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- PDB-6jwh: Yeast Npl4 zinc finger, MPN and CTD domains -

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Basic information

Entry
Database: PDB / ID: 6jwh
TitleYeast Npl4 zinc finger, MPN and CTD domains
ComponentsNuclear protein localization protein 4
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 / 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
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 / MPN domain / MPN domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Nuclear protein localization protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72000253743 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 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,72512
Polymers53,7651
Non-polymers96011
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-2 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.971, 82.936, 92.123
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 BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P33755
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 4% Tacsimat (pH 6.0), 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.2826 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2826 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 62488 / % possible obs: 96.6 % / Redundancy: 15.9 % / Biso Wilson estimate: 28.0897440339 Å2 / Rsym value: 0.078 / Net I/σ(I): 27.8
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.06 / Num. unique obs: 2842 / CC1/2: 0.583 / Rsym value: 0.431 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.72000253743→47.865103903 Å / SU ML: 0.178323398949 / Cross valid method: FREE R-VALUE / σ(F): 1.34884102565 / Phase error: 22.4243122636
RfactorNum. reflection% reflection
Rfree0.192502304034 2876 4.94727607383 %
Rwork0.162781900936 55257 -
obs0.164296845314 58133 93.050020008 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.0671600852 Å2
Refinement stepCycle: LAST / Resolution: 1.72000253743→47.865103903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3687 0 56 406 4149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009953703536183853
X-RAY DIFFRACTIONf_angle_d1.19752096945201
X-RAY DIFFRACTIONf_chiral_restr0.0606564529853549
X-RAY DIFFRACTIONf_plane_restr0.00577906558779671
X-RAY DIFFRACTIONf_dihedral_angle_d14.57550323181439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72000253743-1.74820.361534800356930.2952353512311692X-RAY DIFFRACTION60.7970027248
1.7482-1.77830.268257359498970.2452097984462001X-RAY DIFFRACTION71.5552523874
1.7783-1.81070.2385156271081000.2232444437342174X-RAY DIFFRACTION76.9543147208
1.8107-1.84550.3069043748641260.21670374922367X-RAY DIFFRACTION84.7670860252
1.8455-1.88320.2404200177931200.2061916955862520X-RAY DIFFRACTION90.6593406593
1.8832-1.92410.2267588914971210.2017582828022665X-RAY DIFFRACTION94.5047489824
1.9241-1.96890.2245923103761470.2011258091122688X-RAY DIFFRACTION96.395783747
1.9689-2.01810.2273218333921330.1815840519282708X-RAY DIFFRACTION96.3050847458
2.0181-2.07270.2064438902831440.1662970725542718X-RAY DIFFRACTION97.247706422
2.0727-2.13370.1830406450781470.1642263407062738X-RAY DIFFRACTION97.7634700102
2.1337-2.20260.2114268867211330.1661447155822765X-RAY DIFFRACTION97.9054054054
2.2026-2.28130.1920728605591290.1704147657832752X-RAY DIFFRACTION97.8600543478
2.2813-2.37260.2212975960181590.1724886518022765X-RAY DIFFRACTION97.8580990629
2.3726-2.48060.244259733781530.1711333938892762X-RAY DIFFRACTION98.5796415286
2.4806-2.61140.2166701829551520.1711047894862754X-RAY DIFFRACTION97.7792732167
2.6114-2.7750.2051053625051560.1687570811322774X-RAY DIFFRACTION98.7196765499
2.775-2.98920.2098206152781510.1664678481992816X-RAY DIFFRACTION99.0981963928
2.9892-3.28990.1908500355751310.161524960672859X-RAY DIFFRACTION99.4015957447
3.2899-3.76580.1530146046081470.1471920750122855X-RAY DIFFRACTION99.4368996356
3.7658-4.74390.1683873723591680.1315171535392877X-RAY DIFFRACTION99.7379626597
4.7439-47.8651039030.1749336845271690.1619123218383007X-RAY DIFFRACTION99.4053208138
Refinement TLS params.Method: refined / Origin x: 43.9825603002 Å / Origin y: 28.5329126466 Å / Origin z: 49.2050662592 Å
111213212223313233
T0.141372870179 Å2-0.00531256454932 Å2-0.0219559899276 Å2-0.149490546545 Å20.0080238117342 Å2--0.153761443831 Å2
L0.971737251668 °2-0.297344187641 °2-0.0866111467212 °2-1.70941350911 °20.457388935911 °2--1.1931139189 °2
S0.0589786040051 Å °0.100421779706 Å °-0.0919302724985 Å °-0.00963908383343 Å °-0.110585379932 Å °-0.0426511789369 Å °-0.0370547601454 Å °0.00870567716587 Å °0.0353742683894 Å °
Refinement TLS groupSelection details: all

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