ubiquitin-fold ProteinComplex
Authors: Korolev, S. / Koroleva, O. / Lu, X. / Downes, B.
History
DepositionDec 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 8
B: Membrane-anchored ubiquitin-fold protein 3
C: Ubiquitin-conjugating enzyme E2 8
D: Membrane-anchored ubiquitin-fold protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,26910
Polymers69,6924
Non-polymers5766
Water00
1
A: Ubiquitin-conjugating enzyme E2 8
B: Membrane-anchored ubiquitin-fold protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9423
Polymers34,8462
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-33 kcal/mol
Surface area11700 Å2
MethodPISA
2
C: Ubiquitin-conjugating enzyme E2 8
D: Membrane-anchored ubiquitin-fold protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3267
Polymers34,8462
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-97 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.716, 135.716, 202.134
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRMETMETAA0 - 14731 - 178
21THRTHRMETMETCC0 - 14731 - 178
12GLUGLUPROPROBB4 - 9324 - 113
22GLUGLUPROPRODD4 - 9324 - 113

NCS ensembles :
ID
1
2

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 8 / UBCAT4A / Ubiquitin carrier protein 8 / Ubiquitin-conjugating enzyme E2-17 kDa 8 / Ubiquitin-protein ligase 8


Mass: 19819.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UBC8, UBC4A, At5g41700, MBK23.24 / Production host: Escherichia coli (E. coli) / References: UniProt: P35131, ubiquitin-protein ligase
#2: Protein Membrane-anchored ubiquitin-fold protein 3 / Membrane-anchored ub-fold protein 3 / ATGP4


Mass: 15026.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MUB3, At4g24990, F13M23.130 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SW27
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.86 Å3/Da / Density % sol: 68.1 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 3.0 M (NH4)2SO4 / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 27721 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 30
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.95 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY ID 3NOB, 1QCQ

3nob

1qcq


Resolution: 2.8→10 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 13.175 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25682 1346 5 %RANDOM
Rwork0.22119 ---
obs0.22301 25543 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.553 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.13 Å20 Å2
2--0.25 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3720 0 30 0 3750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193842
X-RAY DIFFRACTIONr_bond_other_d0.0020.023683
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9745226
X-RAY DIFFRACTIONr_angle_other_deg0.81338544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9385478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67724.406143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.19415639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5941514
X-RAY DIFFRACTIONr_chiral_restr0.0920.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214200
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02794
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.2287.1391924
X-RAY DIFFRACTIONr_mcbond_other6.2267.1361923
X-RAY DIFFRACTIONr_mcangle_it8.86710.6842398
X-RAY DIFFRACTIONr_mcangle_other8.86610.6882399
X-RAY DIFFRACTIONr_scbond_it7.9567.8461916
X-RAY DIFFRACTIONr_scbond_other7.7767.7881892
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.42311.3722792
X-RAY DIFFRACTIONr_long_range_B_refined13.73257.0374157
X-RAY DIFFRACTIONr_long_range_B_other13.73257.0254155
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1441MEDIUM POSITIONAL0.040.5
1A866TIGHT THERMAL9.090.5
1A1441MEDIUM THERMAL102
2B809MEDIUM POSITIONAL0.040.5
2B502TIGHT THERMAL10.790.5
2B809MEDIUM THERMAL11.722
LS refinement shellResolution: 2.8→2.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 88 -
Rwork0.391 1736 -
obs--98.59 %

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