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- PDB-5ulf: Crystal Structure of a UbcH5b~Ub conjugate -

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Basic information

Entry
Database: PDB / ID: 5ulf
TitleCrystal Structure of a UbcH5b~Ub conjugate
Components
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsTRANSFERASE/SIGNALING PROTEIN / Open conformation / Isopeptide-linked / TRANSFERASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


(E3-independent) E2 ubiquitin-conjugating enzyme / symbiont entry into host cell via disruption of host cell glycocalyx / E2 ubiquitin-conjugating enzyme / symbiont entry into host cell via disruption of host cell envelope / virus tail / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment ...(E3-independent) E2 ubiquitin-conjugating enzyme / symbiont entry into host cell via disruption of host cell glycocalyx / E2 ubiquitin-conjugating enzyme / symbiont entry into host cell via disruption of host cell envelope / virus tail / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein modification process / protein polyubiquitination / ubiquitin-protein transferase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin protein ligase activity / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / protein ubiquitination / protein-containing complex / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Pectin lyase fold ...Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Ubiquitin family
Similarity search - Domain/homology
Tail fiber / Ubiquitin-conjugating enzyme E2 D2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsMiddleton, A.J. / Day, C.L. / Wright, J.D.
CitationJournal: To be published
Title: Discovery of new non-covalent ubiquitin binding sites on UbcH5
Authors: Middleton, A.J. / Wright, J.D. / Day, C.L.
History
DepositionJan 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D2
B: Ubiquitin
C: Ubiquitin-conjugating enzyme E2 D2
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0439
Polymers51,5834
Non-polymers4605
Water4,522251
1
A: Ubiquitin-conjugating enzyme E2 D2
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9764
Polymers25,7912
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ubiquitin-conjugating enzyme E2 D2
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0685
Polymers25,7912
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.336, 61.356, 62.824
Angle α, β, γ (deg.)102.840, 91.660, 90.020
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A-3 - 147
2010B-3 - 147
1020C1 - 76
2020D1 - 76

NCS ensembles :
ID
1
2

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 D2 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


Mass: 17214.643 Da / Num. of mol.: 2 / Mutation: C21S, S22R, C85K, C107S, C111S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli)
References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#2: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM bis-Tris pH 5.5, 150 mM ammonium sulfate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→48.52 Å / Num. obs: 38416 / % possible obs: 96.8 % / Redundancy: 3.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.06 / Rrim(I) all: 0.119 / Net I/σ(I): 10 / Num. measured all: 150520 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.6 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.840.928683218940.560.5661.0891.580
8.99-48.520.03411423160.9970.0210.0434.898.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimless0.5.28data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.518 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.471 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 1919 5 %RANDOM
Rwork0.2274 ---
obs0.2291 36494 96.76 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.5 Å / Solvent model: MASK
Displacement parametersBiso max: 59.62 Å2 / Biso mean: 23.499 Å2 / Biso min: 4.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20.25 Å21.01 Å2
2---0.91 Å20.27 Å2
3---1.22 Å2
Refinement stepCycle: final / Resolution: 1.8→48.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3624 0 30 251 3905
Biso mean--35.64 29.07 -
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193855
X-RAY DIFFRACTIONr_bond_other_d0.0020.023738
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9765239
X-RAY DIFFRACTIONr_angle_other_deg0.92838647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0055476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17223.714175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81615681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3361530
X-RAY DIFFRACTIONr_chiral_restr0.0770.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214313
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02867
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A99480.06
12B99480.06
21C46900.08
22D46900.08
LS refinement shellResolution: 1.798→1.845 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 143 -
Rwork0.336 2347 -
all-2490 -
obs--83.75 %
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)
12.2131-1.46580.98952.7678-0.5881.454-0.1039-0.0860.09520.24370.0899-0.1438-0.08650.07630.0140.02810.0027-0.02490.0189-0.01210.055914.53734.8510.562
22.2441.16081.00662.14120.45281.7422-0.09310.07420.1234-0.16740.06360.0409-0.0745-0.1040.02950.01840.0013-0.01040.01860.00220.02227.24465.526-12.302
37.02851.0146-0.13493.0520.25712.9263-0.0061-0.28080.01270.0562-0.03210.103-0.1162-0.13630.03830.04760.0101-0.00160.08070.00410.004527.59857.27316.081
48.4724-0.37750.44113.20360.40522.7275-0.10760.41340.2016-0.130.0718-0.2085-0.140.21810.03580.0676-0.0230.01580.109-0.02420.0554-5.7787.79-27.926
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 147
2X-RAY DIFFRACTION2C-3 - 147
3X-RAY DIFFRACTION3B1 - 76
4X-RAY DIFFRACTION4D1 - 76

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