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- PDB-6o82: S. pombe ubiquitin E1 complex with a ubiquitin-AMP mimic -

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Basic information

Entry
Database: PDB / ID: 6o82
TitleS. pombe ubiquitin E1 complex with a ubiquitin-AMP mimic
Components
  • Ubiquitin-60S ribosomal protein L40
  • Ubiquitin-activating enzyme E1 1
KeywordsLIGASE/PROTEIN BINDING / THIOESTER / ADENYLATION / INHIBITOR / ACYL-ADENYLATE INTERMEDIATE / ACETYLATION / LIGASE / NUCLEUS / PHOSPHOPROTEIN / UBL CONJUGATION PATHWAY / ATP-BINDING / NUCLEOTIDE-BINDING / CYTOPLASM / ISOPEPTIDE BOND / LIGASE-PROTEIN BINDING 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 / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / ubiquitin-dependent protein catabolic process / cytosolic large ribosomal subunit / cytoplasmic translation ...Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / ubiquitin-dependent protein catabolic process / cytosolic large ribosomal subunit / cytoplasmic translation / 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, UFD 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, UFD 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-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / 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 / Elongation Factor Tu (Ef-tu); domain 3 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5'-deoxy-5'-(sulfamoylamino)adenosine / PYROPHOSPHATE 2- / 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: 2.604 Å
AuthorsOlsen, S.K. / Lima, C.D.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079196 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118080 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM100477 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA008748 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structural basis for adenylation and thioester bond formation in the ubiquitin E1.
Authors: Hann, Z.S. / Ji, C. / Olsen, S.K. / Lu, X. / Lux, M.C. / Tan, D.S. / Lima, C.D.
History
DepositionMar 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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_conn_type
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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id
Revision 1.5Oct 30, 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-activating enzyme E1 1
D: Ubiquitin-60S ribosomal protein L40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,67022
Polymers240,5584
Non-polymers2,11218
Water5,206289
1
A: Ubiquitin-activating enzyme E1 1
B: Ubiquitin-60S ribosomal protein L40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,56713
Polymers120,2792
Non-polymers1,28811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-93 kcal/mol
Surface area45190 Å2
MethodPISA
2
C: Ubiquitin-activating enzyme E1 1
D: Ubiquitin-60S ribosomal protein L40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,1039
Polymers120,2792
Non-polymers8247
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-55 kcal/mol
Surface area44840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.061, 114.616, 125.967
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: residues 13-1012
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) / References: UniProt: O94609, E1 ubiquitin-activating enzyme
#2: Protein Ubiquitin-60S ribosomal protein L40


Mass: 8514.718 Da / Num. of mol.: 2 / Fragment: residues 1-76 / Mutation: R74C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: uep1, ubi2, SPAC1805.12c / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CH07

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Non-polymers , 6 types, 307 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-JZU / 5'-deoxy-5'-(sulfamoylamino)adenosine


Mass: 345.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N7O5S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 3350, 0.15 M MgSO4, 5 mM MgCl2, 1 mM pyrophosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→42.39 Å / Num. obs: 81217 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 48.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.041 / Rrim(I) all: 0.109 / Net I/σ(I): 12.8
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 7 % / Rmerge(I) obs: 0.597 / Num. unique obs: 7917 / CC1/2: 0.848 / Rpim(I) all: 0.242 / Rrim(I) all: 0.645 / % possible all: 98.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3211refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CMM

3cmm


Resolution: 2.604→42.388 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 22.97
RfactorNum. reflection% reflection
Rfree0.2303 4073 5.02 %
Rwork0.1968 --
obs0.1985 81155 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 182.54 Å2 / Biso mean: 67.3814 Å2 / Biso min: 18.99 Å2
Refinement stepCycle: final / Resolution: 2.604→42.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16599 0 120 289 17008
Biso mean--66.1 43.84 -
Num. residues----2113
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6041-2.63470.28441430.26082525266896
2.6347-2.66680.30451470.255926212768100
2.6668-2.70060.29311510.258226232774100
2.7006-2.73610.30751190.256926662785100
2.7361-2.77360.26811460.239925852731100
2.7736-2.81320.26261200.234426432763100
2.8132-2.85520.26671200.228726782798100
2.8552-2.89980.29541430.234726352778100
2.8998-2.94730.26161290.235826522781100
2.9473-2.99810.28461440.242426152759100
2.9981-3.05260.27951360.237226132749100
3.0526-3.11130.26521590.237326602819100
3.1113-3.17480.31851530.243425832736100
3.1748-3.24380.26141630.245726452808100
3.2438-3.31930.27851650.229126352800100
3.3193-3.40220.25951420.220626292771100
3.4022-3.49420.24351260.213526722798100
3.4942-3.5970.24761360.199926622798100
3.597-3.7130.22441200.198826882808100
3.713-3.84560.23651420.187326292771100
3.8456-3.99950.22371140.173326722786100
3.9995-4.18130.17361600.1626702830100
4.1813-4.40160.18781220.153126802802100
4.4016-4.6770.17471470.142326792826100
4.677-5.03760.18121310.152526992830100
5.0376-5.54360.1931540.170426892843100
5.5436-6.34340.24181530.193327082861100
6.3434-7.98330.21631350.201227512886100
7.9833-42.39320.20471530.186928753028100
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)
11.65530.23930.44611.02150.3831.3596-0.1580.25390.2837-0.46370.04270.0873-0.54830.1097-0.11490.6053-0.0486-0.05040.17360.05180.398724.617238.8931-9.7187
21.52480.717-0.07680.40440.51371.03080.0827-0.520.2218-0.0018-0.26540.23710.0358-0.30840.17050.40990.0231-0.03980.4653-0.08120.5182-3.841620.608112.7263
30.3866-0.33960.02352.2790.76460.7949-0.04720.0312-0.1684-0.2170.05340.24370.0224-0.071-0.02070.3791-0.03550.01880.263-0.02480.474426.1577-1.2197-11.771
41.8896-0.37090.57711.4577-0.22692.82250.0076-0.1918-0.2224-0.06870.053-0.370.16750.3899-0.050.3963-0.01180.01390.202-0.01190.426137.64522.64287.9487
51.06030.03460.31851.01540.16211.55060.3688-0.9202-0.80410.2848-0.264-0.49210.53620.1399-0.06850.7065-0.0881-0.28461.02390.44120.901154.142113.172955.5066
61.4480.299-0.40320.6149-0.07820.52320.2652-0.91620.13340.2884-0.24110.2295-0.0085-0.3189-0.0370.6212-0.17340.02241.2669-0.06450.535622.589633.851459.0106
71.37130.52680.15431.0427-0.46061.7896-0.0091-0.5450.22460.0375-0.0921-0.1225-0.1958-0.2383-0.05890.37120.0132-0.01720.4682-0.08050.392239.971842.789233.457
82.77371.20230.70491.0125-0.2233.88930.2897-0.134-0.6848-0.2256-0.1477-0.30460.9613-0.1293-0.11080.6058-0.0087-0.11590.42240.11530.617740.579914.1332.0799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 538 )A14 - 538
2X-RAY DIFFRACTION2chain 'A' and (resid 539 through 855 )A539 - 855
3X-RAY DIFFRACTION3chain 'A' and (resid 856 through 1012 )A856 - 1012
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 76 )B1 - 76
5X-RAY DIFFRACTION5chain 'C' and (resid 14 through 448 )C14 - 448
6X-RAY DIFFRACTION6chain 'C' and (resid 449 through 833 )C449 - 833
7X-RAY DIFFRACTION7chain 'C' and (resid 834 through 1012 )C834 - 1012
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 76 )D1 - 76

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