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- PDB-6lk8: Structure of Xenopus laevis Cytoplasmic Ring subunit. -

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Basic information

Entry
Database: PDB / ID: 6lk8
TitleStructure of Xenopus laevis Cytoplasmic Ring subunit.
Components
  • (Nuclear pore complex protein ...) x 2
  • (Nup214 complex Coiled coil region 2, helix ...) x 3
  • (Nup214 complex coiled coil region 1, helix ...) x 2
  • GATOR complex protein SEC13
  • MGC154553 protein
  • MGC83295 protein
  • MGC83926 protein
  • Nuclear pore complex protein
  • Nucleoporin SEH1-A
  • Nup214 complex Coiled-coil region 1, helix 1
  • Nup358 complex, clamps
  • bridge domain
  • outer Nup133
  • outer Nup160
KeywordsSTRUCTURAL PROTEIN / building block of vertebrate NPC.
Function / homology
Function and homology information


: / nitrogen compound transport / macromolecule localization / GATOR2 complex / nephron development / macromolecule metabolic process / nuclear pore organization / nuclear pore outer ring / attachment of mitotic spindle microtubules to kinetochore / structural constituent of nuclear pore ...: / nitrogen compound transport / macromolecule localization / GATOR2 complex / nephron development / macromolecule metabolic process / nuclear pore organization / nuclear pore outer ring / attachment of mitotic spindle microtubules to kinetochore / structural constituent of nuclear pore / nucleocytoplasmic transport / mitotic metaphase chromosome alignment / intracellular transport / mRNA transport / cellular response to nutrient levels / nuclear pore / positive regulation of TORC1 signaling / kinetochore / protein transport / nuclear membrane / lysosomal membrane / cell division / structural molecule activity / metal ion binding / cytosol
Similarity search - Function
Nuclear pore complex protein NUP98-NUP96 / Nucleoporin Nup37 / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205 ...Nuclear pore complex protein NUP98-NUP96 / Nucleoporin Nup37 / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205 / Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Sec13/Seh1 family / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Ran binding domain / Ran binding protein RanBP1-like / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / 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 / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Uncharacterized protein / Nuclear pore complex protein Nup133 / Nuclear pore complex protein Nup98-Nup96 / RANBP2-like and GRIP domain-containing protein 3 isoform X2 / Nuclear pore complex protein / MGC154553 protein / Nucleoporin SEH1-A / MGC83295 protein / MGC83926 protein / Nuclear pore complex protein Nup85 / Protein SEC13 homolog
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsShi, Y. / Huang, G. / Yan, C. / Zhang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31430020 China
National Natural Science Foundation of China (NSFC)31621092 China
CitationJournal: Cell Res / Year: 2020
Title: Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex by cryo-electron microscopy single particle analysis.
Authors: Gaoxingyu Huang / Yanqing Zhang / Xuechen Zhu / Chao Zeng / Qifan Wang / Qiang Zhou / Qinghua Tao / Minhao Liu / Jianlin Lei / Chuangye Yan / Yigong Shi /
Abstract: The nuclear pore complex (NPC) exhibits structural plasticity and has only been characterized at local resolutions of up to 15 Å for the cytoplasmic ring (CR). Here we present a single-particle ...The nuclear pore complex (NPC) exhibits structural plasticity and has only been characterized at local resolutions of up to 15 Å for the cytoplasmic ring (CR). Here we present a single-particle cryo-electron microscopy (cryo-EM) structure of the CR from Xenopus laevis NPC at average resolutions of 5.5-7.9 Å, with local resolutions reaching 4.5 Å. Improved resolutions allow identification and placement of secondary structural elements in the majority of the CR components. The two Y complexes in each CR subunit interact with each other and associate with those from flanking subunits, forming a circular scaffold. Within each CR subunit, the Nup358-containing region wraps around the stems of both Y complexes, likely stabilizing the scaffold. Nup205 connects the short arms of the two Y complexes and associates with the stem of a neighboring Y complex. The Nup214-containing region uses an extended coiled-coil to link Nup85 of the two Y complexes and protrudes into the axial pore of the NPC. These previously uncharacterized structural features reveal insights into NPC assembly.
History
DepositionDec 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 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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Assembly

