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- PDB-2bkr: NEDD8 NEDP1 complex -

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Basic information

Entry
Database: PDB / ID: 2bkr
TitleNEDD8 NEDP1 complex
Components
  • NEDDYLIN
  • SENTRIN-SPECIFIC PROTEASE 8
KeywordsPROTEIN-BINDING/HYDROLASE / PROTEIN-BINDING-HYDROLASE COMPLEX / UBIQUITIN / HYDROLASE / PROTEASE / THIOL PROTEASE / UBL CONJUGATION PATHWAY / UBIQUITIN-HYDROLASE COMPLEX
Function / homology
Function and homology information


deNEDDylase activity / protein deneddylation / cellular response to camptothecin / protein neddylation / TGF-beta receptor signaling activates SMADs / regulation of proteolysis / regulation of postsynapse assembly / anatomical structure morphogenesis / protein deubiquitination / cysteine-type peptidase activity ...deNEDDylase activity / protein deneddylation / cellular response to camptothecin / protein neddylation / TGF-beta receptor signaling activates SMADs / regulation of proteolysis / regulation of postsynapse assembly / anatomical structure morphogenesis / protein deubiquitination / cysteine-type peptidase activity / post-translational protein modification / protein modification process / Iron uptake and transport / modification-dependent protein catabolic process / protein tag activity / UCH proteinases / Cargo recognition for clathrin-mediated endocytosis / Neddylation / ubiquitin-dependent protein catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / postsynapse / ubiquitin protein ligase binding / glutamatergic synapse / proteolysis / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
NEDD8-specific protease 1/2-like / Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Nedd8-like ubiquitin / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) ...NEDD8-specific protease 1/2-like / Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Nedd8-like ubiquitin / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like protein NEDD8 / Sentrin-specific protease 8
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsShen, L.N. / Liu, H. / Dong, C. / Xirodimas, D. / Naismith, J.H. / Hay, R.T.
CitationJournal: Embo J. / Year: 2005
Title: Structural Basis of Nedd8 Ubiquitin Discrimination by the Deneddylating Enzyme Nedp1
Authors: Shen, L.N. / Liu, H. / Dong, C. / Xirodimas, D. / Naismith, J.H. / Hay, R.T.
History
DepositionFeb 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SENTRIN-SPECIFIC PROTEASE 8
B: NEDDYLIN


Theoretical massNumber of molelcules
Total (without water)32,7342
Polymers32,7342
Non-polymers00
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.638, 74.226, 79.590
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 SENTRIN-SPECIFIC PROTEASE 8 / NEDP1 / SENTRIN/SUMO-SPECIFIC PROTEASE SENP8 / CYSTEINE PROTEASE FKSG8 / PROTEASE / CYSTEINE 2


Mass: 24073.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q96LD8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein NEDDYLIN / NEDD8 / UBIQUITIN-LIKE PROTEIN NEDD8


Mass: 8661.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15843
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: POSSIBLE INVOLVEMENT IN THE RELEASE OF SENTRINS. POSSIBLE ROLE DURING THE EMBRYONIC ...FUNCTION: POSSIBLE INVOLVEMENT IN THE RELEASE OF SENTRINS. POSSIBLE ROLE DURING THE EMBRYONIC DEVELOPMENT AND DIFFERENTIATION OF THE CENTRAL NERVOUS SYSTEM
Sequence detailsEXTRA N-TERMINAL RESIDUE FROM CLONING SER FOR CHAIN B. THE ORIGINAL SAMPLE FOR CHAIN B CONTAINS 82 ...EXTRA N-TERMINAL RESIDUE FROM CLONING SER FOR CHAIN B. THE ORIGINAL SAMPLE FOR CHAIN B CONTAINS 82 RESIDUES INCLUDING GLY GLY LEU ARG GLN (77-81) BUT THESE RESIDUES ARE CLEAVED OFF BY THE PROTEASE DURING THE COMPLEX FORMATION. THESE RESIDUES ARE NOT THEREFORE PART OF OF THE CRYSTALLIZED COMPLEX.

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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: 2.3 Å3/Da / Density % sol: 46.1 %
Crystal growpH: 4.5
Details: CRYSTALS WERE GROWN BY SETTING-DROP METHOD BY MIXING THE NEDP1-NEDD8 COMPLEX (20MG/ML) WITH EQUAL VOLUME OF RESERVOIR SOLUTION CONTAINING 20%PEG8000, 200MM NACL, 100MM PHOSPHATE CITRATE PH4.5, pH 4.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.008
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.9→54 Å / Num. obs: 25411 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.5
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3 / % possible all: 83.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→54.23 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.177 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1307 5.1 %RANDOM
Rwork0.169 ---
obs0.171 24174 97.8 %-
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: 23.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--1.18 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.9→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 0 214 2464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222297
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9453113
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6795286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27425.094106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1215389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.851159
X-RAY DIFFRACTIONr_chiral_restr0.1090.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021741
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21053
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21603
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2184
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3090.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0991.51477
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61622316
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0183927
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4394.5797
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.241 76
Rwork0.2 1423
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)
11.4071-0.2885-0.181.9757-0.37391.3367-0.0058-0.06670.05450.02720.0539-0.1012-0.10420.0333-0.0481-0.1043-0.02640.0024-0.1385-0.02510.098126.0315.21423.515
24.9434-0.2712-1.41751.01710.07391.9424-0.1091-0.0614-0.40030.07830.00860.15940.031-0.20710.1005-0.1357-0.0268-0.0039-0.11710.02790.14825.721-2.33330.193
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 211
2X-RAY DIFFRACTION2B1 - 76

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