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- PDB-5d0k: Structure of UbE2D2:RNF165:Ub complex -

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Basic information

Entry
Database: PDB / ID: 5d0k
TitleStructure of UbE2D2:RNF165:Ub complex
Components
  • Polyubiquitin-B
  • RING finger protein 165
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsLIGASE / complex / ubiquitin
Function / homology
Function and homology information


muscle structure development / forelimb morphogenesis / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of BMP signaling pathway / motor neuron axon guidance / innervation / 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 ...muscle structure development / forelimb morphogenesis / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of BMP signaling pathway / motor neuron axon guidance / innervation / 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 / protein catabolic process / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein modification process / RING-type E3 ubiquitin transferase / 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 / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase MBR1/2-like / Zinc finger, RING-CH-type / The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. / Ring finger domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. ...E3 ubiquitin-protein ligase MBR1/2-like / Zinc finger, RING-CH-type / The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. / Ring finger domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
Tail fiber / Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase ARK2C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.65 Å
AuthorsWright, J.D. / Day, C.L. / Mace, P.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Secondary ubiquitin-RING docking enhances Arkadia and Ark2C E3 ligase activity.
Authors: Wright, J.D. / Mace, P.D. / Day, C.L.
History
DepositionAug 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Derived calculations
Revision 1.2Dec 30, 2015Group: Database references
Revision 1.3Jan 20, 2016Group: Database references
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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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
C: RING finger protein 165
D: Ubiquitin-conjugating enzyme E2 D2
F: RING finger protein 165
G: Ubiquitin-conjugating enzyme E2 D2
I: RING finger protein 165
J: Ubiquitin-conjugating enzyme E2 D2
L: RING finger protein 165
B: Polyubiquitin-B
E: Polyubiquitin-B
H: Polyubiquitin-B
K: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,85220
Polymers144,32912
Non-polymers5238
Water543
1
A: Ubiquitin-conjugating enzyme E2 D2
C: RING finger protein 165
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2135
Polymers36,0823
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Ubiquitin-conjugating enzyme E2 D2
F: RING finger protein 165
E: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2135
Polymers36,0823
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Ubiquitin-conjugating enzyme E2 D2
I: RING finger protein 165
H: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2135
Polymers36,0823
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Ubiquitin-conjugating enzyme E2 D2
L: RING finger protein 165
K: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2135
Polymers36,0823
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.046, 113.046, 135.667
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein
Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating ...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: 17144.525 Da / Num. of mol.: 4 / Mutation: C21S, C85K, C107S, C111S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli (E. coli) / References: UniProt: P62837, ubiquitin-protein ligase
#2: Protein
RING finger protein 165


Mass: 10360.857 Da / Num. of mol.: 4 / Fragment: UNP residues 255-346 / Mutation: del273-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF165 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZSG1
#3: Protein
Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 4 / Fragment: UNP residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.62 Å3/Da / Density % sol: 66.01 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: MES, sodium chloride, PEG 6000 / PH range: 6

