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- PDB-3rz3: Human Cdc34 E2 in complex with CC0651 inhibitor -

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Basic information

Entry
Database: PDB / ID: 3rz3
TitleHuman Cdc34 E2 in complex with CC0651 inhibitor
ComponentsUbiquitin-conjugating enzyme E2 R1
KeywordsLIGASE/LIGASE INHIBITOR / ubiquitin conjugating enzyme domain / E2 domain / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of inclusion body assembly / (E3-independent) E2 ubiquitin-conjugating enzyme / response to growth factor / negative regulation of cAMP-mediated signaling / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / DNA replication initiation / protein K48-linked ubiquitination / cellular response to interferon-beta / Synthesis of active ubiquitin: roles of E1 and E2 enzymes ...positive regulation of inclusion body assembly / (E3-independent) E2 ubiquitin-conjugating enzyme / response to growth factor / negative regulation of cAMP-mediated signaling / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / DNA replication initiation / protein K48-linked ubiquitination / cellular response to interferon-beta / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / G1/S transition of mitotic cell cycle / protein modification process / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of neuron apoptotic process / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / nuclear speck / nucleoplasm / ATP binding / nucleus / cytosol
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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-U94 / Ubiquitin-conjugating enzyme E2 R1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCeccarelli, D.F. / Webb, D.R. / Sicheri, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: An allosteric inhibitor of the human cdc34 ubiquitin conjugating enzyme
Authors: Ceccarelli, D.F. / Tang, X. / Pelletier, B. / Orlicky, S. / Xie, W. / Plantevin, V. / Neculai, D. / Chou, Y.C. / Ogunjimi, A. / Al-Hakim, A. / Varelas, X. / Koszela, J. / Wasney, G.A. / ...Authors: Ceccarelli, D.F. / Tang, X. / Pelletier, B. / Orlicky, S. / Xie, W. / Plantevin, V. / Neculai, D. / Chou, Y.C. / Ogunjimi, A. / Al-Hakim, A. / Varelas, X. / Koszela, J. / Wasney, G.A. / Vedadi, M. / Dhe-Paganon, S. / Cox, S. / Xu, S. / Lopez-Girona, A. / Mercurio, F. / Wrana, J. / Durocher, D. / Meloche, S. / Webb, D.R. / Tyers, M. / Sicheri, F.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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-conjugating enzyme E2 R1
B: Ubiquitin-conjugating enzyme E2 R1
C: Ubiquitin-conjugating enzyme E2 R1
D: Ubiquitin-conjugating enzyme E2 R1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8078
Polymers83,0384
Non-polymers1,7694
Water1,31573
1
A: Ubiquitin-conjugating enzyme E2 R1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2022
Polymers20,7591
Non-polymers4421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin-conjugating enzyme E2 R1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2022
Polymers20,7591
Non-polymers4421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin-conjugating enzyme E2 R1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2022
Polymers20,7591
Non-polymers4421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin-conjugating enzyme E2 R1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2022
Polymers20,7591
Non-polymers4421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.797, 139.525, 216.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein
Ubiquitin-conjugating enzyme E2 R1 / Ubiquitin-conjugating enzyme E2-32 kDa complementing / Ubiquitin-conjugating enzyme E2-CDC34 / ...Ubiquitin-conjugating enzyme E2-32 kDa complementing / Ubiquitin-conjugating enzyme E2-CDC34 / Ubiquitin-protein ligase R1


Mass: 20759.494 Da / Num. of mol.: 4 / Fragment: unp residues 7-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC34, UBCH3, UBE2R1 / Production host: Escherichia coli (E. coli) / References: UniProt: P49427, ubiquitin-protein ligase
#2: 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.: 4 / Source method: obtained synthetically / Formula: C20H21Cl2NO6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.5M NaH2PO4, 1.6M K2HPO4, 0.1 M Imidazole, 0.2 M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2007
RadiationMonochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 37318 / Num. obs: 32630 / % possible obs: 87.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.2-2.28147.6
2.28-2.37165.7
2.37-2.48178.6
2.48-2.61184.4
4.73-30184.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2OB4

2ob4


Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.899 / SU B: 14.26 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25821 1744 5.1 %RANDOM
Rwork0.22088 ---
obs0.22278 32630 84.17 %-
all-53182 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.088 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å20 Å20 Å2
2--2.93 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4853 0 116 73 5042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0225107
X-RAY DIFFRACTIONr_angle_refined_deg2.0811.9766993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.065622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64623.396212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.6815704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2051529
X-RAY DIFFRACTIONr_chiral_restr0.1590.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213972
X-RAY DIFFRACTIONr_mcbond_it1.1811.53147
X-RAY DIFFRACTIONr_mcangle_it2.18125050
X-RAY DIFFRACTIONr_scbond_it2.74231960
X-RAY DIFFRACTIONr_scangle_it4.4264.51943
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 96 -
Rwork0.298 1897 -
obs--67.24 %
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)
13.00481.11520.51030.99760.28560.83690.0925-0.10190.12290.081-0.03720.0862-0.0161-0.0848-0.05540.374-0.0312-0.00850.19910.00650.30759.12-33.831-32.89
23.7403-0.5683-1.00920.03530.62452.42220.0872-0.24160.0944-0.0112-0.0197-0.1052-0.1002-0.0694-0.06750.38010.00250.0250.16070.00380.3637-8.777-14.128-53.169
31.68651.1684-1.46811.0519-0.37563.22190.09730.1990.02770.18610.02820.0224-0.307-0.1021-0.12550.5252-0.09350.03490.180.00820.2783-24.188-50.698-11.408
40.5470.3728-0.88321.98820.4582.159-0.20760.1056-0.0632-0.18030.2595-0.019-0.0053-0.0858-0.05190.5757-0.0450.05570.15770.02160.2771-31.9826.822-20.128
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 181
2X-RAY DIFFRACTION2B7 - 181
3X-RAY DIFFRACTION3C9 - 181
4X-RAY DIFFRACTION4D13 - 181

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