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- PDB-7mo1: Crystal Structure of the ZnF1 of Nucleoporin NUP153 in complex wi... -

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Entry
Database: PDB / ID: 7mo1
TitleCrystal Structure of the ZnF1 of Nucleoporin NUP153 in complex with Ran-GDP
Components
  • GTP-binding nuclear protein Ran
  • Nuclear pore complex protein Nup153
KeywordsTRANSPORT PROTEIN / nuclear pore complex component / nucleocytoplasmic transport / complex (small GTPase-nuclear protein)
Function / homology
Function and homology information


nucleoplasmic side of nuclear pore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins ...nucleoplasmic side of nuclear pore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / Transcriptional regulation by small RNAs / Regulation of Glucokinase by Glucokinase Regulatory Protein / SUMOylation of DNA damage response and repair proteins / negative regulation of RNA export from nucleus / Regulation of HSF1-mediated heat shock response / annulate lamellae / nuclear pore complex assembly / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / manchette / nuclear inclusion body / cellular response to mineralocorticoid stimulus / nuclear pore nuclear basket / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / structural constituent of nuclear pore / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / RNA export from nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / DNA metabolic process / nuclear localization sequence binding / dynein intermediate chain binding / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / mRNA transport / viral process / ribosomal subunit export from nucleus / nuclear pore / ribosomal small subunit export from nucleus / protein-membrane adaptor activity / protein export from nucleus / centriole / nuclear periphery / mitotic spindle organization / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / molecular condensate scaffold activity / recycling endosome / G protein activity / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / actin cytoskeleton organization / midbody / double-stranded DNA binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / nuclear membrane / amyloid fibril formation / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / small GTPase Ran family profile. / Ran GTPase / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. ...Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / small GTPase Ran family profile. / Ran GTPase / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Nuclear pore complex protein Nup153 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsBley, C.J. / Nie, S. / Mobbs, G.W. / Petrovic, S. / Gres, A.T. / Liu, X. / Mukherjee, S. / Harvey, S. / Huber, F.M. / Lin, D.H. ...Bley, C.J. / Nie, S. / Mobbs, G.W. / Petrovic, S. / Gres, A.T. / Liu, X. / Mukherjee, S. / Harvey, S. / Huber, F.M. / Lin, D.H. / Brown, B. / Tang, A.W. / Rundlet, E.J. / Correia, A.R. / Chen, S. / Regmi, S.G. / Stevens, T.A. / Jette, C.A. / Dasso, M. / Patke, A. / Palazzo, A.F. / Kossiakoff, A.A. / Hoelz, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117360 United States
Howard Hughes Medical Institute (HHMI)55108534 United States
Heritage Medical Research Institute United States
CitationJournal: Science / Year: 2022
Title: Architecture of the cytoplasmic face of the nuclear pore.
Authors: Christopher J Bley / Si Nie / George W Mobbs / Stefan Petrovic / Anna T Gres / Xiaoyu Liu / Somnath Mukherjee / Sho Harvey / Ferdinand M Huber / Daniel H Lin / Bonnie Brown / Aaron W Tang / ...Authors: Christopher J Bley / Si Nie / George W Mobbs / Stefan Petrovic / Anna T Gres / Xiaoyu Liu / Somnath Mukherjee / Sho Harvey / Ferdinand M Huber / Daniel H Lin / Bonnie Brown / Aaron W Tang / Emily J Rundlet / Ana R Correia / Shane Chen / Saroj G Regmi / Taylor A Stevens / Claudia A Jette / Mary Dasso / Alina Patke / Alexander F Palazzo / Anthony A Kossiakoff / André Hoelz /
Abstract: INTRODUCTION The subcellular compartmentalization of eukaryotic cells requires selective transport of folded proteins and protein-nucleic acid complexes. Embedded in nuclear envelope pores, which are ...INTRODUCTION The subcellular compartmentalization of eukaryotic cells requires selective transport of folded proteins and protein-nucleic acid complexes. Embedded in nuclear envelope pores, which are generated by the circumscribed fusion of the inner and outer nuclear membranes, nuclear pore complexes (NPCs) are the sole bidirectional gateways for nucleocytoplasmic transport. The ~110-MDa human NPC is an ~1000-protein assembly that comprises multiple copies of ~34 different proteins, collectively termed nucleoporins. The symmetric core of the NPC is composed of an inner ring encircling the central