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- PDB-2qgx: Ubiquitin-conjugating enzyme E2Q -

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Basic information

Entry
Database: PDB / ID: 2qgx
TitleUbiquitin-conjugating enzyme E2Q
ComponentsUbiquitin-conjugating enzyme E2 Q1
KeywordsLIGASE / ubiquitin conjugating protein / UBC / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


prolactin secretion / reproductive system development / fertilization / mating behavior / E2 ubiquitin-conjugating enzyme / suckling behavior / ubiquitin conjugating enzyme activity / embryo implantation / filopodium / protein polyubiquitination ...prolactin secretion / reproductive system development / fertilization / mating behavior / E2 ubiquitin-conjugating enzyme / suckling behavior / ubiquitin conjugating enzyme activity / embryo implantation / filopodium / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / ATP binding / nucleus / cytosol
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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
Ubiquitin-conjugating enzyme E2 Q1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsNeculai, D. / Avvakumov, G.V. / Xue, S. / Walker, J.R. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Neculai, D. / Avvakumov, G.V. / Xue, S. / Walker, J.R. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Sicheri, F. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Mol Cell Proteomics / Year: 2012
Title: A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen.
Authors: Sheng, Y. / Hong, J.H. / Doherty, R. / Srikumar, T. / Shloush, J. / Avvakumov, G.V. / Walker, J.R. / Xue, S. / Neculai, D. / Wan, J.W. / Kim, S.K. / Arrowsmith, C.H. / Raught, B. / Dhe-Paganon, S.
History
DepositionJun 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 Q1
B: Ubiquitin-conjugating enzyme E2 Q1
C: Ubiquitin-conjugating enzyme E2 Q1
D: Ubiquitin-conjugating enzyme E2 Q1


Theoretical massNumber of molelcules
Total (without water)75,4744
Polymers75,4744
Non-polymers00
Water1,62190
1
A: Ubiquitin-conjugating enzyme E2 Q1


Theoretical massNumber of molelcules
Total (without water)18,8681
Polymers18,8681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin-conjugating enzyme E2 Q1


Theoretical massNumber of molelcules
Total (without water)18,8681
Polymers18,8681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin-conjugating enzyme E2 Q1


Theoretical massNumber of molelcules
Total (without water)18,8681
Polymers18,8681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin-conjugating enzyme E2 Q1


Theoretical massNumber of molelcules
Total (without water)18,8681
Polymers18,8681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Ubiquitin-conjugating enzyme E2 Q1
B: Ubiquitin-conjugating enzyme E2 Q1


Theoretical massNumber of molelcules
Total (without water)37,7372
Polymers37,7372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
MethodPISA
6
C: Ubiquitin-conjugating enzyme E2 Q1
D: Ubiquitin-conjugating enzyme E2 Q1


Theoretical massNumber of molelcules
Total (without water)37,7372
Polymers37,7372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.390, 60.390, 172.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Detailsbiological unit is 1/4 asymmetric unit.

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Components

#1: Protein
Ubiquitin-conjugating enzyme E2 Q1 / Ubiquitin-protein ligase Q1 / Ubiquitin carrier protein Q1 / Protein NICE-5


Mass: 18868.420 Da / Num. of mol.: 4 / Fragment: UBC domain; residues 248-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2Q1, NICE5, UBE2Q / Plasmid: pET28a-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7Z7E8, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 22% PEG4000, 0.1 M Tris-Cl, pH7.5, 0.12 M MgCl2, 1 mM DTT, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 15.81 / Number: 122268 / Rmerge(I) obs: 0.039 / D res high: 2.55 Å / Num. obs: 44274 / % possible obs: 96.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obs
5.438.72299.210.028
4.415.499.510.024
3.834.4197.710.03
3.423.8396.610.042
3.133.4299.310.068
2.893.1399.410.117
2.712.8999.610.202
2.552.7189.310.315
ReflectionResolution: 2.55→38.722 Å / Num. obs: 22493 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 63.455 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 15.81
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2.55-2.710.3153.114601657589.3
2.71-2.890.2025.120165695999.6
2.89-3.130.1178.618691642799.4
3.13-3.420.06813.416980586999.3
3.42-3.830.04221.214742524196.6
3.83-4.410.032713051463297.7
4.41-5.40.02431.611535400499.5
5.40.028328878312699.2

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.87 Å57.61 Å
Translation2.87 Å57.61 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZUO

1zuo


Resolution: 2.56→38.722 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.807 / Stereochemistry target values: twin_lsq_f
RfactorNum. reflection% reflection
Rfree0.208 1126 5.01 %
Rwork0.168 21367 -
obs-22493 99.06 %
Solvent computationBsol: 88.392 Å2 / ksol: 0.394 e/Å3
Displacement parametersBiso max: 593.55 Å2 / Biso mean: 84.773 Å2 / Biso min: 23.96 Å2
Baniso -1Baniso -2Baniso -3
1-8.559 Å2-0 Å2-0 Å2
2--8.559 Å2-0 Å2
3----17.118 Å2
Refinement stepCycle: LAST / Resolution: 2.56→38.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5020 0 0 90 5110
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.3381
X-RAY DIFFRACTIONf_bond_d0.0021
X-RAY DIFFRACTIONf_chiral_restr0.0291
X-RAY DIFFRACTIONf_dihedral_angle_d8.6851
X-RAY DIFFRACTIONf_plane_restr0.0011
X-RAY DIFFRACTIONf_nbd_refined4.0751
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)
11.23891.50533.12793.48364.66627.86140.073-0.2427-0.02230.3930.1986-0.23540.5727-0.0235-0.27020.1347-0.0411-0.16080.437-0.03190.2848-37.164213.54318.3474
21.17690.07040.51311.35773.90868.23870.23510.0185-0.1910.25270.1923-0.10240.81990.0206-0.32690.44090.03660.00020.1447-0.01240.2622-43.9213-0.2212-23.6404
31.55141.1124-2.3163.8474-4.79518.03140.13340.56060.1291-0.28650.07480.25010.284-0.5318-0.33160.08070.07990.00290.43950.15470.1858-60.061527.2631-8.0752
41.15010.6697-2.63341.2128-1.4776.88780.22240.04880.13710.0290.28830.07380.268-0.323-0.35130.2484-0.1421-0.01380.20240.02330.2197-68.831414.26824.1603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 159
2X-RAY DIFFRACTION2chain BB1 - 161
3X-RAY DIFFRACTION3chain CC2 - 162
4X-RAY DIFFRACTION4chain DD1 - 160

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