Deposited unit
A: MGC83295 protein
B: Nuclear pore complex protein Nup85
C: MGC154553 protein
D: Nucleoporin SEH1-A
E: outer Nup160
F: MGC83926 protein
G: Nuclear pore complex protein Nup96
H: GATOR complex protein SEC13
I: Nuclear pore complex protein
J: outer Nup133
S: Nup358 complex, clamps
T: Nup358 complex, clamps
U: Nup358 complex, clamps
V: Nup358 complex, clamps
K: Nup214 complex Coiled-coil region 1, helix 1
L: Nup214 complex coiled coil region 1, helix 2
M: Nup214 complex coiled coil region 1, helix 3
N: Nup214 complex Coiled coil region 2, helix 1
O: Nup214 complex Coiled coil region 2, helix 2
P: Nup214 complex Coiled coil region 2, helix 3
Q: bridge domain
R: bridge domain
a: MGC83295 protein
b: Nuclear pore complex protein Nup85
c: MGC154553 protein
d: Nucleoporin SEH1-A
e: outer Nup160
f: MGC83926 protein
g: Nuclear pore complex protein Nup96
h: GATOR complex protein SEC13
i: Nuclear pore complex protein
j: outer Nup133


Theoretical massNumber of molelcules
Total (without water)3,291,33132
Polymers3,291,33132
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 11 types, 23 molecules AaCcDdEeFfHhIiJjSTUVKQR

#1: Protein MGC83295 protein


Mass: 227854.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q642R6
#3: Protein MGC154553 protein / outer Nup43


Mass: 41744.512 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q05AW3
#4: Protein Nucleoporin SEH1-A / outer Seh1 / GATOR complex protein SEH1-A / Nup107-160 subcomplex subunit seh1-A


Mass: 36037.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q4FZW5
#5: Protein outer Nup160


Mass: 162658.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8GIX3
#6: Protein MGC83926 protein


Mass: 36588.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q66IZ6
#8: Protein GATOR complex protein SEC13 / Protein SEC13 homolog


Mass: 35315.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q7ZYJ8
#9: Protein Nuclear pore complex protein


Mass: 105398.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A2RV69
#10: Protein outer Nup133


Mass: 127551.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8H1I9
#11: Protein
Nup358 complex, clamps


Mass: 322784.344 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8HGL2
#12: Protein Nup214 complex Coiled-coil region 1, helix 1


Mass: 5890.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog)
#18: Protein bridge domain


Mass: 33293.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog)

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Nuclear pore complex protein ... , 2 types, 4 molecules BbGg

#2: Protein Nuclear pore complex protein Nup85 / 85 kDa nucleoporin / Nucleoporin Nup85


Mass: 75160.047 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q68FJ0
#7: Protein Nuclear pore complex protein Nup96 / Nuclear pore complex protein Nup98 / Nuclear pore complex protein Nup98-Nup96 / Nucleoporin Nup96 / ...Nuclear pore complex protein Nup98 / Nuclear pore complex protein Nup98-Nup96 / Nucleoporin Nup96 / Nucleoporin Nup98


Mass: 105079.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8HBE3

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Nup214 complex coiled coil region 1, helix ... , 2 types, 2 molecules LM

#13: Protein Nup214 complex coiled coil region 1, helix 2


Mass: 6826.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog)
#14: Protein Nup214 complex coiled coil region 1, helix 3


Mass: 6230.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog)

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Nup214 complex Coiled coil region 2, helix ... , 3 types, 3 molecules NOP

#15: Protein/peptide Nup214 complex Coiled coil region 2, helix 1


Mass: 2656.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog)
#16: Protein/peptide Nup214 complex Coiled coil region 2, helix 2


Mass: 2996.685 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog)
#17: Protein/peptide Nup214 complex Coiled coil region 2, helix 3


Mass: 2230.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog)

