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- PDB-6jwj: Npl4 in complex with Ufd1 -

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Basic information

Entry
Database: PDB / ID: 6jwj
TitleNpl4 in complex with Ufd1
Components
  • Nuclear protein localization protein 4
  • Peptide from Ubiquitin fusion degradation protein 1
KeywordsPROTEIN BINDING / UBIQUITIN
Function / homology
Function and homology information


Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / DNA replication termination / cytoplasm protein quality control by the ubiquitin-proteasome system / Hrd1p ubiquitin ligase ERAD-L complex / RQC complex / protein localization to vacuole / mitochondria-associated ubiquitin-dependent protein catabolic process / nonfunctional rRNA decay / Translesion Synthesis by POLH ...Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / DNA replication termination / cytoplasm protein quality control by the ubiquitin-proteasome system / Hrd1p ubiquitin ligase ERAD-L complex / RQC complex / protein localization to vacuole / mitochondria-associated ubiquitin-dependent protein catabolic process / nonfunctional rRNA decay / Translesion Synthesis by POLH / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / replisome / ribosome-associated ubiquitin-dependent protein catabolic process / nuclear outer membrane-endoplasmic reticulum membrane network / retrograde protein transport, ER to cytosol / KEAP1-NFE2L2 pathway / Neddylation / protein quality control for misfolded or incompletely synthesized proteins / polyubiquitin modification-dependent protein binding / mRNA transport / ERAD pathway / rescue of stalled ribosome / ubiquitin binding / positive regulation of protein localization to nucleus / ubiquitin-dependent protein catabolic process / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / perinuclear region of cytoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin fusion degradation protein Ufd1-like / Ufd1-like, Nn domain / Ubiquitin fusion degradation protein UFD1 / NPL4, zinc-binding putative / Nuclear protein localization protein 4 / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / NPL4 family / MPN domain / MPN domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Nuclear protein localization protein 4 / Ubiquitin fusion degradation protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear protein localization protein 4
C: Peptide from Ubiquitin fusion degradation protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,42715
Polymers56,2832
Non-polymers1,14413
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-22 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.005, 82.546, 94.1
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Nuclear protein localization protein 4 / HMG-CoA reductase degradation protein 4


Mass: 53765.355 Da / Num. of mol.: 1 / Mutation: E123A,K124A,E125A
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
#2: Protein/peptide Peptide from Ubiquitin fusion degradation protein 1 / UB fusion protein 1 / Polymerase-interacting protein 3


Mass: 2517.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: UFD1, PIP3, YGR048W / Production host: Escherichia coli (E. coli) / References: UniProt: P53044
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 90mM BisTris-HCl (pH 7.5), 19% PEG 3350, 10mM ATP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58001521614→50 Å / Num. obs: 77414 / % possible obs: 99.6 % / Redundancy: 12.4 % / Rsym value: 0.071 / Net I/σ(I): 25.6
Reflection shellResolution: 1.58001521614→1.61 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 0.554 / Num. unique obs: 2809 / CC1/2: 0.496 / % possible all: 70.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JWH

6jwh


Resolution: 1.58→47.5499067827 Å / SU ML: 0.20320713738 / Cross valid method: FREE R-VALUE / σ(F): 1.3378907733 / Phase error: 22.1679964311
RfactorNum. reflection% reflection
Rfree0.205574702564 3905 5.08960573477 %
Rwork0.177654887026 --
obs0.179097620233 76725 96.4718160214 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.6955260253 Å2
Refinement stepCycle: LAST / Resolution: 1.58→47.5499067827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3883 0 68 390 4341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00604153935214039
X-RAY DIFFRACTIONf_angle_d0.9838425851875437
X-RAY DIFFRACTIONf_chiral_restr0.0409494716955568
X-RAY DIFFRACTIONf_plane_restr0.00486295036947699
X-RAY DIFFRACTIONf_dihedral_angle_d13.60927010131504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58001521614-1.59930.4107907091581060.3822474204851717X-RAY DIFFRACTION65.5048508803
1.5993-1.61950.3331098764961040.3591778745441985X-RAY DIFFRACTION74.1042923022
1.6195-1.64080.3476068871041180.3191639499522151X-RAY DIFFRACTION81.3261648746
1.6408-1.66330.3194803987451170.3045766755062340X-RAY DIFFRACTION88.064516129
1.6633-1.68710.2878125364271360.2707777544952528X-RAY DIFFRACTION93.7038339782
1.6871-1.71230.2813794732841350.2721316149232622X-RAY DIFFRACTION97.9396092362
1.7123-1.7390.2897924449991350.2471370198992639X-RAY DIFFRACTION99.3908993192
1.739-1.76750.2594528421541760.2399781403492621X-RAY DIFFRACTION99.9285459093
1.7675-1.7980.2571383224821390.2269384662262680X-RAY DIFFRACTION99.9645390071
1.798-1.83070.2388368510291430.2184675031632662X-RAY DIFFRACTION100
1.8307-1.86590.2646916860181230.2086432728282704X-RAY DIFFRACTION100
1.8659-1.9040.2290693782341450.2036297672552674X-RAY DIFFRACTION99.9645390071
1.904-1.94540.2100383721031490.1922904919732678X-RAY DIFFRACTION99.9646393211
1.9454-1.99070.2231235804181390.1853288222872683X-RAY DIFFRACTION99.9645766915
1.9907-2.04050.1931000029861230.1798568486212706X-RAY DIFFRACTION100
2.0405-2.09560.2030416509561300.1799504826422681X-RAY DIFFRACTION100
2.0956-2.15730.2047187961471600.1678235594392661X-RAY DIFFRACTION100
2.1573-2.22690.1859873408511750.1778615007782673X-RAY DIFFRACTION100
2.2269-2.30650.2278073689641130.1808584847842727X-RAY DIFFRACTION100
2.3065-2.39890.2225780460991260.1750081042982703X-RAY DIFFRACTION100
2.3989-2.5080.211706129211480.1854488416732708X-RAY DIFFRACTION100
2.508-2.64020.2001288658751290.1846418216782721X-RAY DIFFRACTION100
2.6402-2.80560.2067752106151580.1804757419852682X-RAY DIFFRACTION100
2.8056-3.02220.2204922406791400.1836594040542737X-RAY DIFFRACTION100
3.0222-3.32630.1912634578411790.1703815138632692X-RAY DIFFRACTION100
3.3263-3.80750.1787665000731500.1606272374292751X-RAY DIFFRACTION100
3.8075-4.79630.1517696623841490.1350238153442788X-RAY DIFFRACTION100
4.7963-47.54990678270.2166753801111600.158770374982906X-RAY DIFFRACTION99.9673948484
Refinement TLS params.Method: refined / Origin x: 5.41272906256 Å / Origin y: -11.9021059017 Å / Origin z: 4.11072996372 Å
111213212223313233
T0.129490745977 Å2-0.021262830425 Å2-0.0173195400972 Å2-0.153535074987 Å20.0216021538578 Å2--0.171206367724 Å2
L0.569887178606 °2-0.0242737787393 °2-0.172678851825 °2-1.2438885923 °20.473142121639 °2--1.16026472166 °2
S-0.00278323984246 Å °0.023613809919 Å °-0.0378878684576 Å °-0.00248601749449 Å °-0.0249349998173 Å °-0.118421816684 Å °-0.0982271926498 Å °0.0699491863337 Å °0.0394086457828 Å °
Refinement TLS groupSelection details: all

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