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- PDB-7mo0: Crystal Structure of Nucleoporin NUP50 Ran-Binding Domain in Comp... -

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Entry
Database: PDB / ID: 7mo0
TitleCrystal Structure of Nucleoporin NUP50 Ran-Binding Domain in Complex with Ran-GPPNHP
Components
  • GTP-binding nuclear protein Ran
  • Nuclear pore complex protein Nup50Nuclear pore
KeywordsTRANSPORT PROTEIN / nuclear pore complex component / nucleocytoplasmic transport / complex (small GTPase-nuclear protein)
Function / homology
Function and homology information


RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / Nuclear Pore Complex (NPC) Disassembly / manchette / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Regulation of cholesterol biosynthesis by SREBP (SREBF) ...RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / Nuclear Pore Complex (NPC) Disassembly / manchette / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Transport of the SLBP independent Mature mRNA / importin-alpha family protein binding / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / dynein intermediate chain binding / DNA metabolic process / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / mitotic sister chromatid segregation / SUMOylation of DNA replication proteins / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / Regulation of HSF1-mediated heat shock response / mRNA transport / ribosomal small subunit export from nucleus / ribosomal subunit export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / centriole / protein export from nucleus / viral process / SUMOylation of chromatin organization proteins / mitotic spindle organization / G protein activity / HCMV Late Events / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / recycling endosome / ISG15 antiviral mechanism / positive regulation of protein import into nucleus / HCMV Early Events / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / snRNP Assembly / midbody / actin cytoskeleton organization / nuclear membrane / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear pore complex, NUP2/50/61 / NUP50 (Nucleoporin 50 kDa) / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / small GTPase Ran family profile. / Ran GTPase / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases ...Nuclear pore complex, NUP2/50/61 / NUP50 (Nucleoporin 50 kDa) / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / small GTPase Ran family profile. / Ran GTPase / 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 / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTP-binding nuclear protein Ran / Nuclear pore complex protein Nup50
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 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

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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 Nup50
C: GTP-binding nuclear protein Ran
D: Nuclear pore complex protein Nup50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0939
Polymers79,9044
Non-polymers1,1895
Water1,13563
1
A: GTP-binding nuclear protein Ran
B: Nuclear pore complex protein Nup50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4984
Polymers39,9522
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-36 kcal/mol
Surface area17010 Å2
MethodPISA
2
C: GTP-binding nuclear protein Ran
D: Nuclear pore complex protein Nup50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5945
Polymers39,9522
Non-polymers6433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-55 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.590, 73.170, 152.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 24730.764 Da / Num. of mol.: 2
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 Nuclear pore complex protein Nup50 / Nuclear pore / 50 kDa nucleoporin / Nuclear pore-associated protein 60 kDa-like / Nucleoporin Nup50


Mass: 15221.078 Da / Num. of mol.: 2
Fragment: RAN-binding domain of NUP50 (UNP residues 337-468)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP50, NPAP60L, PRO1146 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKX7

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Non-polymers , 4 types, 68 molecules

#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% w/v PEG3350, 0.2 M ammonium sulfate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.45→29.73 Å / Num. obs: 52982 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 56.22 Å2 / Rpim(I) all: 0.034 / Rrim(I) all: 0.125 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all
2.45-2.5413.31.13662927620.7332.693
5.27-29.7312.340.63715530220.0160.058