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Details

Sequence detailsAuthors know the chains K,L,M and N,O,P come from the coiled-coil region from Nup88,Nup62 and ...Authors know the chains K,L,M and N,O,P come from the coiled-coil region from Nup88,Nup62 and Nup214 (termed Nup214 complex). However, at the current resolution, the three helices of the coiled coil cannot be distinguished a nd there are no crystal structure of the three proteins. (1) Xl_Nup214_Q9PVZ2 MEDDTDLPPERETKDFQFRQLKKVRLFDYPADLPKQRSNLLVISNKYGLLFVGGFMGLKV FHTKDILVTVKPKENANKTVVGPQGIHVPMNSPIHHLALSSDNLTLSVCMTSAEQGSSVS FYDVRTLLNESKQNKMPFASCKLLRDPSSSVTDLQWNPTLPSMVAVCLSDGSISVLQVTD TVSVFANLPATLGVTSVCWSPKGKQLAVGKQNGTVVQYLPSLQEKKVIPCPSFYDSDNPV KVLDVLWLSTYVFTVVYAAADGSLEASPQLVIVTLPKKEDKRAERFLNFTETCYSICSER QHHFFLNYIEDWEILLAASAASVDVGVIARPPDQVGWEQWLLEDSSRAEMPMTENNDDTL PMGVALDYTCQLEVFISESQILPPVPVLLLLSTDGVLCPFHVVNLNQGVKPLTTSPEQLS LDGEREMKVVGGTAVSTPPAPLTSVSAPAPPASAAPRSAAPPPYPFGLSTASSGAPTPVL NPPASLAPAATPTKTTSQPAAAATSIFQPAGPAAGSLQPPSLPAFSFSSANNAANASAPS SFPFGAAMVSSNTAKVSAPPAMSFQPAMGTRPFSLATPVTVQAATAPGFTPTPSTVKVNL KDKFNASDTPPPATISSAAALSFTPTSKPNATVPVKSQPTVIPSQASVQPNRPFAVEAPQ APSSVSIASVQKTVRVNPPATKITPQPQRSVALENQAKVTKESDSILNGIREEIAHFQKE LDDLKARTSRACFQVGSEEEKRQLRTESDGLHSFFLEIKETTESLRGEFSAMKIKNLEGF ASIEDVQQRNKLKQDPKYLQLLYKKPLDPKSETQMQEIRRLNQYVKNAVQDVNDVLDLEW DQYLEEKQKKKGIIIPERETLFNSLANHQEIINQQRPKLEQLVENLQKLRLYNQISQWNV PDSSTKSFDVELENMQKTLSQTAIDTQTKPQAKLPAKISPVKQSQLRNFLSKRKTPPVRS LAPANLSRSAFLAPSFFEDLDDVSSTSSLSDMADNDNRNPPPKEIERQETPPPESTPVRV PKHAPVARTTSVQPGLGTASLPFQSGLHPATSTPVAPSQSIRVIPQGADSTMLATKTVKH GAPNITAAQKAAVAAMRRQTASQIPAASLTESTLQTVPQVVNVKELKNNGPGPTIPTVIG PTVPQSAAQVIHQVLATVGSVSARQAAPAAPLKNPPASASSIAPQTWQGSAPNKPAAQAI PKSDPSASQAPAPSVSQVNKPVSFSPAAGGFSFSNVTSAPVTSALGSSSAGCAATARDSN QASSYMFGGTGKSLGSEGSFSFASLKPASSSSSSSVVEPTMSKPSVVTAASTTATVTSTT AASSKPGEGLFQGFSGGETLGSFSGLRVGQADEASKVEVAKTPTAAQPVKLPSNPVLFSF AGAPQPAKVGEAPSTTSSTSASLFGNVQLASAGSTASAFTQSGSKPAFTFGIPQSTSTTA GASSAIPASFQSLLVSAAPATTTPSAPINSGLDVKQPIKPLSEPADSSSSQQQTLTTQSA AEQVPTVTPAATTATALPPPVPTIPSTAEAKIEGAAAPAIPASVISSQTVPFTSTVLASQ TPLASTPAGGPTSQVPVLVTTAPPVTTESAQTVSLTGQPVAGSSAFAQSTVTAASTPVFG