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- PDB-2ogb: Crystal structure of the C-terminal domain of mouse Nrdp1 -

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Basic information

Entry
Database: PDB / ID: 2ogb
TitleCrystal structure of the C-terminal domain of mouse Nrdp1
ComponentsRING finger protein 41
KeywordsLIGASE / E3 ubiquitin ligase / Receptor-binding region
Function / homology
Function and homology information


regulation of lymphocyte differentiation / small GTPase binding => GO:0031267 / interleukin-3 receptor binding / erythropoietin receptor binding / regulation of myeloid cell differentiation / Downregulation of ERBB2:ERBB3 signaling / endoplasmic reticulum tubular network / Antigen processing: Ubiquitination & Proteasome degradation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of reactive oxygen species metabolic process ...regulation of lymphocyte differentiation / small GTPase binding => GO:0031267 / interleukin-3 receptor binding / erythropoietin receptor binding / regulation of myeloid cell differentiation / Downregulation of ERBB2:ERBB3 signaling / endoplasmic reticulum tubular network / Antigen processing: Ubiquitination & Proteasome degradation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of reactive oxygen species metabolic process / regulation of establishment of cell polarity / negative regulation of mitophagy / protein autoubiquitination / proteasomal protein catabolic process / regulation of MAPK cascade / extrinsic apoptotic signaling pathway / negative regulation of cell migration / RING-type E3 ubiquitin transferase / receptor tyrosine kinase binding / autophagy / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of protein catabolic process / positive regulation of reactive oxygen species metabolic process / positive regulation of DNA-binding transcription factor activity / regulation of gene expression / protein ubiquitination / negative regulation of cell population proliferation / protein domain specific binding / perinuclear region of cytoplasm / zinc ion binding / identical protein binding
Similarity search - Function
E3 ubiquitin-protein ligase NRDP1 / NRDP1, C-terminal / USP8 interacting / Zinc finger, SIAH-type / Zinc finger SIAH-type profile. / TRAF-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. ...E3 ubiquitin-protein ligase NRDP1 / NRDP1, C-terminal / USP8 interacting / Zinc finger, SIAH-type / Zinc finger SIAH-type profile. / TRAF-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
THIOCYANATE ION / E3 ubiquitin-protein ligase NRDP1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsBouyain, S. / Leahy, D.J.
CitationJournal: Protein Sci. / Year: 2007
Title: Structure-based mutagenesis of the substrate-recognition domain of Nrdp1/FLRF identifies the binding site for the receptor tyrosine kinase ErbB3.
Authors: Bouyain, S. / Leahy, D.J.
History
DepositionJan 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RING finger protein 41
B: RING finger protein 41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2575
Polymers29,0152
Non-polymers2423
Water2,198122
1
A: RING finger protein 41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7504
Polymers14,5081
Non-polymers2423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RING finger protein 41


Theoretical massNumber of molelcules
Total (without water)14,5081
Polymers14,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: RING finger protein 41

B: RING finger protein 41


Theoretical massNumber of molelcules
Total (without water)29,0152
Polymers29,0152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1390 Å2
ΔGint-10 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.427, 58.227, 37.387
Angle α, β, γ (deg.)90.00, 101.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RING finger protein 41 /


Mass: 14507.568 Da / Num. of mol.: 2 / Fragment: Nrdp1 C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rnf41 / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8BH75, ubiquitin-protein ligase
#2: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 25% (w/v) polyethylene glycol 8000, 180 mM potassium thiocyanate, 100 mM Tris-HCl, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 27, 2005
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 4.5 % / Av σ(I) over netI: 26.1 / Number: 89260 / Rmerge(I) obs: 0.092 / Χ2: 1.01 / D res high: 2 Å / D res low: 30 Å / Num. obs: 19750 / % possible obs: 86.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.313085.510.0780.9615.3
3.424.3189.510.0740.8835.3
2.993.4291.910.0920.9485.2
2.712.9992.210.1170.9375.2
2.522.7192.310.1431.0085.1
2.372.5293.110.1581.0794.9
2.252.3792.710.1831.1554.2
2.152.259110.2271.1393.7
2.072.1579.710.2751.1362.9
22.0760.910.3061.0942.4
ReflectionResolution: 1.95→30 Å / Num. obs: 20628 / % possible obs: 85.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.092 / Χ2: 0.993 / Net I/σ(I): 25.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.022.30.33613480.983156.6
2.02-2.12.70.28617500.958171.9
2.1-2.23.20.25220920.987187.1
2.2-2.313.90.19322110.995192.1
2.31-2.464.60.16222360.977192.8
2.46-2.654.90.14722480.984192.9
2.65-2.9150.1222250.974191.8
2.91-3.335.10.09522061.006191.6
3.33-4.25.10.07521931.001189.6
4.2-305.20.07721191.026185.1

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se26.5320.2550.4980.1660.92
2Se25.3190.7280.1460.2210.938
3Se41.5820.4330.1490.3780.906
4Se44.520.4460.0560.4690.992
5Se25.730.2680.4490.2280.683
6Se46.6780.3720.1550.4450.924
7Se35.9320.2460.1120.1120.797
8Se30.060.7630.1120.3270.646
9Se54.1880.4130.1820.141.09
10Se53.6510.610.1270.4781.121
11Se43.1390.5660.1290.1850.874
12Se46.2760.2160.0310.390.711
Phasing dmFOM : 0.6 / FOM acentric: 0.6 / FOM centric: 0.5 / Reflection: 15198 / Reflection acentric: 14480 / Reflection centric: 718
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.3-29.680.860.890.6761553481
3.9-6.30.870.890.7320151872143
3.1-3.90.80.810.625532425128
2.8-3.10.640.650.4426342515119
2.4-2.80.480.480.3346064447159
2.2-2.40.320.320.222775268788

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
RESOLVE2.03phasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.879 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.234 972 4.8 %RANDOM
Rwork0.212 ---
obs0.213 20090 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.318 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å20.8 Å2
2--0.46 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 15 122 2097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222010
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.952722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.4635245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26324.4998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.97915346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5931516
X-RAY DIFFRACTIONr_chiral_restr0.0920.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021530
X-RAY DIFFRACTIONr_nbd_refined0.2810.2974
X-RAY DIFFRACTIONr_nbtor_refined0.3250.21428
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2128
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3820.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.217
X-RAY DIFFRACTIONr_mcbond_it1.5391.51237
X-RAY DIFFRACTIONr_mcangle_it2.86521999
X-RAY DIFFRACTIONr_scbond_it5.3343773
X-RAY DIFFRACTIONr_scangle_it8.7974.5723
LS refinement shellResolution: 1.95→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 43 -
Rwork0.307 801 -
obs-844 89.12 %
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)
11.8674-2.0104-1.43294.22532.49973.1592-0.0641-0.18690.06220.08860.0978-0.0424-0.01520.054-0.0338-0.25090.0061-0.0143-0.27960.0009-0.1915-38.629-0.4461.433
23.4371-0.3525-0.70832.4146-0.46624.90360.00160.0488-0.0899-0.1765-0.0038-0.21330.29580.89590.0022-0.22110.0497-0.037-0.0405-0.016-0.187-14.677-21.733-13.227
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA198 - 2967 - 105
21AA306 - 314115 - 123
32BB198 - 2967 - 105
42BB306 - 314115 - 123

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