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- PDB-9sob: Structural Model of the Nuclear Pore Complex in Arabidopsis thaliana -

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Entry
Database: PDB / ID: 9sob
TitleStructural Model of the Nuclear Pore Complex in Arabidopsis thaliana
Components
  • (Nuclear pore complex protein ...) x 17
  • Aladin
  • E3 ubiquitin-protein ligase HOS1
  • NUP58
  • Nucleoporin (DUF3414)
  • Nucleoporin protein Ndc1-Nup protein
  • Protein SEH1
  • Protein transport protein SEC13 homolog B
KeywordsNUCLEAR PROTEIN / Nuclear Pore Complex / Nuclear Transport / Nuclear-cytoplasmic transport
Function / homology
Function and homology information


negative regulation of auxin mediated signaling pathway / regulation of timing of transition from vegetative to reproductive phase / long-day photoperiodism, flowering / nuclear pore transmembrane ring / zygote asymmetric cell division / induced systemic resistance / vegetative to reproductive phase transition of meristem / systemic acquired resistance, salicylic acid mediated signaling pathway / systemic acquired resistance / innate immune response-activating signaling pathway ...negative regulation of auxin mediated signaling pathway / regulation of timing of transition from vegetative to reproductive phase / long-day photoperiodism, flowering / nuclear pore transmembrane ring / zygote asymmetric cell division / induced systemic resistance / vegetative to reproductive phase transition of meristem / systemic acquired resistance, salicylic acid mediated signaling pathway / systemic acquired resistance / innate immune response-activating signaling pathway / nuclear pore inner ring / developmental process / nuclear pore organization / response to auxin / embryo development ending in seed dormancy / response to abscisic acid / plasmodesma / structural constituent of nuclear pore / RNA export from nucleus / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / porin activity / ribosomal large subunit export from nucleus / mRNA transport / nuclear pore / mRNA export from nucleus / ribosomal small subunit export from nucleus / vesicle-mediated transport / nuclear periphery / protein export from nucleus / response to cold / response to bacterium / circadian regulation of gene expression / defense response / RING-type E3 ubiquitin transferase / protein import into nucleus / ubiquitin-protein transferase activity / nuclear envelope / protein transport / nuclear membrane / protein-macromolecule adaptor activity / nucleic acid binding / protein ubiquitination / innate immune response / negative regulation of DNA-templated transcription / nucleolus / structural molecule activity / endoplasmic reticulum / Golgi apparatus / mitochondrion / zinc ion binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Nuclear pore complex protein NUP160 / Nuclear pore complex protein NUP214 / E3 ubiquitin-protein ligase HOS1 / NUP160, helical domain / Nucleoporin protein Ndc1-Nup / Aladin seven-bladed propeller / Nucleoporin, NUP53 / Aladin / ELYS-like domain / Nuclear pore complex assembly ...Nuclear pore complex protein NUP160 / Nuclear pore complex protein NUP214 / E3 ubiquitin-protein ligase HOS1 / NUP160, helical domain / Nucleoporin protein Ndc1-Nup / Aladin seven-bladed propeller / Nucleoporin, NUP53 / Aladin / ELYS-like domain / Nuclear pore complex assembly / Nucleoporin Nup88 / Nuclear pore component / : / : / Nup160 C-terminal TPR / NUP160/120 middle TPR / RNA-recognition motif (RRM) Nup35-type domain / Nup53/35/40-type RNA recognition motif / RNA-recognition motif (RRM) Nup35-type domain profile. / Nucleoporin NUP88/NUP82 / Nucleoporin Nup188 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin Nup120/160, beta-propeller domain / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / 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, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin, Nup155-like / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205 / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin interacting component Nup93/Nic96 / Nup93/Nic96 / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / 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 / Sec13/Seh1 family / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / RNA-binding domain superfamily / WD domain, G-beta repeat / Zinc finger, RING/FYVE/PHD-type / G-protein beta WD-40 repeat / Nucleotide-binding alpha-beta