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- PDB-6o83: S. pombe ubiquitin E1~ubiquitin-AMP tetrahedral intermediate mimic -

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Basic information

Entry
Database: PDB / ID: 6o83
TitleS. pombe ubiquitin E1~ubiquitin-AMP tetrahedral intermediate mimic
Components
  • Ubiquitin-60S ribosomal protein L40
  • Ubiquitin-activating enzyme E1 1
KeywordsLIGASE/PROTEIN BINDING / THIOESTER / ADENYLATION / INHIBITOR / TETRAHEDRAL INTERMEDIATE / LIGASE / NUCLEUS / PHOSPHOPROTEIN / UBL CONJUGATION PATHWAY / ATP-BINDING / NUCLEOTIDE-BINDING / ISOPEPTIDE BOND / LIGASE-PROTEIN BINDING complex
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 / 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 / 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 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Chem-VMX / 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: 3.153 Å
AuthorsHann, Z.S. / 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.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)242,95121
Polymers240,5524
Non-polymers2,39917
Water66737
1
A: Ubiquitin-activating enzyme E1 1
B: Ubiquitin-60S ribosomal protein L40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,41610
Polymers120,2762
Non-polymers1,1418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-67 kcal/mol
Surface area42780 Å2
MethodPISA
2
C: Ubiquitin-activating enzyme E1 1
D: Ubiquitin-60S ribosomal protein L40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,53411
Polymers120,2762
Non-polymers1,2599
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-81 kcal/mol
Surface area43220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.575, 150.522, 172.776
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 , 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: 8511.716 Da / Num. of mol.: 2 / Fragment: residues 1-75
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 , 5 types, 54 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-VMX / 5'-{[(3-aminopropyl)sulfonyl]amino}-5'-deoxyadenosine


Mass: 387.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H21N7O5S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.31 Å3/Da / Density % sol: 62.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 27.3% MPD, 6.6% PEG 8000, 100 mM BIS-TRIS propane pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.15→113.5 Å / Num. obs: 53605 / % possible obs: 96 % / Redundancy: 4.2 % / Biso Wilson estimate: 70.5 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.058 / Rrim(I) all: 0.128 / Net I/σ(I): 10.9
Reflection shellResolution: 3.15→3.27 Å / Redundancy: 3 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 2 / Num. unique obs: 4918 / CC1/2: 0.444 / Rpim(I) all: 0.339 / Rrim(I) all: 0.639 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3211refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4II3

4ii3


Resolution: 3.153→113.493 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 25.92
RfactorNum. reflection% reflection
Rfree0.2523 2646 4.94 %
Rwork0.2027 --
obs0.2052 53583 96.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 289.58 Å2 / Biso mean: 89.1432 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 3.153→113.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16183 0 158 37 16378
Biso mean--68.63 24.35 -
Num. residues----2059
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1532-3.21050.3821420.34342341248386
3.2105-3.27230.34911320.31782590272294
3.2723-3.33910.33891230.29532600272394
3.3391-3.41170.34491360.28032624276095
3.4117-3.4910.31521580.27462574273295
3.491-3.57830.29631480.24892620276895
3.5783-3.67510.28081260.24082630275696
3.6751-3.78320.26051320.24092659279196
3.7832-3.90540.27371280.22332673280196
3.9054-4.0450.2431180.19732722284096
4.045-4.20690.22581220.17642644276695
4.2069-4.39840.21591400.16372744288498
4.3984-4.63030.19841440.15262723286798
4.6303-4.92040.19321500.15972759290999
4.9204-5.30030.24881450.16572754289998
5.3003-5.83370.25961280.1832794292298
5.8337-6.67770.261470.19342745289297
6.6777-8.41280.23351640.18372808297299
8.4128-113.56650.21721630.17532933309698
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)
11.4803-0.6277-0.4121.56230.14040.6432-0.1079-0.1357-0.07050.23010.08240.12790.30320.23380.03580.36480.04720.0440.47740.02840.5373-24.38572.0593-26.4859
20.42730.1380.86251.90481.31173.27340.10310.0583-0.0732-0.28280.07010.22070.62760.1117-0.17570.6309-0.0616-0.0740.77940.06750.6721-29.8857-2.7719-52.7587
33.1114-0.4328-0.4656.7014-3.92284.43810.17330.5982-0.0031-0.7829-0.0744-0.40330.09930.3097-0.09270.54030.02650.02560.4555-0.03180.5633-21.273843.2481-51.2273
42.3328-1.2669-0.10510.68840.05220.4967-0.15440.29860.71150.09560.4186-0.6303-0.33190.98340.07880.2651-0.0071-0.02970.9819-0.01470.717-1.836115.9616-32.9859
50.86290.5178-0.31552.53380.23131.40290.16930.01770.30080.1529-0.29630.277-0.2552-0.06390.14980.39110.0895-0.01390.5864-0.1880.7116-83.76714.0308-7.4365
61.67880.01210.80853.846-0.47033.11290.203-0.105-0.09840.2105-0.3490.2580.1964-0.07750.11930.3233-0.04920.00730.5919-0.05170.5432-84.2429-9.8539-9.1231
70.048-0.12430.33221.22360.16922.7756-0.08060.0996-0.31590.27310.03180.2227-0.1719-0.9064-0.10470.688-0.0853-0.00121.31520.02890.5911-89.54472.404410.7442
80.8406-1.3061-0.28774.10470.49923.3378-0.3858-0.1117-0.28270.41190.29020.63340.4102-1.11660.13490.5402-0.05380.11891.26060.11380.6888-102.3333.5127.431
90.0668-0.1679-0.1210.9757-0.22041.6832-0.0112-0.0839-0.00190.10110.13180.0742-0.07980.1659-0.02680.278-0.07510.04670.7418-0.01070.5896-90.90354.003811.5038
101.6623-2.34772.22374.1135-2.90513.0259-0.02360.255-0.00360.3752-0.1522-0.63130.16510.49540.0350.73330.0597-0.22450.99140.24560.9991-57.3748-29.769114.084
111.38341.35940.56921.44470.40070.48970.3592-0.76020.24250.5855-0.4236-0.5105-0.02750.1866-0.15680.3825-0.2887-0.0960.88210.08390.893-58.51625.2633-1.1012
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 38 through 538 )A38 - 538
2X-RAY DIFFRACTION2chain 'A' and (resid 539 through 898 )A539 - 898
3X-RAY DIFFRACTION3chain 'A' and (resid 899 through 1012 )A899 - 1012
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 75 )B1 - 75
5X-RAY DIFFRACTION5chain 'C' and (resid 37 through 304 )C37 - 304
6X-RAY DIFFRACTION6chain 'C' and (resid 305 through 562 )C305 - 562
7X-RAY DIFFRACTION7chain 'C' and (resid 563 through 637 )C563 - 637
8X-RAY DIFFRACTION8chain 'C' and (resid 638 through 753 )C638 - 753
9X-RAY DIFFRACTION9chain 'C' and (resid 754 through 898 )C754 - 898
10X-RAY DIFFRACTION10chain 'C' and (resid 899 through 1012 )C899 - 1012
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 75 )D1 - 75

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