transport channel and outer rings formed by Y‑shaped coat nucleoporin complexes (CNCs) anchored atop both sides of the nuclear envelope. The outer rings are decorated with compartment‑specific asymmetric nuclear basket and cytoplasmic filament nucleoporins, which establish transport directionality and provide docking sites for transport factors and the small guanosine triphosphatase Ran. The cytoplasmic filament nucleoporins also play an essential role in the irreversible remodeling of messenger ribonucleoprotein particles (mRNPs) as they exit the central transport channel. Unsurprisingly, the NPC's cytoplasmic face represents a hotspot for disease‑associated mutations and is commonly targeted by viral virulence factors. RATIONALE Previous studies established a near-atomic composite structure of the human NPC's symmetric core by combining (i) biochemical reconstitution to elucidate the interaction network between symmetric nucleoporins, (ii) crystal and single-particle cryo-electron microscopy structure determination of nucleoporins and nucleoporin complexes to reveal their three-dimensional shape and the molecular details of their interactions, (iii) quantitative docking in cryo-electron tomography (cryo-ET) maps of the intact human NPC to uncover nucleoporin stoichiometry and positioning, and (iv) cell‑based assays to validate the physiological relevance of the biochemical and structural findings. In this work, we extended our approach to the cytoplasmic filament nucleoporins to reveal the near-atomic architecture of the cytoplasmic face of the human NPC. RESULTS Using biochemical reconstitution, we elucidated the protein-protein and protein-RNA interaction networks of the human and cytoplasmic filament nucleoporins, establishing an evolutionarily conserved heterohexameric cytoplasmic filament nucleoporin complex (CFNC) held together by a central heterotrimeric coiled‑coil hub that tethers two separate mRNP‑remodeling complexes. Further biochemical analysis and determination of a series of crystal structures revealed that the metazoan‑specific cytoplasmic filament nucleoporin NUP358 is composed of 16 distinct domains, including an N‑terminal S‑shaped α‑helical solenoid followed by a coiled‑coil oligomerization element, numerous Ran‑interacting domains, an E3 ligase domain, and a C‑terminal prolyl‑isomerase domain. Physiologically validated quantitative docking into cryo-ET maps of the intact human NPC revealed that pentameric NUP358 bundles, conjoined by the oligomerization element, are anchored through their N‑terminal domains to the central stalk regions of the CNC, projecting flexibly attached domains as far as ~600 Å into the cytoplasm. Using cell‑based assays, we demonstrated that NUP358 is dispensable for the architectural integrity of the assembled interphase NPC and RNA export but is required for efficient translation. After NUP358 assignment, the remaining 4-shaped cryo‑ET density matched the dimensions of the CFNC coiled‑coil hub, in close proximity to an outer-ring NUP93. Whereas the N-terminal NUP93 assembly sensor motif anchors the properly assembled related coiled‑coil channel nucleoporin heterotrimer to the inner ring, biochemical reconstitution confirmed that the NUP93 assembly sensor is reused in anchoring the CFNC to the cytoplasmic face of the human NPC. By contrast, two CFNCs are anchored by a divergent mechanism that involves assembly sensors located in unstructured portions of two CNC nucleoporins. Whereas unassigned cryo‑ET density occupies the NUP358 and CFNC binding sites on the nuclear face, docking of the nuclear basket component ELYS established that the equivalent position on the cytoplasmic face is unoccupied, suggesting that mechanisms other than steric competition promote asymmetric distribution of nucleoporins. CONCLUSION We have substantially advanced the biochemical and structural characterization of the asymmetric nucleoporins' architecture and attachment at the cytoplasmic and nuclear faces of the NPC. Our near‑atomic composite structure of the human NPC's cytoplasmic face provides a biochemical and structural framework for elucidating the molecular basis of mRNP remodeling, viral virulence factor interference with NPC function, and the underlying mechanisms of nucleoporin diseases at the cytoplasmic face of the NPC. [Figure: see text].
History
DepositionMay 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP-binding nuclear protein Ran
B: Nuclear pore complex protein Nup153
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5895
Polymers29,0562
Non-polymers5333
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-29 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.276, 79.619, 55.063
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

