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- PDB-6jwi: Yeast Npl4 in complex with Lys48-linked diubiquitin -

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Basic information

Entry
Database: PDB / ID: 6jwi
TitleYeast Npl4 in complex with Lys48-linked diubiquitin
Components
  • Nuclear protein localization protein 4
  • Ubiqutin
KeywordsPROTEIN BINDING / UBIQUITIN
Function / homology
Function and homology information


translation at postsynapse / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / Formation of a pool of free 40S subunits / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / IRAK2 mediated activation of TAK1 complex ...translation at postsynapse / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / Formation of a pool of free 40S subunits / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / IRAK2 mediated activation of TAK1 complex / Negative regulation of FLT3 / SRP-dependent cotranslational protein targeting to membrane / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of expression of SLITs and ROBOs / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Major pathway of rRNA processing in the nucleolus and cytosol / Endosomal Sorting Complex Required For Transport (ESCRT) / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Downregulation of ERBB4 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Alpha-protein kinase 1 signaling pathway / Stabilization of p53 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Pexophagy / Regulation of NF-kappa B signaling / Cdc48p-Npl4p-Vms1p AAA ATPase complex / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of BACH1 activity / Doa10p ubiquitin ligase complex / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Recognition of DNA damage by PCNA-containing replication complex / p75NTR recruits signalling complexes / HDR through Homologous Recombination (HRR) / Interferon alpha/beta signaling / Regulation of innate immune responses to cytosolic DNA / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / PINK1-PRKN Mediated Mitophagy / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Termination of translesion DNA synthesis / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Inactivation of CSF3 (G-CSF) signaling / DNA replication termination / Senescence-Associated Secretory Phenotype (SASP) / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR1-induced NF-kappa-B signaling pathway / Josephin domain DUBs / Dual Incision in GG-NER / Downregulation of ERBB2 signaling / Regulation of FZD by ubiquitination / Dual incision in TC-NER / IKK complex recruitment mediated by RIP1 / KEAP1-NFE2L2 pathway / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Oncogene Induced Senescence / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / : / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / Metalloprotease DUBs / Gap-filling DNA repair synthesis and ligation in TC-NER / Degradation of AXIN / Regulation of TNFR1 signaling / Neddylation / EGFR downregulation / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / G2/M Checkpoints
Similarity search - Function
NPL4, zinc-binding putative / Nuclear protein localization protein 4 / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / NPL4 family / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / MPN domain ...NPL4, zinc-binding putative / Nuclear protein localization protein 4 / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / NPL4 family / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / MPN domain / MPN domain profile. / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
trehalose / Ubiqutin subunit 1 / Nuclear protein localization protein 4 / Ubiquitin-ribosomal protein eL40 fusion protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Saccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSato, Y. / Fukai, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16H04750 Japan
Japan Society for the Promotion of Science15H01175 Japan
Japan Society for the Promotion of Science18H05501 Japan
CitationJournal: Nat Commun / Year: 2019
Title: Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4.
Authors: Sato, Y. / Tsuchiya, H. / Yamagata, A. / Okatsu, K. / Tanaka, K. / Saeki, Y. / Fukai, S.
History
DepositionApr 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Ubiqutin
A: Nuclear protein localization protein 4
E: Nuclear protein localization protein 4
G: Ubiqutin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,64931
Polymers125,1274
Non-polymers6,52227
Water3,063170
1
I: Ubiqutin
A: Nuclear protein localization protein 4
G: Ubiqutin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,87218
Polymers71,1873
Non-polymers3,68515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Nuclear protein localization protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,77713
Polymers53,9401
Non-polymers2,83712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.351, 103.103, 99.620
Angle α, β, γ (deg.)90.000, 100.401, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 113 through 181 or resid 189 through 580))A113 - 181
121(chain 'A' and (resid 113 through 181 or resid 189 through 580))A189 - 443
131(chain 'A' and (resid 113 through 181 or resid 189 through 580))A447 - 580
241(chain 'D' and resid 113 through 580)D113 - 181
251(chain 'D' and resid 113 through 580)D189 - 443
261(chain 'D' and resid 113 through 580)D447 - 580
172chain 'G'G2 - 71
282(chain 'I' and resid 1 through 71)I2 - 71

