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- PDB-4ii3: Crystal structure of S. pombe Ubiquitin activating enzyme 1 (Uba1... -

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Basic information

Entry
Database: PDB / ID: 4ii3
TitleCrystal structure of S. pombe Ubiquitin activating enzyme 1 (Uba1) in complex with ubiquitin and ATP/Mg
Components
  • Ubiquitin-60S ribosomal protein L40
  • Ubiquitin-activating enzyme E1 1
KeywordsLIGASE / Rossmann-like Fold / ubiquitin-like fold / Ubiquitin activating enzyme activity / ATP binding / Ligase activity / ATP/Mg binding / Ubiquitin E2 binding
Function / homology
Function and homology information


Neddylation / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / cytoplasmic translation / cytosolic large ribosomal subunit / ubiquitin-dependent protein catabolic process / protein ubiquitination ...Neddylation / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / cytoplasmic translation / cytosolic large ribosomal subunit / ubiquitin-dependent protein catabolic process / protein ubiquitination / structural constituent of ribosome / DNA damage response / ubiquitin protein ligase binding / 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. / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / 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 / Ubiquitin conserved site / Ubiquitin domain / 3-Layer(bba) Sandwich / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / NAD(P)-binding Rossmann-like Domain / 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
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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: Refinement description / Category: 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: Data collection / Database references ...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 / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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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-activating enzyme E1 1
D: Ubiquitin-60S ribosomal protein L40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,52120
Polymers245,0084
Non-polymers1,51216
Water2,684149
1
A: Ubiquitin-activating enzyme E1 1
B: Ubiquitin-60S ribosomal protein L40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,2209
Polymers122,5042
Non-polymers7167
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-66 kcal/mol
Surface area44460 Å2
MethodPISA
2
C: Ubiquitin-activating enzyme E1 1
D: Ubiquitin-60S ribosomal protein L40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,30011
Polymers122,5042
Non-polymers7969
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-74 kcal/mol
Surface area44600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.500, 113.300, 126.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 111764.047 Da / Num. of mol.: 2 / 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: 10740.132 Da / Num. of mol.: 2 / Fragment: UNP residues 1-76
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 4 types, 165 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium Cacodylate, 0.2M Calcium Acetate, 11.5% Peg8000, 3% 1,5 diaminopentane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 3.4 % / Av σ(I) over netI: 8 / Number: 189068 / Rmerge(I) obs: 0.113 / Χ2: 1.07 / D res high: 2.9 Å / D res low: 50 Å / Num. obs: 55035 / % possible obs: 95.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.245098.610.050.9724.3
4.966.2498.310.1071.2584
4.334.9698.310.0971.1574.1
3.944.3397.610.1151.2023.9
3.653.9496.610.1581.2023.6
3.443.6595.410.2041.1613.4
3.273.4494.110.2621.0133.1
3.123.2792.610.3190.8652.8
33.1290.710.3650.7532.6
2.9389.410.3970.6632.4
ReflectionResolution: 2.9→50 Å / Num. all: 57810 / Num. obs: 55035 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.113 / Χ2: 1.07 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-32.40.39750940.663189.4
3-3.122.60.36551760.753190.7
3.12-3.272.80.31952790.865192.6
3.27-3.443.10.26253851.013194.1
3.44-3.653.40.20454701.161195.4
3.65-3.943.60.15855541.202196.6
3.94-4.333.90.11556131.202197.6
4.33-4.964.10.09756921.157198.3
4.96-6.2440.10757611.258198.3
6.24-504.30.0560110.972198.6

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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: 2.9→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2829 2770 4.8 %Random
Rwork0.2392 ---
all0.2392 58242 --
obs0.2392 55008 94.4 %-
Solvent computationBsol: 11.0687 Å2
Displacement parametersBiso max: 136.35 Å2 / Biso mean: 61.8011 Å2 / Biso min: 2.79 Å2
Baniso -1Baniso -2Baniso -3
1--4.782 Å20 Å20 Å2
2--1.663 Å20 Å2
3---3.119 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16623 0 76 149 16848
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d0.966
X-RAY DIFFRACTIONc_mcbond_it1.1551.5
X-RAY DIFFRACTIONc_scbond_it1.5482
X-RAY DIFFRACTIONc_mcangle_it2.0522
X-RAY DIFFRACTIONc_scangle_it2.5372.5
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 (%)
2.9-30.3812170.38874473469081.5
3-3.120.38672810.36164907518890.6
3.12-3.270.37542790.33495068534792.6
3.27-3.440.3482850.29985156544194.1
3.44-3.650.31832690.26615218548795.4
3.65-3.940.28862620.24155343560596.7
3.94-4.330.25382840.20785378566297.6
4.33-4.960.22873030.18525452575598.4
4.96-6.240.26962930.20675503579698.3
6.24-500.2182970.1835740603798.6
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 DIFFRACTION7cis_peptide.param

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