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- PDB-6cdd: Npl4 zinc finger and MPN domains (Chaetomium thermophilum) -

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Basic information

Entry
Database: PDB / ID: 6cdd
TitleNpl4 zinc finger and MPN domains (Chaetomium thermophilum)
ComponentsNpl4 zinc finger
KeywordsPROTEIN BINDING / AAA ATPase cofactor / zinc finger / MPN
Function / homology
Function and homology information


mRNA transport / protein transport / ubiquitin-dependent protein catabolic process / nuclear membrane / perinuclear region of cytoplasm / metal ion binding
Similarity search - Function
NPL4, zinc-binding putative / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / Nuclear protein localization protein 4 / NPL4 family / MPN domain / MPN domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Nuclear protein localization protein 4
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58233712092 Å
AuthorsBodnar, N.O. / Rapoport, T.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM052586 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007753 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4.
Authors: Nicholas O Bodnar / Kelly H Kim / Zhejian Ji / Thomas E Wales / Vladimir Svetlov / Evgeny Nudler / John R Engen / Thomas Walz / Tom A Rapoport /
Abstract: Many polyubiquitinated proteins are extracted from membranes or complexes by the conserved ATPase Cdc48 (in yeast; p97 or VCP in mammals) before proteasomal degradation. Each Cdc48 hexamer contains ...Many polyubiquitinated proteins are extracted from membranes or complexes by the conserved ATPase Cdc48 (in yeast; p97 or VCP in mammals) before proteasomal degradation. Each Cdc48 hexamer contains two stacked ATPase rings (D1 and D2) and six N-terminal (N) domains. Cdc48 binds various cofactors, including the Ufd1-Npl4 heterodimer. Here, we report structures of the Cdc48-Ufd1-Npl4 complex from Chaetomium thermophilum. Npl4 interacts through its UBX-like domain with a Cdc48 N domain, and it uses two Zn-finger domains to anchor the enzymatically inactive Mpr1-Pad1 N-terminal (MPN) domain, homologous to domains found in several isopeptidases, to the top of the D1 ATPase ring. The MPN domain of Npl4 is located above Cdc48's central pore, a position similar to the MPN domain from deubiquitinase Rpn11 in the proteasome. Our results indicate that Npl4 is unique among Cdc48 cofactors and suggest a mechanism for binding and translocation of polyubiquitinated substrates into the ATPase.
History
DepositionFeb 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Npl4 zinc finger
B: Npl4 zinc finger
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4936
Polymers107,2312
Non-polymers2624
Water4,107228
1
A: Npl4 zinc finger
hetero molecules


  • defined by author&software
  • Evidence: microscopy, One copy of this protein forms a heterodimer with another cofactor, Ufd1. This heterodimer in turn associates in a 1:1 manner with the hexameric ATPase Cdc48. There is no ...Evidence: microscopy, One copy of this protein forms a heterodimer with another cofactor, Ufd1. This heterodimer in turn associates in a 1:1 manner with the hexameric ATPase Cdc48. There is no described role for an Npl4 dimer.
  • 53.7 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)53,7473
Polymers53,6161
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Npl4 zinc finger
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7473
Polymers53,6161
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.858, 72.221, 193.543
Angle α, β, γ (deg.)90.000, 96.714, 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-IDDetails
111
212

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLUGLU(chain 'A' and resid 132 through 596)AA132 - 4484 - 320
12THRTHRTHRTHR(chain 'A' and resid 132 through 596)AA458 - 596330 - 468
21PROPROGLUGLUchain 'B'BB132 - 4484 - 320
22THRTHRTHRTHRchain 'B'BB458 - 596330 - 468

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Components

#1: Protein Npl4 zinc finger


Mass: 53615.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0009420 / Plasmid: K27SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0S0B4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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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: 3.81 Å3/Da / Density % sol: 67.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Na/K phosphate pH 7, 9.2% wt/vol poly-gamma-glutamic acid, 0.2 M potassium thiocyanate, 5% propylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.283 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 2.582→96.11 Å / Num. obs: 96089 / % possible obs: 95.15 % / Redundancy: 2.9 % / Biso Wilson estimate: 81.4323024304 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06434 / Rpim(I) all: 0.04406 / Net I/σ(I): 9.82
Reflection shellResolution: 2.582→2.675 Å / Redundancy: 2.7 % / Rmerge(I) obs: 2.031 / Num. unique obs: 7754 / CC1/2: 0.322 / Rpim(I) all: 1.443 / % possible all: 77.79

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.12_2829refinement
PHENIX1.12_2829phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: cryo-EM density

