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- PDB-5ulk: Crystal Structure of RNF165 in complex with a UbcH5b~Ub conjugate -

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Basic information

Entry
Database: PDB / ID: 5ulk
TitleCrystal Structure of RNF165 in complex with a UbcH5b~Ub conjugate
Components
  • E3 ubiquitin-protein ligase RNF165
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsTRANSFERASE / Open conformation / Backside / Isopeptide-linked
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 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 ...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 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Herpes Virus-1 / 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 / 2-Layer Sandwich / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.38 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 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D2
B: Ubiquitin
C: E3 ubiquitin-protein ligase RNF165
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1535
Polymers36,0223
Non-polymers1312
Water00
1
A: Ubiquitin-conjugating enzyme E2 D2
C: E3 ubiquitin-protein ligase RNF165
hetero molecules

B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)36,1535
Polymers36,0223
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_444-x-1/2,y-1/2,-z-1/21
Buried area2400 Å2
ΔGint-14 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.109, 73.714, 121.559
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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: 17144.525 Da / Num. of mol.: 1 / 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 / 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.: 1
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: Protein E3 ubiquitin-protein ligase RNF165 / RING finger protein 165


Mass: 10300.740 Da / Num. of mol.: 1 / Fragment: residues 292-340 / Mutation: M313A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF165 / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6ZSG1, RING-type E3 ubiquitin transferase
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 2.15 Å3/Da / Density % sol: 42.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 200 mM ammonium nitrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.381→60.779 Å / Num. all: 12481 / Num. obs: 12481 / % possible obs: 97.5 % / Redundancy: 6.9 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Rsym value: 0.068 / Net I/av σ(I): 7.1 / Net I/σ(I): 13.3 / Num. measured all: 85553
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.38-2.515.50.7341861515680.3250.8070.7341.985.2
2.51-2.667.30.5011.51274617410.1980.5390.5013.3100
2.66-2.857.30.2862.71193016310.1130.3080.2865.1100
2.85-3.077.30.1584.71106115200.0630.170.1587.9100
3.07-3.377.20.171031714320.040.1080.112.2100
3.37-3.7770.0679.8890912700.0270.0720.06718.7100
3.77-4.356.80.05311.5781611480.0220.0570.05325.8100
4.35-5.336.50.04911.463959780.020.0540.04929.399.9
5.33-7.536.80.0461352337740.0190.050.04630.2100
7.53-31.51560.04213.925314190.0180.0460.0423491.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
SCALA3.3.21data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→60.78 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 39.609 / SU ML: 0.368 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.416 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 612 4.9 %RANDOM
Rwork0.2065 ---
obs0.2096 11834 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 137.93 Å2 / Biso mean: 83.06 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-9.73 Å20 Å2-0 Å2
2---2.75 Å20 Å2
3----6.98 Å2
Refinement stepCycle: final / Resolution: 2.38→60.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 2 0 2166
Biso mean--71.81 --
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192209
X-RAY DIFFRACTIONr_bond_other_d0.0020.022151
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9752993
X-RAY DIFFRACTIONr_angle_other_deg0.95134974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1485267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20524.12497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73315401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1681515
X-RAY DIFFRACTIONr_chiral_restr0.0810.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212429
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02476
LS refinement shellResolution: 2.381→2.443 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.535 26 -
Rwork0.497 628 -
all-654 -
obs--70.4 %
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)
12.59220.0174-2.60834.15020.779910.3533-0.11340.3828-0.11990.02910.1501-0.11670.0972-0.1563-0.03670.098-0.04620.01850.08-0.05260.1695-19.857-25.112-22.379
29.21681.7468-0.06719.2053-1.83978.38770.3160.2573-0.30150.0751-0.1809-0.13430.40690.2326-0.13510.28090.0326-0.06760.0205-0.02770.1266-2.809-6.947-45.949
35.4241-1.56460.116.7436-0.2698.8849-0.27060.1901-0.1518-0.20170.0764-0.2332-0.0414-0.16570.19420.3684-0.05940.04860.0379-0.05420.0882-24.986-5.775-5.78
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 147
2X-RAY DIFFRACTION2B1 - 73
3X-RAY DIFFRACTION3C293 - 340

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