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- PDB-2fzp: Crystal structure of the USP8 interaction domain of human NRDP1 -

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Basic information

Entry
Database: PDB / ID: 2fzp
TitleCrystal structure of the USP8 interaction domain of human NRDP1
Componentsring finger protein 41 isoform 1
KeywordsLIGASE / E3 Ligase / protein ubiquitination / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of lymphocyte differentiation / interleukin-3 receptor binding / erythropoietin receptor binding / regulation of myeloid cell differentiation / endoplasmic reticulum tubular network / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of reactive oxygen species metabolic process / negative regulation of mitophagy / regulation of MAPK cascade / protein autoubiquitination ...regulation of lymphocyte differentiation / interleukin-3 receptor binding / erythropoietin receptor binding / regulation of myeloid cell differentiation / endoplasmic reticulum tubular network / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of reactive oxygen species metabolic process / negative regulation of mitophagy / regulation of MAPK cascade / protein autoubiquitination / proteasomal protein catabolic process / extrinsic apoptotic signaling pathway / negative regulation of cell migration / Downregulation of ERBB2:ERBB3 signaling / RING-type E3 ubiquitin transferase / receptor tyrosine kinase binding / autophagy / small GTPase binding / positive regulation of reactive oxygen species metabolic process / protein polyubiquitination / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / protein domain specific binding / negative regulation of cell population proliferation / perinuclear region of cytoplasm / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase NRDP1 / NRDP1, C-terminal / USP8 interacting / Zinc finger, SIAH-type / Zinc finger SIAH-type profile. / Zinc finger, C3HC4 type (RING finger) / 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. / Zinc finger, C3HC4 type (RING finger) / 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
E3 ubiquitin-protein ligase NRDP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Amino-terminal Dimerization, NRDP1-Rhodanese Interaction, and Inhibited Catalytic Domain Conformation of the Ubiquitin-specific Protease 8 (USP8).
Authors: Avvakumov, G.V. / Walker, J.R. / Xue, S. / Finerty Jr., P.J. / Mackenzie, F. / Newman, E.M. / Dhe-Paganon, S.
#1: Journal: Mol.Cell.Biol. / Year: 2004
Title: Stabilization of the E3 ubiquitin ligase Nrdp1 by the deubiquitinating enzyme USP8.
Authors: Wu, X. / Yen, L. / Irwin, L. / Sweeney, C. / Carraway, K.L.
#2: Journal: Embo J. / Year: 2004
Title: Nrdp1-mediated degradation of the gigantic IAP, BRUCE, is a novel pathway for triggering apoptosis.
Authors: Qiu, X.B. / Markant, S.L. / Yuan, J. / Goldberg, A.L.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: An RBCC protein implicated in maintenance of steady-state neuregulin receptor levels.
Authors: Diamonti, A.J. / Guy, P.M. / Ivanof, C. / Wong, K. / Sweeney, C. / Carraway, K.L.
#4: Journal: Blood Cells Mol.Dis. / Year: 2001
Title: FLRF, a novel evolutionarily conserved RING finger gene, is differentially expressed in mouse fetal and adult hematopoietic stem cells and progenitors.
Authors: Abdullah, J.M. / Li, X. / Nachtman, R.G. / Jurecic, R.
History
DepositionFeb 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ring finger protein 41 isoform 1


Theoretical massNumber of molelcules
Total (without water)16,1721
Polymers16,1721
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.796, 44.262, 88.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ring finger protein 41 isoform 1 / NRDP1