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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 210 / Detector: CCD / Date: May 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.65→43.42 Å / Num. obs: 56144 / % possible obs: 99.7 % / Redundancy: 5.7 % / Net I/σ(I): 12.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.65→35.699 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2377 2825 5.04 %
Rwork0.1919 --
obs0.1943 56056 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→35.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9351 0 8 3 9362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149653
X-RAY DIFFRACTIONf_angle_d1.30313044
X-RAY DIFFRACTIONf_dihedral_angle_d16.2533698
X-RAY DIFFRACTIONf_chiral_restr0.0531461
X-RAY DIFFRACTIONf_plane_restr0.0061679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6503-2.6960.37651480.31482650X-RAY DIFFRACTION99
2.696-2.7450.34471560.30112652X-RAY DIFFRACTION99
2.745-2.79780.33461740.27792644X-RAY DIFFRACTION100
2.7978-2.85490.28281260.26862667X-RAY DIFFRACTION99
2.8549-2.91690.27481380.24952612X-RAY DIFFRACTION99
2.9169-2.98470.28911540.25132686X-RAY DIFFRACTION99
2.9847-3.05930.35891440.24752673X-RAY DIFFRACTION100
3.0593-3.1420.35871350.25132660X-RAY DIFFRACTION100
3.142-3.23440.26331000.23942696X-RAY DIFFRACTION100
3.2344-3.33870.3211080.2312702X-RAY DIFFRACTION100
3.3387-3.4580.2571640.2392642X-RAY DIFFRACTION100
3.458-3.59630.28131580.22412626X-RAY DIFFRACTION100
3.5963-3.75980.30371230.21182726X-RAY DIFFRACTION100
3.7598-3.95780.29721820.19682596X-RAY DIFFRACTION100
3.9578-4.20540.22981200.1742717X-RAY DIFFRACTION100
4.2054-4.52950.15571200.14352699X-RAY DIFFRACTION100
4.5295-4.98420.18961700.14062615X-RAY DIFFRACTION100
4.9842-5.70290.18241260.15872693X-RAY DIFFRACTION100
5.7029-7.17550.19821320.18132676X-RAY DIFFRACTION100
7.1755-35.70220.19551470.16072599X-RAY DIFFRACTION97
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)
12.5477-1.23860.38531.7808-0.25975.34410.18880.2276-0.065-0.15910.0286-0.0390.19520.35240.00190.5917-0.035-0.17980.74850.12080.739782.1348-268.6829534.9412
22.34960.93620.90351.71971.49092.82830.2601-0.5426-0.18580.4999-0.07370.10680.254-0.8868-0.00270.6568-0.065-0.02490.81460.24390.754276.5552-264.1189563.3853
31.02760.18-0.46473.1117-0.33545.04650.0753-0.11450.13450.32340.09630.1024-0.3520.03530.00090.6715-0.0655-0.04930.64060.20960.702790.9137-284.0488586.4565
43.14320.742-1.24861.2282-0.08662.6170.00160.5893-0.1663-0.49480.10020.22160.5726-0.43880.00230.6585-0.0946-0.17710.68230.14090.69692.6862-291.4995558.2937
52.4595-0.9343-0.22551.1953-0.2184.45810.0209-0.14830.06220.10590.14040.0443-0.2167-0.29440.00150.73370.0417-0.20620.62370.07160.72765.3624-259.0367518.6241
61.58140.3568-0.4453.3641-1.5192.4936-0.03050.4082-0.1424-0.56310.09120.10680.79440.33090.00080.78510-0.22490.6348-0.09220.703972.4623-261.4206490.232
72.33091.105-0.16671.40730.26854.88690.00850.2664-0.0178-0.15210.1345-0.109-0.30980.32830.00020.7091-0.0542-0.19420.6525-0.07210.74947.715-258.9797467.1028
81.13670.5904-0.37952.85782.35662.79990.1458-0.3314-0.03120.50350.02840.11880.9309-0.15390.00080.77450.0101-0.21720.66450.07820.707940.6739-261.5286495.5326
92.4006-1.1746-1.07591.08010.00342.5222-0.07810.51860.0782-0.26390.18110.01640.1050.07510.00320.63260.011-0.10630.7507-0.00150.6674109.801-283.5443547.887
101.07870.32890.77442.84970.4912.33390.3845-0.3706-0.0710.4027-0.1408-0.0144-0.2064-0.03860.00210.7367-0.04020.05510.62170.09830.678291.8252-252.5933573.538
112.3193-1.5459-0.89621.4850.41392.42240.0329-0.2648-0.02770.61380.09290.0866-0.0355-0.2263-00.72270.0487-0.05930.70710.09190.72938.6722-242.6373505.7171
121.9790.874-0.68921.5057-0.65642.37570.00450.20880.0245-0.63020.1125-0.008-0.02950.190500.7187-0.0564-0.06010.6749-0.06710.688174.4732-242.3512480.0691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:147 )A0 - 147
2X-RAY DIFFRACTION2( CHAIN C AND ( RESID 257:342 OR RESID 401:401 OR RESID 402:402 ) )C257 - 342
3X-RAY DIFFRACTION2( CHAIN C AND ( RESID 257:342 OR RESID 401:401 OR RESID 402:402 ) )C401
4X-RAY DIFFRACTION2( CHAIN C AND ( RESID 257:342 OR RESID 401:401 OR RESID 402:402 ) )C402
5X-RAY DIFFRACTION3( CHAIN D AND RESID 0:147 )D0 - 147
6X-RAY DIFFRACTION4( CHAIN F AND ( RESID 258:342 OR RESID 401:401 OR RESID 402:402 ) )F258 - 342
7X-RAY DIFFRACTION4( CHAIN F AND ( RESID 258:342 OR RESID 401:401 OR RESID 402:402 ) )F401
8X-RAY DIFFRACTION4( CHAIN F AND ( RESID 258:342 OR RESID 401:401 OR RESID 402:402 ) )F402
9X-RAY DIFFRACTION5( CHAIN G AND RESID 0:147 )G0 - 147
10X-RAY DIFFRACTION6( CHAIN I AND ( RESID 258:342 OR RESID 401:401 OR RESID 402:402 ) )I258 - 342
11X-RAY DIFFRACTION6( CHAIN I AND ( RESID 258:342 OR RESID 401:401 OR RESID 402:402 ) )I401
12X-RAY DIFFRACTION6( CHAIN I AND ( RESID 258:342 OR RESID 401:401 OR RESID 402:402 ) )I402
13X-RAY DIFFRACTION7( CHAIN J AND RESID 0:147 )J0 - 147
14X-RAY DIFFRACTION8( CHAIN L AND ( RESID 258:342 OR RESID 401:401 OR RESID 402:402 ) )L258 - 342
15X-RAY DIFFRACTION8( CHAIN L AND ( RESID 258:342 OR RESID 401:401 OR RESID 402:402 ) )L401
16X-RAY DIFFRACTION8( CHAIN L AND ( RESID 258:342 OR RESID 401:401 OR RESID 402:402 ) )L402
17X-RAY DIFFRACTION9( CHAIN B AND RESID 1:76 )B1 - 76
18X-RAY DIFFRACTION10( CHAIN E AND RESID 1:76 )E1 - 76
19X-RAY DIFFRACTION11( CHAIN H AND RESID 1:76 )H1 - 76
20X-RAY DIFFRACTION12( CHAIN K AND RESID 1:76 )K1 - 76

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