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- PDB-3cmm: Crystal Structure of the Uba1-Ubiquitin Complex -

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Basic information

Entry
Database: PDB / ID: 3cmm
TitleCrystal Structure of the Uba1-Ubiquitin Complex
Components
  • Ubiquitin-activating enzyme E1 1
  • Ubiquitin
KeywordsLIGASE/PROTEIN BINDING / Ubiquitin / E1 / Uba1 / Protein turnover / ligase / Conformational change / thioester / adenylation / transthioesterification / ATP-binding / Nucleotide-binding / Nucleus / Phosphoprotein / Ubl conjugation pathway / DNA damage / DNA repair / LIGASE-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


: / : / Metalloprotease DUBs / : / : / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Interleukin-1 signaling / Negative regulators of DDX58/IFIH1 signaling ...: / : / Metalloprotease DUBs / : / : / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Interleukin-1 signaling / Negative regulators of DDX58/IFIH1 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Translesion Synthesis by POLH / Translesion synthesis by POLK / Translesion synthesis by POLI / : / UCH proteinases / Regulation of PTEN stability and activity / Aggrephagy / Regulation of TP53 Degradation / Translesion synthesis by REV1 / E1 ubiquitin-activating enzyme / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Endosomal Sorting Complex Required For Transport (ESCRT) / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Peroxisomal protein import / Neddylation / Orc1 removal from chromatin / ubiquitin activating enzyme activity / ABC-family proteins mediated transport / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / MAPK6/MAPK4 signaling / Antigen processing: Ubiquitination & Proteasome degradation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Formation of TC-NER Pre-Incision Complex / Ub-specific processing proteases / Dual incision in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Gap-filling DNA repair synthesis and ligation in TC-NER / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / modification-dependent protein catabolic process / ribosomal large subunit assembly / 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 / 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, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain ...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, conserved site / Ubiquitin-activating enzyme signature 1. / 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
PROLINE / Polyubiquitin / Ubiquitin-activating enzyme E1 1 / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsLee, I. / Schindelin, H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structural insights into E1-catalyzed ubiquitin activation and transfer to conjugating enzymes.
Authors: Lee, I. / Schindelin, H.
History
DepositionMar 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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
C: Ubiquitin-activating enzyme E1 1
B: Ubiquitin
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,4006
Polymers244,1694
Non-polymers2302
Water3,171176
1
A: Ubiquitin-activating enzyme E1 1
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2003
Polymers122,0852
Non-polymers1151
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-9.6 kcal/mol
Surface area47550 Å2
MethodPISA
2
C: Ubiquitin-activating enzyme E1 1
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2003
Polymers122,0852
Non-polymers1151
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-11.7 kcal/mol
Surface area47040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.363, 118.564, 207.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEPHEPHEAA14 - 9055 - 896
21ILEILEPHEPHECB14 - 9055 - 896
12METMETGLYGLYBC1 - 761 - 76
22METMETGLYGLYDD1 - 761 - 76

NCS ensembles :
ID
1
2

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Components

#1: Protein Ubiquitin-activating enzyme E1 1


Mass: 113515.977 Da / Num. of mol.: 2 / Fragment: Residues 10-1024
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBA1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: P22515, ubiquitin-protein ligase
#2: Protein Ubiquitin /


