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- PDB-4ii2: Crystal structure of Ubiquitin activating enzyme 1 (Uba1) in comp... -

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Basic information

Entry
Database: PDB / ID: 4ii2
TitleCrystal structure of Ubiquitin activating enzyme 1 (Uba1) in complex with the Ub E2 Ubc4, ubiquitin, and ATP/Mg
Components
  • Ubiquitin-60S ribosomal protein L40
  • Ubiquitin-activating enzyme E1 1
  • Ubiquitin-conjugating enzyme E2 4
KeywordsLIGASE / ubiquitin / E1 / E2 / Uba1 / Ubc4 / conformational change / thioester / adenylation / thioester transfer (transthioesterification) / ATP-binding / Rossmann-like Fold / ubiquitin-like fold / Ligase activity / ATP/Mg binding / Ubiquitin E2 binding / ubiquitination / nucleus
Function / homology
Function and homology information


Peroxisomal protein import / E3 ubiquitin ligases ubiquitinate target proteins / nuclear SCF ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / SREBP signaling pathway / positive regulation of mitotic metaphase/anaphase transition / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ...Peroxisomal protein import / E3 ubiquitin ligases ubiquitinate target proteins / nuclear SCF ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / SREBP signaling pathway / positive regulation of mitotic metaphase/anaphase transition / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / modification-dependent protein catabolic process / protein polyubiquitination / ubiquitin-protein transferase activity / protein tag activity / ribosome biogenesis / ubiquitin-dependent protein catabolic process / cytoplasmic translation / cytosolic large ribosomal subunit / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / DNA damage response / nucleolus / magnesium ion binding / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2 / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, UFD domain / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily ...Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2 / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, UFD domain / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme e1 C-terminal domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / 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 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Elongation Factor Tu (Ef-tu); domain 3 / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Arc Repressor Mutant, subunit A / NAD(P)-binding Rossmann-like Domain / Ubiquitin-like domain superfamily / Roll / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Ubiquitin-activating enzyme E1 1 / Ubiquitin-ribosomal protein eL40B fusion protein / Ubiquitin-conjugating enzyme E2 4
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOlsen, S.K. / Lima, C.D.
CitationJournal: Mol.Cell / Year: 2013
Title: Structure of a ubiquitin E1-E2 complex: insights to E1-E2 thioester transfer.
Authors: Olsen, S.K. / Lima, C.D.
History
DepositionDec 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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 1.4Nov 6, 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-activating enzyme E1 1
B: Ubiquitin-60S ribosomal protein L40
C: Ubiquitin-conjugating enzyme E2 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,13718
Polymers139,6423
Non-polymers1,49515
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10220 Å2
ΔGint-59 kcal/mol
Surface area49140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.600, 111.200, 181.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Ubiquitin-activating enzyme E1 1 / Poly(A)+ RNA transport protein 3


Mass: 111764.047 Da / Num. of mol.: 1 / Fragment: Uba1, UNP residues 13-1012
Source method: isolated from a genetically manipulated source
Details: N-terminal SMT3 fusion(Ulp-cleavable)
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843
Gene: ptr3, SPBC1604.21c, SPBC211.09, Ubiquitin activating enzyme 1 (Uba1)
Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: O94609, ubiquitin-protein ligase
#2: Protein Ubiquitin-60S ribosomal protein L40


Mass: 9692.942 Da / Num. of mol.: 1 / Fragment: UNP residues 1-76 / Mutation: K6R/K11R/K27R/S28A/K29R/K33R/K48R/S57A/K63R
Source method: isolated from a genetically manipulated source
Details: N-term His tag
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: strain 972 / ATCC 24843 / Gene: ubi2 / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: P0CH07
#3: Protein Ubiquitin-conjugating enzyme E2 4 / Ubiquitin carrier protein 4 / Ubiquitin-protein ligase 4


Mass: 18185.438 Da / Num. of mol.: 1 / Mutation: C21S/C107S
Source method: isolated from a genetically manipulated source
Details: C-term His tag
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843
Gene: SPBC119.02, ubc4, Ubiquitin conjugating enzyme 4 (Ubc4)
Plasmid: pET-29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: P46595, ubiquitin-protein ligase

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Non-polymers , 6 types, 583 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1M Bis Tris Propane, 0.2M Ammonium Sulfate, 22% Peg8000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 84591 / Num. obs: 84422 / % possible obs: 99.8 % / Observed criterion σ(I): -1 / Redundancy: 8.2 % / Rmerge(I) obs: 0.085 / Χ2: 1.07 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.2-2.287.50.458483651.00399.8
2.28-2.377.60.3685.283291.038100
2.37-2.487.80.2867.183811.07999.9
2.48-2.6180.2229.983171.13799.9
2.61-2.778.20.16513.884101.20599.9
2.77-2.998.30.1221783941.029100
2.99-3.298.50.09222.384611.007100
3.29-3.768.60.07825.284631.01799.9
3.76-4.748.50.06529.885371.0799.8
4.74-408.40.06228.187651.11498.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CMM

3cmm


Resolution: 2.2→40 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2536 4253 5 %Random
Rwork0.2135 ---
all0.2135 84419 --
obs0.2135 84266 99.8 %-
Solvent computationBsol: 59.5637 Å2
Displacement parametersBiso max: 148.82 Å2 / Biso mean: 54.5483 Å2 / Biso min: 25.45 Å2
Baniso -1Baniso -2Baniso -3
1-20.884 Å20 Å20 Å2
2---7.163 Å20 Å2
3----13.721 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9491 0 88 568 10147
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.176
X-RAY DIFFRACTIONc_mcbond_it1.3311.5
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_mcangle_it2.1742
X-RAY DIFFRACTIONc_scangle_it3.0412.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.280.37784090.35727932834199.8
2.28-2.370.35713960.322179258321100
2.37-2.480.31614120.27667951836399.9
2.48-2.610.29794200.24837907832799.9
2.61-2.770.2864680.23627933840199.9
2.77-2.990.29054070.234879668373100
2.99-3.290.26444130.224180138426100
3.29-3.760.24144580.201379998457100
3.76-4.740.20944270.17138100852799.9
4.74-400.22364430.18428287873098.9
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6atp.par
X-RAY DIFFRACTION7EDO.par
X-RAY DIFFRACTION8PGO.par
X-RAY DIFFRACTION9cis_peptide.param

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