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
Cootmodel building
AutoSolphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.45→29.73 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2387 2618 4.94 %
Rwork0.212 50364 -
obs0.2134 52982 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 203.36 Å2 / Biso mean: 87.1956 Å2 / Biso min: 36.84 Å2
Refinement stepCycle: final / Resolution: 2.45→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5345 0 95 63 5503
Biso mean--69.97 58.58 -
Num. residues----671
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.490.4018960.38122674277099
2.49-2.540.34511310.348626572788100
2.54-2.590.32881050.354826752780100
2.59-2.650.32261230.322926462769100
2.65-2.710.34921260.329226572783100
2.71-2.780.39681420.316926742816100
2.78-2.860.33691300.307426282758100
2.86-2.940.29361450.283926792824100
2.94-3.030.28841840.266726462830100
3.03-3.140.29111500.260826022752100
3.14-3.270.32821800.252426042784100
3.27-3.420.31761240.234526932817100
3.42-3.60.23241470.220226042751100
3.6-3.820.2881500.210926672817100
3.82-4.110.17741250.179826762801100
4.12-4.530.18781640.156426102774100
4.53-5.180.15281410.154526572798100
5.18-6.520.22261290.187126582787100
6.52-29.730.21161260.182326572783100
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)
12.9513-0.73270.30242.95230.28633.1298-0.1507-0.15970.07560.25930.1725-0.28430.2220.1689-0.00890.5090.05290.01420.4737-0.00880.53248.0796-13.605818.8852
22.8356-3.0234-0.10635.4532-0.36985.6387-0.27250.10840.27730.31230.1726-0.2592-0.10040.11350.15480.5430.0001-0.03680.4785-0.00920.64215.0105-1.768715.0275
31.5446-0.00950.41730.8311-0.07270.682-0.108-0.5182-0.59310.4097-0.32570.20250.5504-0.40110.44950.9819-0.26140.15081.22320.09741.0338-26.5511-16.915521.9122
44.8041-0.00150.55941.23680.30031.6578-0.425-0.037-0.11350.21520.18390.0755-0.3987-0.26520.17270.71360.11270.06490.592-0.01320.6833-14.11213.189221.7534
52.26360.56140.65283.44850.1853.37680.2186-0.4297-0.34580.3022-0.13220.07660.6373-0.6459-0.07830.7259-0.07310.05610.74620.07520.6416-21.3379-10.587218.9155
63.6963-0.39240.36454.4745-0.00383.60310.1321-0.9712-0.46710.4076-0.11270.63770.7609-0.63460.02580.7819-0.22120.1030.84840.03290.7128-26.9063-10.972821.2452
72.98290.14810.33652.33161.0253.0290.0291-0.26050.11890.30210.058-0.1367-0.21770.063-0.05970.55370.0603-0.0170.46530.01890.516517.7598-40.94314.3856
83.1071-0.0915-0.45372.9346-0.61012.6831-0.1493-0.0603-0.28470.14630.10140.27340.2538-0.45730.05690.5635-0.0261-0.00010.5095-0.00120.55077.2493-47.52799.7622
91.7397-0.9905-0.57141.3850.47082.5201-0.2307-0.16120.2087-0.0135-0.0572-0.141-0.24010.3570.20390.9054-0.0765-0.11430.75130.08920.756840.4792-45.89128.8117
103.84681.40720.7984.8569-0.11278.4697-0.12730.1637-0.1665-0.24120.0493-0.08130.63570.14640.0870.51650.11880.03980.44290.05010.498235.9724-51.136516.7895
114.87441.2407-0.17473.9242-2.12727.3258-0.1833-0.5824-0.18130.1806-0.2725-0.37030.18541.07270.46220.57690.0991-0.02730.69020.05460.553442.2724-48.592125.6437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 140 )A6 - 140
2X-RAY DIFFRACTION2chain 'A' and (resid 141 through 179 )A141 - 179
3X-RAY DIFFRACTION3chain 'A' and (resid 180 through 216 )A180 - 216
4X-RAY DIFFRACTION4chain 'B' and (resid 343 through 362 )B343 - 362
5X-RAY DIFFRACTION5chain 'B' and (resid 363 through 435 )B363 - 435
6X-RAY DIFFRACTION6chain 'B' and (resid 436 through 468 )B436 - 468
7X-RAY DIFFRACTION7chain 'C' and (resid 4 through 66 )C4 - 66
8X-RAY DIFFRACTION8chain 'C' and (resid 67 through 178 )C67 - 178
9X-RAY DIFFRACTION9chain 'C' and (resid 179 through 216 )C179 - 216
10X-RAY DIFFRACTION10chain 'D' and (resid 345 through 408 )D345 - 408
11X-RAY DIFFRACTION11chain 'D' and (resid 409 through 468 )D409 - 468

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