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- PDB-6nyo: Crystal structure of a human Cdc34-ubiquitin thioester mimetic -

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Basic information

Entry
Database: PDB / ID: 6nyo
TitleCrystal structure of a human Cdc34-ubiquitin thioester mimetic
Components
  • Ubiquitin-conjugating enzyme E2 R2
  • Ubiquitin
KeywordsLIGASE/TRANSFERASE / CONFORMATIONAL CHANGE / THIOESTER / ADENYLATION / THIOESTER TRANSFER / TRANSTHIOESTERIFICATION / ATP-BINDING / UBIQUITIN E2-BINDING / UBIQUITINATION / LIGASE / LIGASE-TRANSFERASE complex
Function / homology
Function and homology information


E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein monoubiquitination / ribosomal large subunit export from nucleus / protein K48-linked ubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / modification-dependent protein catabolic process / protein tag activity / ribosomal large subunit assembly / protein polyubiquitination ...E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein monoubiquitination / ribosomal large subunit export from nucleus / protein K48-linked ubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / modification-dependent protein catabolic process / protein tag activity / ribosomal large subunit assembly / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ribosome biogenesis / cytoplasmic translation / cytosolic large ribosomal subunit / ubiquitin-dependent protein catabolic process / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Ribosomal L40e family ...Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Chem-U94 / Ubiquitin-ribosomal protein eL40A fusion protein / Ubiquitin-conjugating enzyme E2 R2
Similarity search - Component
Biological speciesHomo sapiens (human)
Schizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.502 Å
AuthorsOlsen, S.K. / Williams, K.M. / Atkison, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115568 United States
CitationJournal: Nat Commun / Year: 2019
Title: Structural insights into E1 recognition and the ubiquitin-conjugating activity of the E2 enzyme Cdc34.
Authors: Williams, K.M. / Qie, S. / Atkison, J.H. / Salazar-Arango, S. / Alan Diehl, J. / Olsen, S.K.
History
DepositionFeb 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 R2
E: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6307
Polymers33,9062
Non-polymers7235
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-1 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.585, 55.737, 119.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AE

#1: Protein Ubiquitin-conjugating enzyme E2 R2 / E2 ubiquitin-conjugating enzyme R2 / Ubiquitin carrier protein R2 / Ubiquitin-conjugating enzyme E2- ...E2 ubiquitin-conjugating enzyme R2 / Ubiquitin carrier protein R2 / Ubiquitin-conjugating enzyme E2-CDC34B / Ubiquitin-protein ligase R2


Mass: 23166.207 Da / Num. of mol.: 1 / Fragment: residues 1-202 / Mutation: C93K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2R2, CDC34B, UBC3B / Plasmid: pET29NTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) codon plus
References: UniProt: Q712K3, E2 ubiquitin-conjugating enzyme
#2: Protein Ubiquitin /


Mass: 10740.132 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) codon plus / References: UniProt: P0CH08*PLUS

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Non-polymers , 4 types, 324 molecules

#3: Chemical ChemComp-U94 / 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid


Mass: 442.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21Cl2NO6
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.03 M potassium dihydrogen phosphate, 23% PEG 8,000

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Data collection

DiffractionMean temperature: 108 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 48439 / % possible obs: 99.9 % / Redundancy: 5.67 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.032 / Net I/σ(I): 17.5
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.976 / CC1/2: 0.582 / Rpim(I) all: 0.464

