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- PDB-1x23: Crystal structure of ubch5c -

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Basic information

Entry
Database: PDB / ID: 1x23
TitleCrystal structure of ubch5c
ComponentsUbiquitin-conjugating enzyme E2 D3
KeywordsLIGASE / Ubiquitin conjugating enzyme / Ubiquitin / E2
Function / homology
Function and homology information


Signaling by BMP / protein K6-linked ubiquitination / (E3-independent) E2 ubiquitin-conjugating enzyme / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein monoubiquitination / negative regulation of BMP signaling pathway / protein K48-linked ubiquitination ...Signaling by BMP / protein K6-linked ubiquitination / (E3-independent) E2 ubiquitin-conjugating enzyme / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein monoubiquitination / negative regulation of BMP signaling pathway / protein K48-linked ubiquitination / protein autoubiquitination / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / protein modification process / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endosome membrane / protein ubiquitination / DNA repair / apoptotic process / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
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 / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 D3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNakanishi, M. / Teshima, N. / Mizushima, T. / Murata, S. / Tanaka, K. / Yamane, T.
CitationJournal: To be Published
Title: Crystal structure of ubch5c
Authors: Nakanishi, M. / Teshima, N. / Mizushima, T. / Murata, S. / Tanaka, K. / Yamane, T.
History
DepositionApr 19, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_ref_seq_dif
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.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D3
B: Ubiquitin-conjugating enzyme E2 D3
C: Ubiquitin-conjugating enzyme E2 D3
D: Ubiquitin-conjugating enzyme E2 D3


Theoretical massNumber of molelcules
Total (without water)69,9644
Polymers69,9644
Non-polymers00
Water12,196677
1
A: Ubiquitin-conjugating enzyme E2 D3


Theoretical massNumber of molelcules
Total (without water)17,4911
Polymers17,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin-conjugating enzyme E2 D3


Theoretical massNumber of molelcules
Total (without water)17,4911
Polymers17,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ubiquitin-conjugating enzyme E2 D3


Theoretical massNumber of molelcules
Total (without water)17,4911
Polymers17,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin-conjugating enzyme E2 D3


Theoretical massNumber of molelcules
Total (without water)17,4911
Polymers17,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.998, 44.334, 97.584
Angle α, β, γ (deg.)90.00, 93.36, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: MET / End label comp-ID: MET / Refine code: 5 / Auth seq-ID: 1 - 147 / Label seq-ID: 9 - 155

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Ubiquitin-conjugating enzyme E2 D3 / Ubiquitin-protein ligase D3 / Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2-17 kDa ...Ubiquitin-protein ligase D3 / Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2-17 kDa 3 / E217 / KB 3


Mass: 17490.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61077, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-Na, 10% iso-propanol, 20% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Nov 27, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 46077 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.9
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.249 / % possible all: 83.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QCQ

1qcq


Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.902 / SU B: 4.156 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28222 2178 5 %RANDOM
Rwork0.19949 ---
all0.20376 46077 --
obs0.20376 41012 94.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20.57 Å2
2---0.55 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4867 0 0 677 5544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225012
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9736829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0895603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40423.636220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03915808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4521532
X-RAY DIFFRACTIONr_chiral_restr0.1030.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023872
X-RAY DIFFRACTIONr_nbd_refined0.240.22627
X-RAY DIFFRACTIONr_nbtor_refined0.3210.23400
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2470.2549
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.2138
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.289
X-RAY DIFFRACTIONr_mcbond_it0.9931.53157
X-RAY DIFFRACTIONr_mcangle_it1.61125046
X-RAY DIFFRACTIONr_scbond_it2.53832115
X-RAY DIFFRACTIONr_scangle_it3.7634.51783
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A588medium positional0.350.5
2B588medium positional0.430.5
3C588medium positional0.440.5
4D588medium positional0.290.5
1A586loose positional1.015
2B586loose positional0.965
3C586loose positional0.985
4D586loose positional0.925
1A588medium thermal1.342
2B588medium thermal1.992
3C588medium thermal1.832
4D588medium thermal2.022
1A586loose thermal2.1610
2B586loose thermal2.9310
3C586loose thermal2.7510
4D586loose thermal2.4910
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 151 -
Rwork0.196 2682 -
obs--86 %

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