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- PDB-5a9q: Human nuclear pore complex -

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Entry
Database: PDB / ID: 5a9q
TitleHuman nuclear pore complex
Components
  • (NUCLEAR PORE COMPLEX PROTEIN ...) x 6
  • NUCLEOPORIN NUP37
  • NUCLEOPORIN NUP43
  • NUCLEOPORIN SEH1
  • PROTEIN SEC13 HOMOLOG
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


nephron development / GATOR2 complex / Seh1-associated complex / protein localization to nuclear inner membrane / nuclear envelope organization / nuclear pore inner ring / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore complex assembly ...nephron development / GATOR2 complex / Seh1-associated complex / protein localization to nuclear inner membrane / nuclear envelope organization / nuclear pore inner ring / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore complex assembly / COPII-coated vesicle cargo loading / telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore organization / somite development / atrial cardiac muscle cell action potential / nuclear pore cytoplasmic filaments / COPII vesicle coat / paraxial mesoderm development / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Amino acids regulate mTORC1 / miRNA processing / attachment of mitotic spindle microtubules to kinetochore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / protein-containing complex localization / nuclear localization sequence binding / structural constituent of nuclear pore / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of mRNA splicing, via spliceosome / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / COPII-mediated vesicle transport / lamellipodium assembly / neural tube development / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / poly(A)+ mRNA export from nucleus / mitotic metaphase chromosome alignment / female gonad development / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / macrophage chemotaxis / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Regulation of HSF1-mediated heat shock response / positive regulation of TOR signaling / mRNA transport / nuclear pore / mRNA export from nucleus / cellular response to nutrient levels / SUMOylation of DNA damage response and repair proteins / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / negative regulation of TORC1 signaling / neurogenesis / serine-type peptidase activity / Mitotic Prometaphase / positive regulation of TORC1 signaling / EML4 and NUDC in mitotic spindle formation / MHC class II antigen presentation / cellular response to amino acid starvation / nuclear periphery / Resolution of Sister Chromatid Cohesion / SUMOylation of chromatin organization proteins / HCMV Late Events / chromosome segregation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / promoter-specific chromatin binding / molecular condensate scaffold activity / RHO GTPases Activate Formins / ER to Golgi transport vesicle membrane / Transcriptional regulation by small RNAs / kinetochore / ISG15 antiviral mechanism / spindle / protein import into nucleus / HCMV Early Events / Separation of Sister Chromatids / nuclear envelope / protein transport / actin cytoskeleton / snRNP Assembly / nuclear membrane / transcription coactivator activity / defense response to Gram-positive bacterium
Similarity search - Function
: / Nucleoporin NUP160, helical domain / : / : / Nup160 C-terminal TPR / NUP160/120 middle TPR / Nucleoporin Nup37 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin Nup120/160, beta-propeller domain / Nup98, Gle2-binding sequence ...: / Nucleoporin NUP160, helical domain / : / : / Nup160 C-terminal TPR / NUP160/120 middle TPR / Nucleoporin Nup37 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin Nup120/160, beta-propeller domain / Nup98, Gle2-binding sequence / 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, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / 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. / WD domain, G-beta repeat / 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. / 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 Nup98-Nup96 / Protein SEC13 homolog / Nuclear pore complex protein Nup107 / Nuclear pore complex protein Nup160 / Nucleoporin Nup43 / Nucleoporin Nup37 / Nuclear pore complex protein Nup133 / Nucleoporin SEH1 / Nuclear pore complex protein Nup85
