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- PDB-7wwp: Crystal structure of human Npl4 -

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Basic information

Entry
Database: PDB / ID: 7wwp
TitleCrystal structure of human Npl4
ComponentsNuclear protein localization protein 4 homolog
KeywordsPROTEIN BINDING / p97 / Ufd1 / Npl4 / edoplasmid reticulum-associated degradation / ubiquitin
Function / homology
Function and homology information


UFD1-NPL4 complex / negative regulation of RIG-I signaling pathway / : / VCP-NPL4-UFD1 AAA ATPase complex / K48-linked polyubiquitin modification-dependent protein binding / negative regulation of type I interferon production / K63-linked polyubiquitin modification-dependent protein binding / nuclear outer membrane-endoplasmic reticulum membrane network / retrograde protein transport, ER to cytosol / Golgi organization ...UFD1-NPL4 complex / negative regulation of RIG-I signaling pathway / : / VCP-NPL4-UFD1 AAA ATPase complex / K48-linked polyubiquitin modification-dependent protein binding / negative regulation of type I interferon production / K63-linked polyubiquitin modification-dependent protein binding / nuclear outer membrane-endoplasmic reticulum membrane network / retrograde protein transport, ER to cytosol / Golgi organization / ubiquitin binding / Translesion Synthesis by POLH / KEAP1-NFE2L2 pathway / Neddylation / ATPase binding / ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Nuclear pore localisation protein Npl4, ubiquitin-like domain / Nuclear pore localisation protein NPL4 / NPL4, zinc-binding putative / Nuclear protein localization protein 4 / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / NPL4 family / Zinc finger domain / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. ...Nuclear pore localisation protein Npl4, ubiquitin-like domain / Nuclear pore localisation protein NPL4 / NPL4, zinc-binding putative / Nuclear protein localization protein 4 / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / NPL4 family / Zinc finger domain / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / MPN domain / MPN domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Nuclear protein localization protein 4 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsNguyen, T.Q. / Le, L.T.M. / Kim, D.H. / Ko, K.S. / Lee, H.T. / Nguyen, Y.T.K. / Kim, H.S. / Han, B.W. / Kang, W. / Yang, J.K.
Funding support Korea, Republic Of, 4items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2014R1A2A2A01006834 Korea, Republic Of
National Research Foundation (NRF, Korea)2017R1D1A1B03035446 Korea, Republic Of
National Research Foundation (NRF, Korea)2019R1F1A106326813 Korea, Republic Of
National Research Foundation (NRF, Korea)2021R1A6A1A10044154 Korea, Republic Of
CitationJournal: Structure / Year: 2022
Title: Structural basis for the interaction between human Npl4 and Npl4-binding motif of human Ufd1.
Authors: Nguyen, T.Q. / My Le, L.T. / Kim, D.H. / Ko, K.S. / Lee, H.T. / Kim Nguyen, Y.T. / Kim, H.S. / Han, B.W. / Kang, W. / Yang, J.K.
History
DepositionFeb 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear protein localization protein 4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6602
Polymers53,5941
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.325, 136.325, 126.875
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3

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Components

#1: Protein Nuclear protein localization protein 4 homolog / Protein NPL4


Mass: 53594.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPLOC4, NPL4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TAT6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
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: 3.18 Å3/Da / Density % sol: 61.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M HEPES (pH6.5), 16 % (w/v) PEG 3350, and 5 % (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 14503 / % possible obs: 99 % / Redundancy: 27.4 % / Biso Wilson estimate: 69.86 Å2 / Rsym value: 0.108 / Net I/σ(I): 22.5
Reflection shellResolution: 3→3.05 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 708 / Rsym value: 1.124

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WWQ

7wwq


Resolution: 2.99→46.44 Å / SU ML: 0.4006 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.819
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2905 736 5.09 %
Rwork0.2309 13716 -
obs0.2339 14452 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.87 Å2
Refinement stepCycle: LAST / Resolution: 2.99→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3357 0 1 0 3358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00883439
X-RAY DIFFRACTIONf_angle_d1.05794672
X-RAY DIFFRACTIONf_chiral_restr0.0556513
X-RAY DIFFRACTIONf_plane_restr0.0092612
X-RAY DIFFRACTIONf_dihedral_angle_d6.9843455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.230.33111360.30042675X-RAY DIFFRACTION99.26
3.23-3.550.31881490.23572689X-RAY DIFFRACTION99.86
3.55-4.060.32281560.22652728X-RAY DIFFRACTION100
4.06-5.120.23121480.20482720X-RAY DIFFRACTION99
5.12-46.440.29851470.23412904X-RAY DIFFRACTION98.71
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)
11.747088998390.442686647646-0.4067909257291.75391184753-0.1704184207792.4105879483-0.01406564673-0.616393616301-0.23483095080.5712322557090.0290314509422-0.01286913178720.2743186268780.109797777525-0.06902555679160.5511713116810.1036009794240.004879308571550.4686008792120.0990646615030.41757335813232.308015709533.13926866933.56054236019
22.023944578361.90051435944-0.7179091890242.17845959116-1.435565545751.66278173811-0.0988848288510.151915991516-0.218970582348-0.03844353896460.02930719490230.06018677416240.249643945094-0.2858431869770.0639171814370.3881906583940.05511824719110.004221027660840.332679476883-0.01966486270820.40155473138520.931438155635.4739038561-11.91410775
33.27093922361.02011631736-0.6344178044161.81220227409-0.8583740917621.612892796850.1677031580070.06193465805520.181980503841-0.163834650804-0.214066522543-0.227970156128-0.01957510649710.2557138089070.06527499900390.4378098639410.1505888434560.02163436934080.279595304417-0.02012537989340.42880671249141.030184708643.6258576887-19.5392038195
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 105 through 274 )105 - 2741 - 134
22chain 'A' and (resid 275 through 427 )275 - 427135 - 284
33chain 'A' and (resid 428 through 563 )428 - 563285 - 420

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