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Processing

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

4mdk


Resolution: 1.502→41.784 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.12
RfactorNum. reflection% reflection
Rfree0.2022 2000 4.14 %
Rwork0.1748 --
obs0.1759 48361 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.502→41.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 46 319 2497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062251
X-RAY DIFFRACTIONf_angle_d0.7863055
X-RAY DIFFRACTIONf_dihedral_angle_d11.1251362
X-RAY DIFFRACTIONf_chiral_restr0.052336
X-RAY DIFFRACTIONf_plane_restr0.006395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5019-1.53950.26191380.25793204X-RAY DIFFRACTION98
1.5395-1.58110.28591420.24083266X-RAY DIFFRACTION100
1.5811-1.62760.23071390.21883248X-RAY DIFFRACTION100
1.6276-1.68020.25881420.21563286X-RAY DIFFRACTION100
1.6802-1.74020.22861430.19023303X-RAY DIFFRACTION100
1.7402-1.80990.21721410.18673267X-RAY DIFFRACTION100
1.8099-1.89230.17351410.17473270X-RAY DIFFRACTION100
1.8923-1.9920.20841430.17083331X-RAY DIFFRACTION100
1.992-2.11680.19721420.16933284X-RAY DIFFRACTION100
2.1168-2.28030.19561420.16183312X-RAY DIFFRACTION100
2.2803-2.50970.20521440.16943334X-RAY DIFFRACTION100
2.5097-2.87280.21641450.17593348X-RAY DIFFRACTION100
2.8728-3.61910.18541450.17023386X-RAY DIFFRACTION100
3.6191-41.80060.18691530.16113522X-RAY DIFFRACTION99
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)
10.3103-0.3466-0.50112.06990.57461.48170.1050.24240.0738-0.3626-0.38120.4935-0.3385-0.9676-0.22390.13340.0331-0.02640.2101-0.00710.167873.1801233.4834258.6227
21.5165-0.8595-0.25880.90510.00560.76770.05350.0566-0.134-0.0353-0.07170.0980.0426-0.0778-0.00340.0913-0.014-0.00510.0781-0.00250.10586.5073222.5284260.7504
30.04250.0777-0.0050.03670.01470.02370.03930.24780.48060.0069-0.1411-0.224-0.02150.4598-0.00010.4567-0.0590.02460.58410.04380.838199.7932242.6792266.0045
40.7104-0.583-0.14250.3495-0.41750.52150.20.22240.39570.0628-0.184-0.2559-0.15780.17990.13940.1219-0.02990.01170.11230.0230.159495.3761230.1236258.443
50.65640.0669-0.27680.8352-0.71661.38730.17330.2169-0.483-0.3431-0.2549-0.35630.47030.8087-0.10920.17490.07420.05690.33270.01860.2259110.0262212.6431258.101
60.5298-0.04170.07210.2591-0.08731.03190.08160.1184-0.4373-0.0185-0.02760.06280.5426-0.0020.03270.2589-0.0056-0.03930.1328-0.00720.239792.7275206.213258.0892
70.7001-0.4001-0.05080.6978-0.29010.26940.11780.30310.2147-0.51610.04570.58850.5137-0.1419-0.01910.3171-0.0574-0.04760.3488-0.06680.292484.2182212.8818245.3019
80.46030.13560.41240.89490.03640.39190.1073-0.02220.2884-0.31690.0677-0.2635-0.3360.00270.01850.16570.02130.00310.1978-0.00020.133891.4045233.4707237.3396
90.5986-0.1263-0.18630.3427-0.03170.18960.17320.36490.4088-0.2476-0.0546-0.25590.053-0.00570.00340.21790.02670.04860.23130.02510.178997.1564231.8173232.5296
100.8978-0.66420.17310.86690.37310.89-0.21260.18290.4141-0.1930.2583-0.1861-0.26210.36890.06750.1558-0.0278-0.00410.18490.04940.1333102.3204236.1102238.281
111.3333-1.3708-0.86412.18180.56210.76160.2071-0.33430.3256-0.0451-0.1062-0.6691-0.22150.15730.14740.107-0.0313-0.0090.15920.05980.0641102.0877234.1006246.5293
120.1360.2735-0.21910.5756-0.54490.5608-0.12360.0376-0.3045-0.2186-0.1329-0.31020.30580.3013-0.03450.17260.03650.00030.23220.02980.181100.4193223.0571241.9065
130.0760.061-0.03670.11770.01990.04270.19630.3298-0.2987-0.3225-0.11170.0960.334-0.132400.26870.0118-0.01630.2098-0.00850.185894.6549222.4734234.0104
140.207-0.14210.18970.0991-0.13570.17810.2282-0.2436-0.3251-0.0404-0.0505-0.07340.1165-0.1340.0110.12090.0043-0.01620.20390.00310.126593.6224231.1104245.2463
150.1662-0.5801-0.04432.11730.09210.11760.09020.15440.09240.5763-0.0698-0.4046-0.51140.89330.03010.1985-0.0881-0.00750.3460.04280.2377102.6118232.7403257.8111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 97 )
3X-RAY DIFFRACTION3chain 'A' and (resid 98 through 109 )
4X-RAY DIFFRACTION4chain 'A' and (resid 110 through 141 )
5X-RAY DIFFRACTION5chain 'A' and (resid 142 through 159 )
6X-RAY DIFFRACTION6chain 'A' and (resid 160 through 178 )
7X-RAY DIFFRACTION7chain 'A' and (resid 179 through 192 )
8X-RAY DIFFRACTION8chain 'E' and (resid -1 through 11 )
9X-RAY DIFFRACTION9chain 'E' and (resid 12 through 22 )
10X-RAY DIFFRACTION10chain 'E' and (resid 23 through 34 )
11X-RAY DIFFRACTION11chain 'E' and (resid 35 through 44 )
12X-RAY DIFFRACTION12chain 'E' and (resid 45 through 56 )
13X-RAY DIFFRACTION13chain 'E' and (resid 57 through 65 )
14X-RAY DIFFRACTION14chain 'E' and (resid 66 through 71 )
15X-RAY DIFFRACTION15chain 'E' and (resid 72 through 76 )

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