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 23 Å
Authorsvon Appen, A. / Kosinski, J. / Sparks, L. / Ori, A. / DiGuilio, A. / Vollmer, B. / Mackmull, M. / Banterle, N. / Parca, L. / Kastritis, P. ...von Appen, A. / Kosinski, J. / Sparks, L. / Ori, A. / DiGuilio, A. / Vollmer, B. / Mackmull, M. / Banterle, N. / Parca, L. / Kastritis, P. / Buczak, K. / Mosalaganti, S. / Hagen, W. / Andres-Pons, A. / Lemke, E.A. / Bork, P. / Antonin, W. / Glavy, J.S. / Bui, K.H. / Beck, M.
CitationJournal: Nature / Year: 2015
Title: In situ structural analysis of the human nuclear pore complex.
Authors: Alexander von Appen / Jan Kosinski / Lenore Sparks / Alessandro Ori / Amanda L DiGuilio / Benjamin Vollmer / Marie-Therese Mackmull / Niccolo Banterle / Luca Parca / Panagiotis Kastritis / ...Authors: Alexander von Appen / Jan Kosinski / Lenore Sparks / Alessandro Ori / Amanda L DiGuilio / Benjamin Vollmer / Marie-Therese Mackmull / Niccolo Banterle / Luca Parca / Panagiotis Kastritis / Katarzyna Buczak / Shyamal Mosalaganti / Wim Hagen / Amparo Andres-Pons / Edward A Lemke / Peer Bork / Wolfram Antonin / Joseph S Glavy / Khanh Huy Bui / Martin Beck /
Abstract: Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and ...Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and requires in situ structural biology approaches. Of approximately 30 nucleoporins (Nups), 15 are structured and form the Y and inner-ring complexes. These two major scaffolding modules assemble in multiple copies into an eight-fold rotationally symmetric structure that fuses the inner and outer nuclear membranes to form a central channel of ~60 nm in diameter. The scaffold is decorated with transport-channel Nups that often contain phenylalanine-repeat sequences and mediate the interaction with cargo complexes. Although the architectural arrangement of parts of the Y complex has been elucidated, it is unclear how exactly it oligomerizes in situ. Here we combine cryo-electron tomography with mass spectrometry, biochemical analysis, perturbation experiments and structural modelling to generate, to our knowledge, the most comprehensive architectural model of the human nuclear pore complex to date. Our data suggest previously unknown protein interfaces across Y complexes and to inner-ring complex members. We show that the transport-channel Nup358 (also known as Ranbp2) has a previously unanticipated role in Y-complex oligomerization. Our findings blur the established boundaries between scaffold and transport-channel Nups. We conclude that, similar to coated vesicles, several copies of the same structural building block--although compositionally identical--engage in different local sets of interactions and conformations.
History
DepositionJul 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4May 8, 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
0: NUCLEOPORIN NUP43
1: NUCLEAR PORE COMPLEX PROTEIN NUP160
2: NUCLEOPORIN NUP37
3: NUCLEAR PORE COMPLEX PROTEIN NUP133
4: NUCLEAR PORE COMPLEX PROTEIN NUP107
5: NUCLEAR PORE COMPLEX PROTEIN NUP96
6: PROTEIN SEC13 HOMOLOG
7: NUCLEOPORIN SEH1
8: NUCLEAR PORE COMPLEX PROTEIN NUP85
9: NUCLEOPORIN NUP43
A: NUCLEAR PORE COMPLEX PROTEIN NUP155
B: NUCLEAR PORE COMPLEX PROTEIN NUP155
C: NUCLEAR PORE COMPLEX PROTEIN NUP133
D: NUCLEAR PORE COMPLEX PROTEIN NUP107
E: NUCLEAR PORE COMPLEX PROTEIN NUP96
F: PROTEIN SEC13 HOMOLOG
G: NUCLEOPORIN SEH1
H: NUCLEAR PORE COMPLEX PROTEIN NUP85
I: NUCLEOPORIN NUP43
J: NUCLEAR PORE COMPLEX PROTEIN NUP160
K: NUCLEOPORIN NUP37
L: NUCLEAR PORE COMPLEX PROTEIN NUP133
M: NUCLEAR PORE COMPLEX PROTEIN NUP107
N: NUCLEAR PORE COMPLEX PROTEIN NUP96
O: PROTEIN SEC13 HOMOLOG
P: NUCLEOPORIN SEH1
Q: NUCLEAR PORE COMPLEX PROTEIN NUP85
R: NUCLEOPORIN NUP43
S: NUCLEAR PORE COMPLEX PROTEIN NUP160
T: NUCLEOPORIN NUP37
U: NUCLEAR PORE COMPLEX PROTEIN NUP133
V: NUCLEAR PORE COMPLEX PROTEIN NUP107
W: NUCLEAR PORE COMPLEX PROTEIN NUP96
X: PROTEIN SEC13 HOMOLOG
Y: NUCLEOPORIN SEH1
Z: NUCLEAR PORE COMPLEX PROTEIN NUP85
a: NUCLEAR PORE COMPLEX PROTEIN NUP160
b: NUCLEOPORIN NUP37


