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- PDB-5um6: Crystal Structure of S. pombe Uba1 in a closed conformation -

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Basic information

Entry
Database: PDB / ID: 5um6
TitleCrystal Structure of S. pombe Uba1 in a closed conformation
ComponentsUbiquitin-activating enzyme E1 1
Keywordsligase/ligase inhibitor / ROSSMANN-LIKE FOLD / UBIQUITIN-LIKE FOLD / UBIQUITIN ACTIVATING ENZYME / ATP BINDING / LIGASE ACTIVITY / ATP/MG BINDING / UBIQUITIN E2 BINDING / LIGASE / TRANSFERASE / ligase-ligase inhibitor complex
Function / homology
Function and homology information


Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA damage response / magnesium ion binding / ATP hydrolysis activity / ATP binding ...Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA damage response / magnesium ion binding / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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-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 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Elongation Factor Tu (Ef-tu); domain 3 / Arc Repressor Mutant, subunit A / 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
2-(decylamino)ethane-1-thiol / Chem-8EA / Ubiquitin-activating enzyme E1 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.794 Å
AuthorsLv, Z. / Yuan, L. / Aldana-Masangkay, G. / Atkison, J.H. / Chen, Y. / Olsen, S.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM115568 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM086171 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Domain alternation and active site remodeling are conserved structural features of ubiquitin E1.
Authors: Lv, Z. / Yuan, L. / Atkison, J.H. / Aldana-Masangkay, G. / Chen, Y. / Olsen, S.K.
History
DepositionJan 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-activating enzyme E1 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,3324
Polymers111,6451
Non-polymers6883
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)145.102, 145.102, 145.102
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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


Mass: 111644.906 Da / Num. of mol.: 1 / Mutation: C593A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: ptr3, SPBC1604.21c, SPBC211.09 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: O94609, E1 ubiquitin-activating enzyme
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-8EA / N-(2-{[(4-chlorophenyl)methyl]disulfanyl}ethyl)decan-1-amine


Mass: 374.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H32ClNS2
#4: Chemical ChemComp-8E7 / 2-(decylamino)ethane-1-thiol


Mass: 217.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H27NS

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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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium Citrate pH5.6-6.0 1.0-1.2 Ammonium Sulfate
PH range: 5.6-6.0

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.08 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.794→50 Å / Num. obs: 25520 / % possible obs: 100 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.2 / Rsym value: 0.051 / Net I/σ(I): 39.2
Reflection shellResolution: 2.79→2.9 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.726 / Num. unique all: 2515 / CC1/2: 0.89 / Rsym value: 0.672 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000v705bdata reduction
HKL-2000v705bdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ii3

4ii3


Resolution: 2.794→40.244 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.41
RfactorNum. reflection% reflection
Rfree0.2395 1292 5.07 %
Rwork0.2057 --
obs0.2075 25461 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.794→40.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7551 0 42 0 7593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037760
X-RAY DIFFRACTIONf_angle_d0.50810494
X-RAY DIFFRACTIONf_dihedral_angle_d15.3774706
X-RAY DIFFRACTIONf_chiral_restr0.041167
X-RAY DIFFRACTIONf_plane_restr0.0041359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.794-2.90590.29041130.27412651X-RAY DIFFRACTION99
2.9059-3.03810.31741490.27572657X-RAY DIFFRACTION100
3.0381-3.19820.2911530.25182630X-RAY DIFFRACTION100
3.1982-3.39850.26691320.23572692X-RAY DIFFRACTION100
3.3985-3.66070.25441520.21512656X-RAY DIFFRACTION100
3.6607-4.02880.2261580.19272685X-RAY DIFFRACTION100
4.0288-4.61110.21721430.16872656X-RAY DIFFRACTION100
4.6111-5.80670.21071520.17832744X-RAY DIFFRACTION100
5.8067-40.24820.20691400.18522798X-RAY DIFFRACTION100
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)
11.4298-0.11160.20460.33580.00230.65580.170.4433-0.2619-0.02610.1313-0.19540.24120.4862-0.0014-0.08560.02980.01830.501-0.2050.2912145.6818173.1186264.2506
21.5424-0.71980.17293.2962-0.46032.4926-0.0429-0.09860.2634-0.1738-0.0465-0.1341-0.69760.34210.04330.5009-0.2022-0.06520.37650.01980.1353119.2938210.1948244.7353
33.5597-1.8529-1.72934.39763.51022.834-0.1679-0.1932-0.14480.0796-0.23470.4401-0.0852-0.38950.21760.70080.05690.01770.7074-0.12620.5505134.2829186.067303.1516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 39:172) or (resseq 261:580) or (resseq 852:899))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 918:1012))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 173:260))

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