plait domain superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Nuclear pore complex protein NUP155 / Nuclear pore complex protein NUP214 / Nuclear pore complex protein NUP133 / Nucleoporin (DUF3414) / Nuclear pore complex protein NUP205 / Nuclear pore complex protein NUP35 / Nuclear pore complex protein NUP93A / Protein transport protein SEC13 homolog B / Nuclear pore complex protein NUP43 / E3 ubiquitin-protein ligase HOS1 ...Nuclear pore complex protein NUP155 / Nuclear pore complex protein NUP214 / Nuclear pore complex protein NUP133 / Nucleoporin (DUF3414) / Nuclear pore complex protein NUP205 / Nuclear pore complex protein NUP35 / Nuclear pore complex protein NUP93A / Protein transport protein SEC13 homolog B / Nuclear pore complex protein NUP43 / E3 ubiquitin-protein ligase HOS1 / Aladin / Nuclear pore complex protein NUP54 / Nuclear pore complex protein NUP107 / Nuclear pore complex protein NUP62 / Nucleoporin protein Ndc1-Nup protein / Nuclear pore complex protein NUP96 / Nuclear pore complex protein NUP85 / Protein SEH1 / Nuclear pore complex protein NUP160 / Nuclear pore complex protein NUP88
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 35 Å
AuthorsObarska-Kosinska, A. / Sanchez Carrillo, I.B. / Hoffmann, P.C. / Fourcassie, V. / Beck, M. / Germain, H.
Funding support Germany, European Union, Canada, 4items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)NPCvalve 101054823European Union
Natural Sciences and Engineering Research Council (NSERC, Canada)RG2020-04002 Canada
European Molecular Biology Organization (EMBO)ALTF 33-2021European Union
CitationJournal: Nat.Plants / Year: 2025
Title: In situ architecture of the nuclear pore complex of the higher plant Arabidopsis thaliana
Authors: Sanchez Carrillo, I.B. / Hoffmann, P.C. / Obarska-Kosinska, A. / Fourcassie, V. / Beck, M. / Germain, H.
History
DepositionSep 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: Nuclear pore complex protein NUP160
M: Nuclear pore complex protein NUP96
N: Protein transport protein SEC13 homolog B
R8: Nuclear pore complex protein NUP160
M8: Nuclear pore complex protein NUP96
N8: Protein transport protein SEC13 homolog B
R16: Nuclear pore complex protein NUP160
M16: Nuclear pore complex protein NUP96
N16: Protein transport protein SEC13 homolog B
T: E3 ubiquitin-protein ligase HOS1
T8: E3 ubiquitin-protein ligase HOS1
T16: E3 ubiquitin-protein ligase HOS1
P: Nuclear pore complex protein NUP85
O: Protein SEH1
Q: Nuclear pore complex protein NUP43
P8: Nuclear pore complex protein NUP85
O8: Protein SEH1
Q8: Nuclear pore complex protein NUP43
P16: Nuclear pore complex protein NUP85
O16: Protein SEH1
Q16: Nuclear pore complex protein NUP43
L: Nuclear pore complex protein NUP107
L8: Nuclear pore complex protein NUP107
L16: Nuclear pore complex protein NUP107
K: Nuclear pore complex protein NUP133
K8: Nuclear pore complex protein NUP133
K16: Nuclear pore complex protein NUP133
C16: Nuclear pore complex protein NUP205
A24: Nuclear pore complex protein NUP93A
C24: Nuclear pore complex protein NUP205
A40: Nuclear pore complex protein NUP93A
A: Nuclear pore complex protein NUP93A
V: Nuclear pore complex protein NUP214
W: Nuclear pore complex protein NUP88
J: Nuclear pore complex protein NUP62
C: Nuclear pore complex protein NUP205
C8: Nuclear pore complex protein NUP205
A8: Nuclear pore complex protein NUP93A
A16: Nuclear pore complex protein NUP93A
F8: Nuclear pore complex protein NUP35
F: Nuclear pore complex protein NUP35
A32: Nuclear pore complex protein NUP93A
F24: Nuclear pore complex protein NUP35
F16: Nuclear pore complex protein NUP35
B: Nucleoporin (DUF3414)
B8: Nucleoporin (DUF3414)
4: Aladin
E: Nucleoporin protein Ndc1-Nup protein
48: Aladin
E8: Nucleoporin protein Ndc1-Nup protein
H: Nuclear pore complex protein NUP54
I: NUP58
J32: Nuclear pore complex protein NUP62
H8: Nuclear pore complex protein NUP54
I8: NUP58
J8: Nuclear pore complex protein NUP62
H24: Nuclear pore complex protein NUP54
I24: NUP58
J24: Nuclear pore complex protein NUP62
H16: Nuclear pore complex protein NUP54
I16: NUP58
J16: Nuclear pore complex protein NUP62
D: Nuclear pore complex protein NUP155
D8: Nuclear pore complex protein NUP155
D16: Nuclear pore complex protein NUP155
D24: Nuclear pore complex protein NUP155
D32: Nuclear pore complex protein NUP155
D40: Nuclear pore complex protein NUP155
C32: Nuclear pore complex protein NUP205
A48: Nuclear pore complex protein NUP93A