QALASGAAPSPFAQPTSSSVSTSANSSTGFGTSAFGATGGNGGFGQPSFGQAPLWKGPAT SQSTLPFSQPTFGTQPAFGQPAASTATSSAGSLFGCTSSASSFSFGQASNTSGTSTSGVL FGQSSAPVFGQSAAFPQAAPAFGSASVSTTTTASFGFGQPAGFASGTSGSLFNPSQSGST SVFGQQPASSSGGLFGAGSGGASTVGLFSGLGAKPSQEAANKNPFGSPGSSGFGSAGASN SSNLFGNSGAKAFGFGGTSFGDKPSATFSAGGSVASQGFSFNSPTKTGGFGAAPVFGSPP TFGGSPGFGGSPAFGTAAAFSNTLGSTGGKVFGEGTSAATTGGFGFGSNSSTAAFGSLAT QNTPTFGSISQQSPGFGGQSSGFSGFGAGPGAAAGNTGGFGFGVSNPTSPGFGCWRS (2) Xl_Nup88A_Q4KLQ6 MAAGEHWQSALSEHALFSSLKERLRDVEELREEGERRASKDKQLRNLLCVLDGDLLVWDA EECAFHTVTLRSLSVESTGSSSSGEQKLLCTNPPLFDVNEVLLSPTQHHVALVGSKGVMV LEIPKRWGKKSEFEGGEKTVNCRTIPIAERIFTSSTSLLLKQAIWYPSETQEPHLILLTS DNILRLYNLQDLFTPVKVISLSSAEEETTLPHNGRSYKASLGETAVACDFGPLAVLPKGF GQHSKEDTVAYPLYILYETGETYLMYIDLQKSNITVGKLLGPLPMYPAAEDNYGYDACAL LCLPCVPNIIVIATESGLLYHCVVLEGEEDDEQTSNKSWNSSCDLIPSLYVFECVELELA LKFATEEEESLELDFACPIKLHRDPICPSRYHCTHVAGVHSVGLTWFNKLEKFLSSGEED KDSLQELAAEQKCLVEHILCTKPLRCRLPSPIQGFWIISDLFLGTSMICITCDFECIVRP LLTTIRPPSPPLLCSQSDKSSTEILPHVLADVKGPFEEHIRGILRRNSANPLLLNSSSKD SSPPPEECLQLLSRATQVFREEYLLKQDLANEEIQRRVKLLIAQKEKQLEDLRYCREERK SLTETAERLAEKFEEAKEKQEDLINRLKRILRSFHTQLPVLSESERDMKKELQATNQQLQ QLGNSINQVNRKMSYQEKQMEKGKSPRKSSLTLSDYQKKNIKAVLKEHGEHIQEMVKQIN NIRNHVNF (3) Xl_Nup62_Q91349 MSGFNFGAASAGGFSFGNPKSTTTTAPTGFSFGAATAAPSGGFSFGTATPTPASTTGQTS GLFSFSNPAPSLAPTSGFSFGAQVTSTPAPSSGGLAFGANTSKLNSGVGNQPAGGTTQTS QPMGGFSFGAATTQTQPSATSVGGFSFAGGVGSTSTNVFAQPAASTGITLQSAVSTAAAP TATTSQPTSTFSFGTQPQAAPALNFGLLSSSSVLSTASTPAAAQPVAPTTGLSLNFGKPA DTSAAVTSTGSTTTNTPSLSSLLGTSGPSLFSSVATSTVPSVVSTVASGLSLTSTATSTG FGMKTLASSAVPTGTLATSTASLGVKAPLAGTIVQANAVGSAAATGISTATAMTYAQLEN LINKWSLELEDQEKHFLQQATQVNAWDRTLMQNGERITTLHREMEKVKLDQKRLDQELDF ILSQQKELEDLLTPLEESVKEQSGTIYLQHADEEREKTYKLAENIDAQLKRMAQDLKEVI EHLNTSAGPGDASNPLQQICKILNAHMDSLQWIDQNSALLQRKVEQVTKECESRRKEQER GFSIAFD

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: TISSUE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cytoplasmic Ring Subunit of Xenopus laevis NPC / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm
Image recordingElectron dose: 75 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 616547 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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