Mass: 16172.340 Da / Num. of mol.: 1 / Fragment: USP8 interaction Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF41 / Plasmid: PET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q9H4P4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.1 Å3/Da / Density % sol: 41.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.8M (NH4)2SO4, 0.1M HEPES pH 7.0,0.2M NaCl, 0.001M DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.00769 Å
DetectorType: SBC-3 / Detector: CCD / Date: Nov 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00769 Å / Relative weight: 1
ReflectionResolution: 1.87→27.36 Å / Num. all: 12100 / Num. obs: 12100 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.97
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 1.52 / Num. unique all: 1173 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→27.36 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.882 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23163 549 4.8 %RANDOM
Rwork0.16916 ---
obs0.172 10951 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.627 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2--0.52 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.87→27.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 0 99 1146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221067
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.951448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6595133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.21724.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17815184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.452159
X-RAY DIFFRACTIONr_chiral_restr0.1060.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02812
X-RAY DIFFRACTIONr_nbd_refined0.2150.2471
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2752
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.26
X-RAY DIFFRACTIONr_mcbond_it2.0453686
X-RAY DIFFRACTIONr_mcangle_it2.5141078
X-RAY DIFFRACTIONr_scbond_it3.8095435
X-RAY DIFFRACTIONr_scangle_it5.7787370
LS refinement shellResolution: 1.873→1.922 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 43 -
Rwork0.213 663 -
obs--99.58 %
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)
18.812.5347-2.14032.6035-1.91312.701-0.10080.06760.0002-0.11070.0690.02010.01830.10290.03180.05770.00840.00960.0025-0.01830.015623.615549.788928.8869
22.86481.07581.67559.4554-1.4434.00140.05320.2196-0.0176-0.0952-0.0027-0.00630.06480.1255-0.05050.02210.0066-0.01640.0201-0.02190.029930.565346.621329.9534
34.7921-0.60222.309917.41820.34287.5784-0.1095-0.1559-0.03030.53710.0132-0.46350.1520.29120.09630.04660.0145-0.00430.01710.00520.003528.872936.759928.0206
410.6085-12.8552-16.100116.019918.331627.5745-0.28170.2591-0.21360.5311-0.11890.10580.9733-0.30750.40060.04450.0112-0.02480.02290.00880.041429.623726.535520.2231
523.2979-21.30798.114720.7336-6.20117.38990.79631.0086-0.0691-0.9149-0.8756-0.04670.28270.66750.0794-0.0149-0.01790.03610.03650.0027-0.030626.946827.99716.3042
613.75741.7117-11.79156.88294.680115.772-0.11720.59720.0801-0.11780.15340.0791-0.055-1.1157-0.0362-0.00260.0001-0.00940.11240.0336-0.018916.908437.66845.4436
75.9986-0.60565.93680.7618-0.073213.82420.0293-0.05270.05320.0606-0.08410.08080.145-0.32180.05480.0248-0.01960.00970.0189-0.0120.044314.952236.341618.777
81.3853-1.1261-1.21122.3932-2.02337.18170.002-0.0147-0.00650.0281-0.00160.0421-0.0864-0.3776-0.00040.00880.00250.0221-0.0058-0.02350.041721.204543.982723.4995
94.37521.24141.04621.59522.94859.97640.0959-0.09580.43790.0138-0.1920.0231-0.4084-0.39140.09610.0390.0326-0.00450.00050.00390.047121.521443.318113.3797
1010.59370.78258.346215.98084.79677.673-0.2242-0.50550.5283-0.12460.04930.4174-0.3051-0.50.17490.0370.03480.01550.0719-0.0077-0.029923.447943.07816.0021
119.5948-2.6287-0.13195.31326.829417.61450.0474-0.07270.5641-0.2041-0.1216-0.2034-0.4009-0.49730.07420.04610.03440.01570.02140.03830.025929.956541.57512.2407
1215.2077-3.43772.85414.4438-2.72916.94290.09850.588-0.1411-0.26280.06910.00310.1507-0.3236-0.16760.07-0.00620.01610.0505-0.0105-0.028132.600335.3828-1.0083
134.2576-2.49360.29191.5102-0.90110.72530.04730.14680.1596-0.14740.0975-0.19050.01890.2856-0.14480.0479-0.01340.01240.00360.00420.04236.807432.30547.6527
1425.82876.8507-3.71554.869-1.94183.54850.1086-0.1371-0.86070.0676-0.0613-0.21410.2584-0.1823-0.04740.03590.0033-0.01990.01630.00550.007626.628230.367619.2596
157.20043.04090.24383.21640.3710.75380.0456-0.21080.0370.08960.0278-0.19010.04390.0649-0.07340.03290.0179-0.00270.03460.00220.021227.979334.297417.3636
1615.8619-8.239110.37677.2159-5.910617.823-0.07470.10240.97520.0265-0.1707-0.5665-0.91930.26960.24540.057-0.0380.0331-0.0254-0.0060.07738.371641.311112.1031
1731.9843-16.8025-38.791221.688221.9147.48511.2079-0.14921.3553-0.87610.3045-1.0326-1.83220.363-1.51240.0313-0.01880.0218-0.0007-0.04850.057131.575845.267515.4688
185.08158.1225.495413.9657.80076.9254-0.04740.2675-0.1091-0.36880.0083-0.3965-0.31940.38680.03910.045-0.0067-0.01170.0251-0.00030.029226.419138.119913.1151
198.762-1.4971-1.17547.2956-0.83780.3109-0.30520.3152-0.4727-0.46970.35740.17230.2325-0.0382-0.05230.0356-0.019-0.01330.018-0.02420.008822.112828.20428.1873
2019.509-17.672221.738816.0087-19.795253.1618-0.0935-0.626-0.85250.63840.3789-0.28720.45181.0382-0.28530.029-0.01070.0109-0.0210.01730.045527.928722.854816.2622
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA184 - 19111 - 18
2X-RAY DIFFRACTION2AA192 - 19819 - 25
3X-RAY DIFFRACTION3AA199 - 20526 - 32
4X-RAY DIFFRACTION4AA206 - 21033 - 37
5X-RAY DIFFRACTION5AA211 - 21838 - 45
6X-RAY DIFFRACTION6AA219 - 22246 - 49
7X-RAY DIFFRACTION7AA223 - 23750 - 64
8X-RAY DIFFRACTION8AA238 - 24465 - 71
9X-RAY DIFFRACTION9AA245 - 25172 - 78
10X-RAY DIFFRACTION10AA252 - 25579 - 82
11X-RAY DIFFRACTION11AA256 - 26283 - 89
12X-RAY DIFFRACTION12AA263 - 26990 - 96
13X-RAY DIFFRACTION13AA270 - 27597 - 102
14X-RAY DIFFRACTION14AA276 - 281103 - 108
15X-RAY DIFFRACTION15AA282 - 293109 - 120
16X-RAY DIFFRACTION16AA294 - 300121 - 127
17X-RAY DIFFRACTION17AA301 - 304128 - 131
18X-RAY DIFFRACTION18AA305 - 308132 - 135
19X-RAY DIFFRACTION19AA309 - 312136 - 139
20X-RAY DIFFRACTION20AA313 - 317140 - 144

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