Mass: 8568.769 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBI1, RPL40A / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P61864, UniProt: P0CG63*PLUS
#3: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: L-proline, PEG 5000 MME, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 77706 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 7.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.412 / % possible all: 86.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
PHASERphasing
RefinementResolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.901 / SU B: 25.795 / SU ML: 0.248 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.029 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24687 3899 5 %RANDOM
Rwork0.19077 ---
obs0.19365 73486 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.161 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--0.74 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17051 0 14 176 17241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02217403
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.9723536
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28952152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15525.394825
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.808153100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1191574
X-RAY DIFFRACTIONr_chiral_restr0.0990.22639
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213144
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.27770
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.211833
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2601
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4131.510973
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.737217451
X-RAY DIFFRACTIONr_scbond_it1.22837042
X-RAY DIFFRACTIONr_scangle_it2.0844.56085
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3512medium positional0.50.5
2B304medium positional0.20.5
1A3408loose positional0.75
2B297loose positional0.475
1A3512medium thermal0.442
2B304medium thermal0.382
1A3408loose thermal1.0510
2B297loose thermal0.9610
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 229 -
Rwork0.286 4539 -
obs--84.12 %
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)
12.81820.2077-0.09251.1996-0.36311.44850.0873-0.370.09690.1637-0.05120.0182-0.22020.0187-0.0361-0.0982-0.0396-0.004-0.1361-0.0535-0.175511.212.334-29.882
24.83310.67721.12855.50231.05196.32090.09950.3379-0.63770.00120.04720.08810.40920.0124-0.1467-0.0957-0.0016-0.0411-0.1525-0.0778-0.0542-20.768-7.428-52.814
32.66150.5036-0.46731.8641-0.35411.6196-0.0040.49910.1271-0.24530.03180.1219-0.18670.1081-0.0277-0.0848-0.0329-0.0254-0.08060.0075-0.138117.97316.172-54.321
42.66260.65840.15936.3927-1.00012.05-0.07820.44990.0695-0.6860.1025-0.4454-0.01930.1545-0.0243-0.0853-0.02120.02940.0768-0.0255-0.1763-18.46619.337-76.451
52.72852.3229-0.51063.64170.35078.4079-0.19140.7176-0.1348-0.68690.5592-0.5954-0.23750.7536-0.36780.0486-0.05580.06510.526-0.21280.006231.7084.89-83.232
69.26330.04280.979510.64171.21292.13610.23590.7776-1.5325-0.29240.03960.10410.3420.052-0.2756-0.0291-0.017-0.0325-0.0388-0.19280.25227.234-10.833-53.038
72.5352-0.2628-0.29251.1354-0.12091.28750.07120.30840.1156-0.1311-0.0525-0.0331-0.13940.0473-0.0187-0.0506-0.03020.0073-0.13510.0119-0.194-43.50324.102-44.442
83.7969-0.17440.82865.4484-0.77856.45010.0981-0.1795-0.5480.0120.1224-0.04170.6147-0.0362-0.2205-0.0276-0.0151-0.0086-0.16540.0115-0.012-21.182-11.038-29.448
91.8456-0.1228-0.56951.86410.06531.47960.0137-0.34010.02150.3935-0.0049-0.0066-0.1567-0.0263-0.0087-0.0222-0.03770.0065-0.0783-0.0163-0.1848-50.45821.701-19.911
102.3395-0.3794-3.25742.0797-2.4098.81030.221-0.36390.27220.38330.22540.0271-0.308-0.2373-0.44640.0758-0.05180.08060.30450.06640.0511-71.4666.4133.334
112.4266-0.5651-0.15062.51740.8613.257-0.0906-0.3527-0.13960.48780.16330.01630.09830.0613-0.07270.01270.0001-0.02560.00440.0527-0.1913-15.7177.2710.956
124.8457-0.31260.59416.3775-0.12372.443-0.0056-0.0303-0.9605-0.1580.06680.15110.4265-0.065-0.06110.0026-0.06710.0146-0.082-0.00160.0675-48.594-5.399-29.829
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 1773 - 168
2X-RAY DIFFRACTION1AA263 - 426254 - 417
3X-RAY DIFFRACTION2AA178 - 262169 - 253
4X-RAY DIFFRACTION3AA427 - 596418 - 587
5X-RAY DIFFRACTION3AA862 - 916853 - 907
6X-RAY DIFFRACTION4AA597 - 860588 - 851
7X-RAY DIFFRACTION5AA920 - 1024911 - 1015
8X-RAY DIFFRACTION6BC1 - 761 - 76
9X-RAY DIFFRACTION7CB12 - 1773 - 168
10X-RAY DIFFRACTION7CB263 - 426254 - 417
11X-RAY DIFFRACTION8CB178 - 262169 - 253
12X-RAY DIFFRACTION9CB427 - 596418 - 587
13X-RAY DIFFRACTION9CB862 - 916853 - 907
14X-RAY DIFFRACTION10CB920 - 1024911 - 1015
15X-RAY DIFFRACTION11CB597 - 860588 - 851
16X-RAY DIFFRACTION12DD1 - 761 - 76

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