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- PDB-5d0i: Structure of RING finger protein 165 -

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Basic information

Entry
Database: PDB / ID: 5d0i
TitleStructure of RING finger protein 165
ComponentsRING finger protein 165
KeywordsMETAL BINDING PROTEIN / RING finger protein
Function / homology
Function and homology information


muscle structure development / forelimb morphogenesis / innervation / positive regulation of BMP signaling pathway / motor neuron axon guidance / protein catabolic process / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin protein ligase activity / protein-containing complex ...muscle structure development / forelimb morphogenesis / innervation / positive regulation of BMP signaling pathway / motor neuron axon guidance / protein catabolic process / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin protein ligase activity / protein-containing complex / zinc ion binding / nucleus
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 / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type ...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 / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ARK2C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 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 30, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Mar 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

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Assembly

Deposited unit
A: RING finger protein 165
B: RING finger protein 165
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3897
Polymers22,0312
Non-polymers3585
Water1,17165
1
A: RING finger protein 165
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2424
Polymers11,0161
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RING finger protein 165
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1463
Polymers11,0161
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.220, 76.220, 103.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein RING finger protein 165 /


Mass: 11015.576 Da / Num. of mol.: 2 / Fragment: UNP residues 255-346
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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.4 Å3/Da / Density % sol: 63.86 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: HEPES, sodium chloride, ammonium sulfate, ethylene glycol
PH range: 6.8-7.5

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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: Nov 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→32.37 Å / Num. obs: 23021 / % possible obs: 94.3 % / Redundancy: 10.8 % / Net I/σ(I): 14.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.9→32.369 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1998 1177 5.12 %Random selection
Rwork0.1734 ---
obs0.1747 22990 93.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→32.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms889 0 9 65 963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008924
X-RAY DIFFRACTIONf_angle_d1.0131222
X-RAY DIFFRACTIONf_dihedral_angle_d14.465336
X-RAY DIFFRACTIONf_chiral_restr0.045141
X-RAY DIFFRACTIONf_plane_restr0.004151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.98650.30221540.27212633X-RAY DIFFRACTION93
1.9865-2.09120.21921470.21822654X-RAY DIFFRACTION93
2.0912-2.22220.20741630.19112716X-RAY DIFFRACTION95
2.2222-2.39370.19541550.17522725X-RAY DIFFRACTION95
2.3937-2.63450.19911310.1712744X-RAY DIFFRACTION94
2.6345-3.01550.19591340.1782776X-RAY DIFFRACTION95
3.0155-3.79820.2051470.17262761X-RAY DIFFRACTION93
3.7982-32.37330.18261460.15272804X-RAY DIFFRACTION90
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)
14.16390.1547-0.44194.8508-2.87053.6399-0.1686-0.4631-0.77480.16880.11290.23680.25640.0813-0.03730.28620.02950.06410.28290.10620.373523.409741.029132.2337
24.9188-0.3031-1.04695.5340.43833.25460.3233-0.78990.91840.3868-0.14120.1046-0.27360.4082-0.08490.3356-0.0790.07380.3406-0.15740.358522.442363.050733.2997
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 259:339 OR RESID 401:402 ) )A259 - 339
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 259:339 OR RESID 401:402 ) )A401 - 402
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 292:344 OR RESID 401:402 ) )B292 - 344
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 292:344 OR RESID 401:402 ) )B401 - 402

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