Resolution: 2.58233712092→96.107851877 Å / SU ML: 0.459566972743 / Cross valid method: FREE R-VALUE / σ(F): 1.33489028264 / Phase error: 30.4847135538
RfactorNum. reflection% reflection
Rfree0.228609406897 4617 4.8855591886 %
Rwork0.19152216146 --
obs0.193296283219 94503 95.1528942678 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 105.883376985 Å2
Refinement stepCycle: LAST / Resolution: 2.58233712092→96.107851877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7283 0 4 228 7515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002294968139057487
X-RAY DIFFRACTIONf_angle_d0.52937384996910168
X-RAY DIFFRACTIONf_chiral_restr0.04181418935851098
X-RAY DIFFRACTIONf_plane_restr0.002624535288021335
X-RAY DIFFRACTIONf_dihedral_angle_d16.9327508834529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5823-2.61170.511459568419680.4468432033941916X-RAY DIFFRACTION61.3861386139
2.6117-2.64240.4760451679141630.4412530589282748X-RAY DIFFRACTION87.0774753216
2.6424-2.67460.4195513096511630.416439470372693X-RAY DIFFRACTION84.3224092117
2.6746-2.70850.3797031988991280.3919668996842758X-RAY DIFFRACTION90.3852176636
2.7085-2.74410.394614226361330.3759890713243103X-RAY DIFFRACTION96.9152440851
2.7441-2.78170.3937920833241360.3512651055663068X-RAY DIFFRACTION96.7683479311
2.7817-2.82150.3535493771811760.3336007633183149X-RAY DIFFRACTION99.0762812872
2.8215-2.86360.355913663461740.3057083065863015X-RAY DIFFRACTION97.8220858896
2.8636-2.90830.335136766511600.3029848239113091X-RAY DIFFRACTION97.921686747
2.9083-2.9560.304394359541590.2688285583553074X-RAY DIFFRACTION98.2376177454
2.956-3.0070.3125281930831470.2628352459963148X-RAY DIFFRACTION97.5429248076
3.007-3.06170.2921363152461650.2448619407633049X-RAY DIFFRACTION98.5285101165
3.0617-3.12060.3103214423341890.2533550254393127X-RAY DIFFRACTION98.4268328881
3.1206-3.18430.3353893990161620.2597406681833014X-RAY DIFFRACTION97.5729646697
3.1843-3.25350.3112473707591590.2639647643213035X-RAY DIFFRACTION95.8583433373
3.2535-3.32920.2765765997931300.2385003762333049X-RAY DIFFRACTION96.2167070218
3.3292-3.41250.2698410009141730.2285109710513090X-RAY DIFFRACTION98.3423749247
3.4125-3.50470.2977448453341510.2123545256293071X-RAY DIFFRACTION98.441796517
3.5047-3.60790.263804051991530.1983475427773129X-RAY DIFFRACTION97.6495090747
3.6079-3.72430.2753533342431350.1918886126753134X-RAY DIFFRACTION98.2566877066
3.7243-3.85740.2504515887971520.1744747890453063X-RAY DIFFRACTION97.6609963548
3.8574-4.01190.2018096786221510.1733941548443064X-RAY DIFFRACTION96.8081903041
4.0119-4.19450.1902319002721070.1560879777943067X-RAY DIFFRACTION95.8333333333
4.1945-4.41560.1827838061361140.1299275939873018X-RAY DIFFRACTION94.9954504095
4.4156-4.69230.1520016617871780.1298956745033065X-RAY DIFFRACTION98.2727272727
4.6923-5.05450.1448185150432050.1398935437073031X-RAY DIFFRACTION98.3287754482
5.0545-5.56320.1995421201351790.1573357739463083X-RAY DIFFRACTION97.7524722805
5.5632-6.3680.2211574086821840.1813948715032916X-RAY DIFFRACTION94.0819423369
6.368-8.02240.1962894692611800.1777413544463088X-RAY DIFFRACTION97.8443113772
8.0224-96.17440.2051648237671430.1758272948383030X-RAY DIFFRACTION95.7742227588
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)
10.2731162005990.3018091023310.4199862738320.6418425361260.3559947327350.6836181620040.004053570134430.666007567880.3512492780910.194146442814-0.00106529167310.1105233253190.0367077641445-0.2689225504076.52589023665E-50.7259680391520.1107276572260.1464729347241.161406682130.1901384764010.983060143693-5.2421076987641.772802931913.9209616118
21.609656984260.225057393993-0.3508280053011.646439274410.6292709967371.274006898940.1743349768970.0623940830070.08806240209550.3519299078730.00272712199382-0.1602904837450.0239543980187-0.01406591928788.41949274842E-60.5975483965460.0009485307869470.04236441454770.775642053576-0.001980436071580.76890725350716.599355643632.384953312425.6075846022
30.667092141390.1822898047970.1301594051290.5880322740890.5240465586010.553900122641-0.117169538590.370425584825-0.403882157378-0.04526266522280.10482059145-0.1941146673590.449384954359-0.0811234565564-1.83681564813E-50.6946175264340.03411260999760.07750609676721.17843402629-0.212592993711.0969907494424.019088837510.83636683230.556390941258
40.138068547182-0.194391142567-0.04056387728910.3254150438680.03310739116180.0228440406123-0.07628334985140.329134772605-0.391770481097-0.1122894754750.2105683048940.2655498838690.4548888581440.05288097847744.22646158759E-51.22297991559-0.111333297089-0.1173309776121.05182921684-0.1455142009911.0460539541512.268857777-18.869267119646.8402752123
50.618650980499-0.148014404791-0.2248501478340.2705873581660.1531855783821.41473292912-0.09636189275660.1901864233020.0174403080553-0.02709083895580.01910858917650.0203335059357-0.1951121452820.0476939935647-6.47543236199E-61.02107862624-0.0671326174498-0.08589461347290.7495947014610.02381935577910.79613794616418.59511263132.4466854797163.0310072731
60.41719853027-0.211033064803-0.1218680496730.411826197756-0.3700414790660.645591091492-0.173361776904-0.0166575376252-0.07553275994860.2985913882560.1126677276590.0809409804040.0490829182456-0.0279484174527-2.28543723936E-81.2857613948-0.0483076091695-0.04146033715760.803893438864-0.01667567253440.94534042165319.7288746834-15.185644381791.861939438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 129 through 178 )
2X-RAY DIFFRACTION2chain 'A' and (resid 179 through 497 )
3X-RAY DIFFRACTION3chain 'A' and (resid 498 through 596 )
4X-RAY DIFFRACTION4chain 'B' and (resid 132 through 178 )
5X-RAY DIFFRACTION5chain 'B' and (resid 179 through 497 )
6X-RAY DIFFRACTION6chain 'B' and (resid 498 through 596 )

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