Theoretical massNumber of molelcules
Total (without water)5,802,82970
Polymers5,802,82970
Non-polymers00
Water00
1
R: Nuclear pore complex protein NUP160
M: Nuclear pore complex protein NUP96
N: Protein transport protein SEC13 homolog B
R8: Nuclear pore complex protein NUP160
M8: Nuclear pore complex protein NUP96
N8: Protein transport protein SEC13 homolog B
R16: Nuclear pore complex protein NUP160
M16: Nuclear pore complex protein NUP96
N16: Protein transport protein SEC13 homolog B
T: E3 ubiquitin-protein ligase HOS1
T8: E3 ubiquitin-protein ligase HOS1
T16: E3 ubiquitin-protein ligase HOS1
P: Nuclear pore complex protein NUP85
O: Protein SEH1
Q: Nuclear pore complex protein NUP43
P8: Nuclear pore complex protein NUP85
O8: Protein SEH1
Q8: Nuclear pore complex protein NUP43
P16: Nuclear pore complex protein NUP85
O16: Protein SEH1
Q16: Nuclear pore complex protein NUP43
L: Nuclear pore complex protein NUP107
L8: Nuclear pore complex protein NUP107
L16: Nuclear pore complex protein NUP107
K: Nuclear pore complex protein NUP133
K8: Nuclear pore complex protein NUP133
K16: Nuclear pore complex protein NUP133
C16: Nuclear pore complex protein NUP205
A24: Nuclear pore complex protein NUP93A
C24: Nuclear pore complex protein NUP205
A40: Nuclear pore complex protein NUP93A
A: Nuclear pore complex protein NUP93A
V: Nuclear pore complex protein NUP214
W: Nuclear pore complex protein NUP88
J: Nuclear pore complex protein NUP62
C: Nuclear pore complex protein NUP205
C8: Nuclear pore complex protein NUP205
A8: Nuclear pore complex protein NUP93A
A16: Nuclear pore complex protein NUP93A
F8: Nuclear pore complex protein NUP35
F: Nuclear pore complex protein NUP35
A32: Nuclear pore complex protein NUP93A
F24: Nuclear pore complex protein NUP35
F16: Nuclear pore complex protein NUP35
B: Nucleoporin (DUF3414)
B8: Nucleoporin (DUF3414)
4: Aladin
E: Nucleoporin protein Ndc1-Nup protein
48: Aladin
E8: Nucleoporin protein Ndc1-Nup protein
H: Nuclear pore complex protein NUP54
I: NUP58
J32: Nuclear pore complex protein NUP62
H8: Nuclear pore complex protein NUP54
I8: NUP58
J8: Nuclear pore complex protein NUP62
H24: Nuclear pore complex protein NUP54
I24: NUP58
J24: Nuclear pore complex protein NUP62
H16: Nuclear pore complex protein NUP54
I16: NUP58
J16: Nuclear pore complex protein NUP62
D: Nuclear pore complex protein NUP155
D8: Nuclear pore complex protein NUP155
D16: Nuclear pore complex protein NUP155
D24: Nuclear pore complex protein NUP155
D32: Nuclear pore complex protein NUP155
D40: Nuclear pore complex protein NUP155
C32: Nuclear pore complex protein NUP205
A48: Nuclear pore complex protein NUP93A
x 15


Theoretical massNumber of molelcules
Total (without water)87,042,4371050
Polymers87,042,4371050
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation14

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Components

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Nuclear pore complex protein ... , 17 types, 51 molecules RR8R16MM8M16PP8P16QQ8Q16LL8L16KK8K16C16C24CC8C32A24A40A16A32AA48V...