21A-601-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 24483.086 Da / Num. of mol.: 1 / Mutation: F35S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Production host: Escherichia coli (E. coli) / References: UniProt: P62826
#2: Protein/peptide Nuclear pore complex protein Nup153 / 153 kDa nucleoporin / Nucleoporin Nup153


Mass: 4573.210 Da / Num. of mol.: 1 / Fragment: ZINC FINGER 1 of NUP153 (UNP residues 648-687)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nup153 / Production host: Escherichia coli (E. coli) / References: UniProt: P49791

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Non-polymers , 4 types, 225 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 22% w/v PEG3350, 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.6→28.44 Å / Num. obs: 67816 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 1 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.022 / Rrim(I) all: 0.081 / Net I/σ(I): 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.6312.61.7172214417620.6530.4981.791.599.5
8.75-28.4411.40.03230322650.9990.0090.03368.797.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→28.44 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 18.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1754 3328 4.91 %
Rwork0.151 64488 -
obs0.1523 67816 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.95 Å2 / Biso mean: 39.0357 Å2 / Biso min: 14.89 Å2
Refinement stepCycle: final / Resolution: 1.6→28.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 42 222 2158
Biso mean--25.46 39.44 -
Num. residues----240
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.620.32611430.29162679282299
1.62-1.640.25891490.259526562805100
1.64-1.670.26291440.250527182862100
1.67-1.70.26031280.230927122840100
1.7-1.730.25491410.214426802821100
1.73-1.760.22461430.205926422785100
1.76-1.790.22071290.194426982827100
1.79-1.830.20981150.187927272842100
1.83-1.870.20811240.182827012825100
1.87-1.910.22481500.172226582808100
1.91-1.960.17031420.165927182860100
1.96-2.010.20651410.161726692810100
2.01-2.070.16521320.148126902822100
2.07-2.140.19471380.144126822820100
2.14-2.220.17721220.140127282850100
2.22-2.30.16331380.137426672805100
2.3-2.410.13951190.149227282847100
2.41-2.540.16311480.134926522800100
2.54-2.690.17431410.141126792820100
2.69-2.90.14231560.14626902846100
2.9-3.190.18481280.138826742802100
3.2-3.660.15861530.132126942847100
3.66-4.60.15951420.119326822824100
4.6-28.440.16551620.161826642826100
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)
10.4870.26590.72510.71340.2361.3036-0.5931-0.82080.49791.63220.331-0.6666-0.52580.4916-0.04560.71720.0775-0.12610.4915-0.11290.5577-6.756934.91637.902
20.9491-0.0401-0.2421.85630.11581.2497-0.0178-0.0803-0.03970.1350.0674-0.10080.10390.113600.16610.0028-0.02080.1712-0.00150.17861.19626.8782-3.0842
30.39930.19420.40610.25980.21640.41110.0623-0.3027-0.28220.19780.170.10350.3305-0.02290.00040.26920.0309-0.01390.2420.05260.2523-0.739815.73372.9205
41.7682-0.51830.67681.9705-0.06760.9185-0.09720.1084-0.5622-0.17980.09910.22670.6046-0.0704-0.00280.3472-0.02790.00060.1863-0.04320.3201-1.456811.8551-12.4014
50.2165-0.00750.34550.001-0.01210.55030.26130.1345-0.7850.02220.23230.30171.4172-0.31670.0490.642-0.1782-0.10330.54270.09080.8111-11.394711.1198-13.8566
60.945-0.24320.16911.35790.16331.1078-0.01030.2624-0.0221-0.26990.11470.08560.1154-0.03220.00020.2048-0.0313-0.02780.229-0.00440.1878-3.770126.5701-17.9472
70.1807-0.10510.25460.0773-0.14060.3641-0.1802-0.1301-0.1550.4249-0.5240.59910.04-1.3262-0.05580.5455-0.1144-0.09370.7008-0.28290.599-11.637414.1555-28.1317
80.03080.0211-0.00260.02170.00640.02210.0526-0.06140.7186-0.0449-0.02920.0858-0.2746-0.11110.00320.50840.11140.00530.89580.07760.7935-19.475939.1394-2.9159
90.0106-0.0081-0.01980.04910.03790.06840.072-0.26420.77050.1665-0.04380.2669-0.5931-0.2550.00340.52920.1532-0.03570.4645-0.05540.4404-4.6131.041212.0218
100.00720.0079-0.00750.05650.0160.0291-0.1605-0.14020.49180.26430.18490.421-0.0815-0.53060.00120.4380.0458-0.01690.4413-0.0210.3289-3.548527.78528.9588
110.26-0.0105-0.20880.30120.13990.50610.005-0.05910.00640.0656-0.13230.08770.0019-0.1557-0.40060.79290.24110.20.9889-0.02330.3209-7.669824.951918.6185
120.05310.0397-0.01560.0653-0.06030.0682-0.1601-0.95990.17891.3975-0.03210.27340.2527-0.58020.00170.70230.10820.02360.6006-0.02180.3361-1.274525.093116.0425
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 10 )A0 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 70 )A11 - 70
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 87 )A71 - 87
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 137 )A88 - 137
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 145 )A138 - 145
6X-RAY DIFFRACTION6chain 'A' and (resid 146 through 199 )A146 - 199
7X-RAY DIFFRACTION7chain 'A' and (resid 200 through 208 )A200 - 208
8X-RAY DIFFRACTION8chain 'B' and (resid 649 through 654 )B649 - 654
9X-RAY DIFFRACTION9chain 'B' and (resid 661 through 665 )B661 - 665
10X-RAY DIFFRACTION10chain 'B' and (resid 666 through 671 )B666 - 671
11X-RAY DIFFRACTION11chain 'B' and (resid 672 through 677 )B672 - 677
12X-RAY DIFFRACTION12chain 'B' and (resid 678 through 686 )B678 - 686

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