Theoretical massNumber of molelcules
Total (without water)3,243,76138
Polymers3,243,76138
Non-polymers00
Water00
1
0: NUCLEOPORIN NUP43
1: NUCLEAR PORE COMPLEX PROTEIN NUP160
2: NUCLEOPORIN NUP37
3: NUCLEAR PORE COMPLEX PROTEIN NUP133
4: NUCLEAR PORE COMPLEX PROTEIN NUP107
5: NUCLEAR PORE COMPLEX PROTEIN NUP96
6: PROTEIN SEC13 HOMOLOG
7: NUCLEOPORIN SEH1
8: NUCLEAR PORE COMPLEX PROTEIN NUP85
9: NUCLEOPORIN NUP43
A: NUCLEAR PORE COMPLEX PROTEIN NUP155
B: NUCLEAR PORE COMPLEX PROTEIN NUP155
C: NUCLEAR PORE COMPLEX PROTEIN NUP133
D: NUCLEAR PORE COMPLEX PROTEIN NUP107
E: NUCLEAR PORE COMPLEX PROTEIN NUP96
F: PROTEIN SEC13 HOMOLOG
G: NUCLEOPORIN SEH1
H: NUCLEAR PORE COMPLEX PROTEIN NUP85
I: NUCLEOPORIN NUP43
J: NUCLEAR PORE COMPLEX PROTEIN NUP160
K: NUCLEOPORIN NUP37
L: NUCLEAR PORE COMPLEX PROTEIN NUP133
M: NUCLEAR PORE COMPLEX PROTEIN NUP107
N: NUCLEAR PORE COMPLEX PROTEIN NUP96
O: PROTEIN SEC13 HOMOLOG
P: NUCLEOPORIN SEH1
Q: NUCLEAR PORE COMPLEX PROTEIN NUP85
R: NUCLEOPORIN NUP43
S: NUCLEAR PORE COMPLEX PROTEIN NUP160
T: NUCLEOPORIN NUP37
U: NUCLEAR PORE COMPLEX PROTEIN NUP133
V: NUCLEAR PORE COMPLEX PROTEIN NUP107
W: NUCLEAR PORE COMPLEX PROTEIN NUP96
X: PROTEIN SEC13 HOMOLOG
Y: NUCLEOPORIN SEH1
Z: NUCLEAR PORE COMPLEX PROTEIN NUP85
a: NUCLEAR PORE COMPLEX PROTEIN NUP160
b: NUCLEOPORIN NUP37
x 8


Theoretical massNumber of molelcules
Total (without water)25,950,092304
Polymers25,950,092304
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation7

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Components

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Protein , 4 types, 16 molecules 09IR2KTb6FOX7GPY

#1: Protein
NUCLEOPORIN NUP43 / NUP107-160 SUBCOMPLEX SUBUNIT NUP43 / P42 / NUP43


Mass: 42195.652 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: Q8NFH3
#3: Protein
NUCLEOPORIN NUP37 / P37 / NUP107-160 SUBCOMPLEX SUBUNIT NUP37 / NUP37