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules IGAE

#1: Protein Ubiqutin


Mass: 8623.726 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ubc, EG216818 / Production host: Escherichia coli (E. coli) / References: UniProt: A5JUZ1, UniProt: P62984*PLUS
#2: Protein Nuclear protein localization protein 4 / HMG-CoA reductase degradation protein 4


Mass: 53939.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: NPL4, HRD4, YBR170C, YBR1231 / Production host: Escherichia coli (E. coli) / References: UniProt: P33755

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Sugars , 1 types, 14 molecules

#3: Polysaccharide
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 183 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.49 Å3/Da / Density % sol: 64.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM Bicine-NaOH (pH 6.5), 18% PEG 3350, 200mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97904 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 55810 / % possible obs: 99.1 % / Redundancy: 19.3 % / Rsym value: 0.252 / Net I/σ(I): 10.3
Reflection shellResolution: 2.55→2.58 Å / Redundancy: 6.1 % / Num. unique obs: 2546 / CC1/2: 0.504 / Rsym value: 1.307 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JWH

6jwh


Resolution: 2.55→48.99 Å / SU ML: 0.3147 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.3071
RfactorNum. reflection% reflection
Rfree0.2257 2831 5.08 %
Rwork0.1905 --
obs0.1924 55737 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 58.12 Å2
Refinement stepCycle: LAST / Resolution: 2.55→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8521 0 425 170 9116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00979131
X-RAY DIFFRACTIONf_angle_d1.214712345
X-RAY DIFFRACTIONf_chiral_restr0.06381424
X-RAY DIFFRACTIONf_plane_restr0.00621524
X-RAY DIFFRACTIONf_dihedral_angle_d16.18426002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.590.31931200.29792354X-RAY DIFFRACTION88.77
2.59-2.640.28861370.2722507X-RAY DIFFRACTION94.29
2.64-2.690.36591380.25952605X-RAY DIFFRACTION97.86
2.69-2.740.30821440.25772606X-RAY DIFFRACTION99.24
2.74-2.80.27511320.25442720X-RAY DIFFRACTION99.58
2.8-2.870.31621450.25462648X-RAY DIFFRACTION99.79
2.87-2.940.25621440.22482656X-RAY DIFFRACTION100
2.94-3.020.23161440.20142640X-RAY DIFFRACTION100
3.02-3.110.23791420.22689X-RAY DIFFRACTION99.93
3.11-3.210.2271460.20462681X-RAY DIFFRACTION100
3.21-3.320.2671440.20142654X-RAY DIFFRACTION100
3.32-3.460.24741440.20362672X-RAY DIFFRACTION99.86
3.46-3.610.24011320.18672654X-RAY DIFFRACTION100
3.61-3.80.19911470.16122656X-RAY DIFFRACTION100
3.8-4.040.20161410.15772680X-RAY DIFFRACTION100
4.04-4.350.17691390.13612702X-RAY DIFFRACTION100
4.35-4.790.15681550.13932665X-RAY DIFFRACTION99.44
4.79-5.480.19671460.16042664X-RAY DIFFRACTION99.93
5.48-6.910.21721400.19542707X-RAY DIFFRACTION99.93
6.91-48.990.22871510.20892746X-RAY DIFFRACTION99.48
Refinement TLS params.Method: refined / Origin x: 10.915840126 Å / Origin y: -21.2792471351 Å / Origin z: 28.5387213383 Å
111213212223313233
T0.267078227512 Å2-0.00742127019569 Å2-6.02208972909E-5 Å2-0.272040068451 Å20.0118402555631 Å2--0.154569998296 Å2
L0.799688498586 °2-0.415267705222 °20.00306696403485 °2-1.18254054277 °2-0.0308048953253 °2--0.313266811932 °2
S0.0909000765111 Å °0.229867940301 Å °0.0367626975864 Å °-0.427484615562 Å °-0.0773110130383 Å °-0.0175243262569 Å °0.000497824023099 Å °-0.00875630157758 Å °-0.0184121893955 Å °
Refinement TLS groupSelection details: all

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