#1: Protein Nuclear pore complex protein NUP160 / AtNUP160 / Nucleoporin 160 / Protein SUPPRESSOR OF AUXIN RESISTANCE 1


Mass: 168456.297 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9C811
#2: Protein Nuclear pore complex protein NUP96 / AtNUP96 / Nucleoporin 96 / Nucleoporin PRECOCIOUS / Nucleoporin PRECOZ / Protein MODIFIER OF SNC1 3 ...AtNUP96 / Nucleoporin 96 / Nucleoporin PRECOCIOUS / Nucleoporin PRECOZ / Protein MODIFIER OF SNC1 3 / Protein SUPPRESSOR OF AUXIN RESISTANCE 3


Mass: 80453.953 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LLD0
#5: Protein Nuclear pore complex protein NUP85 / Nuclear pore complex protein NUP75 / Nucleoporin 75 / Nucleoporin 85


Mass: 80946.992 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8RXH2
#7: Protein Nuclear pore complex protein NUP43 / Nucleoporin 43


Mass: 39388.680 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q24JJ9
#8: Protein Nuclear pore complex protein NUP107 / Nucleoporin 107


Mass: 111106.227 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8L748
#9: Protein Nuclear pore complex protein NUP133 / Nucleoporin 133 / Nucleoporin Nup155-like


Mass: 81469.633 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: F4IGA5
#10: Protein
Nuclear pore complex protein NUP205 / Nucleoporin 205 / Protein EMBRYO DEFECTIVE 3142


Mass: 206947.188 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: F4KBW6
#11: Protein
Nuclear pore complex protein NUP93A / Nucleoporin 93A


Mass: 96591.953 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O22224
#12: Protein Nuclear pore complex protein NUP93A / Nucleoporin 93A


Mass: 85783.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O22224
#13: Protein Nuclear pore complex protein NUP214 / Nucleoporin 214 / Protein EMBRYO DEFECTIVE 1011 / Protein LNO1 / Protein LONO1


Mass: 22728.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: F4I1T7
#14: Protein Nuclear pore complex protein NUP88 / Nucleoporin 88 / Protein EMBRYO DEFECTIVE 2789 / Protein MODIFIER OF SNC1 / 7


Mass: 89832.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FFK6
#15: Protein Nuclear pore complex protein NUP62 / Nucleoporin 62 / NP62 / Protein EMBRYO DEFECTIVE 2766


Mass: 21492.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8L7F7
#16: Protein Nuclear pore complex protein NUP93A / Nucleoporin 93A


Mass: 7520.575 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O22224
#17: Protein/peptide
Nuclear pore complex protein NUP35 / Nucleoporin 35


Mass: 3045.227 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O04326
#21: Protein
Nuclear pore complex protein NUP54 / Nucleoporin 54


Mass: 28956.146 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8GYF7
#23: Protein
Nuclear pore complex protein NUP62 / Nucleoporin 62 / NP62 / Protein EMBRYO DEFECTIVE 2766


Mass: 22892.584 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8L7F7
#24: Protein
Nuclear pore complex protein NUP155 / Nucleoporin 155


Mass: 160181.938 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: F4HXV6

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Protein , 7 types, 19 molecules NN8N16TT8T16OO8O16BB8448EE8II8I24I16

#3: Protein Protein transport protein SEC13 homolog B / SEC13-like protein B


Mass: 32674.375 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O64740
#4: Protein E3 ubiquitin-protein ligase HOS1 / Protein HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 1 / RING finger protein HOS1 / RING-type E3 ...Protein HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 1 / RING finger protein HOS1 / RING-type E3 ubiquitin transferase HOS1


Mass: 78435.930 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q84JU6, RING-type E3 ubiquitin transferase
#6: Protein Protein SEH1


Mass: 35729.016 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q93VR9
#18: Protein Nucleoporin (DUF3414)


Mass: 219705.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: F4JUG3
#19: Protein Aladin


Mass: 48532.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8GWR1
#20: Protein Nucleoporin protein Ndc1-Nup protein


Mass: 57475.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LAF4
#22: Protein
NUP58


Mass: 27626.533 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Nuclear Pore Complex / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 5.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 2500 nm
Image recordingElectron dose: 2.2 e/Å2 / Avg electron dose per subtomogram: 130 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1novaSTAvolume selection
13novaSTA3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C8 (8 fold cyclic)
3D reconstructionResolution: 35 Å / Resolution method: OTHER / Num. of particles: 75 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 37 / Num. of volumes extracted: 79

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