Mass: 36748.512 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: Q8NFH4
#7: Protein
PROTEIN SEC13 HOMOLOG / SEC13-LIKE PROTEIN 1 / SEC13-RELATED PROTEIN / SEC13


Mass: 35578.438 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: P55735
#8: Protein
NUCLEOPORIN SEH1 / NUP107-160 SUBCOMPLEX SUBUNIT SEH1 / SEC13-LIKE PROTEIN / SEH 1


Mass: 39700.566 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: Q96EE3

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NUCLEAR PORE COMPLEX PROTEIN ... , 6 types, 22 molecules 1JSa3CLU4DMV5ENW8HQZAB

#2: Protein
NUCLEAR PORE COMPLEX PROTEIN NUP160 / 160 KDA NUCLEOPORIN / NUCLEOPORIN NUP160 / NUP160


Mass: 162280.203 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: Q12769
#4: Protein
NUCLEAR PORE COMPLEX PROTEIN NUP133 / 133 KDA NUCLEOPORIN / NUCLEOPORIN NUP133 / NUP133


Mass: 129108.461 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: Q8WUM0
#5: Protein
NUCLEAR PORE COMPLEX PROTEIN NUP107 / 107 KDA NUCLEOPORIN / NUCLEOPORIN NUP107 / NUP107


Mass: 106504.969 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: P57740
#6: Protein
NUCLEAR PORE COMPLEX PROTEIN NUP96 / 96 KDA NUCLEOPORIN / NUCLEOPORIN NUP96 / NUP96


Mass: 106039.656 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: P52948
#9: Protein
NUCLEAR PORE COMPLEX PROTEIN NUP85 / 85 KDA NUCLEOPORIN / FROUNT / NUCLEOPORIN NUP75 / NUCLEOPORIN NUP85 / PERICENTRIN-1 / NUP85


Mass: 75105.266 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: Q9BW27
#10: Protein NUCLEAR PORE COMPLEX PROTEIN NUP155 / 155 KDA NUCLEOPORIN / NUCLEOPORIN NUP155 / NUP155


Mass: 155357.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: O75694

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: electron tomography

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Sample preparation

ComponentName: HUMAN NUCLEAR PORE COMPLEX / Type: ORGANELLE OR CELLULAR COMPONENT
Buffer solutionName: 20MM TRIS, 0.2-0.4% TREHALOSE / pH: 7.5 / Details: 20MM TRIS, 0.2-0.4% TREHALOSE
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, INSTRUMENT- HOMEMADE PLUNGER,

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Oct 17, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 42000 X / Calibrated magnification: 42000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm
Specimen holderTilt angle max: 60 ° / Tilt angle min: -45 °
Image recordingElectron dose: 110 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)

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Processing

EM software
IDNameCategory
1AV33D reconstruction
2IMOD3D reconstruction
3TOM Toolbox3D reconstruction
CTF correctionDetails: PHASE FLIPPING OF TILT SERIES
SymmetryPoint symmetry: C8 (8 fold cyclic)
3D reconstructionMethod: SUBTOMOGRAM AVERAGING / Resolution: 23 Å
Details: THIS PDB STRUCTURE INCLUDES UNAMBIGUOUS FITS ONLY. THE STRUCTURE WITH LESS CONFIDENT FITS CAN BE OBTAINED FROM AUTHORS. PROTEIN-PROTEIN INTERFACES SHALL NOT BE INTERPRETED AT RESIDUE-LEVEL ...Details: THIS PDB STRUCTURE INCLUDES UNAMBIGUOUS FITS ONLY. THE STRUCTURE WITH LESS CONFIDENT FITS CAN BE OBTAINED FROM AUTHORS. PROTEIN-PROTEIN INTERFACES SHALL NOT BE INTERPRETED AT RESIDUE-LEVEL RESOLUTION. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3103. (DEPOSITION ID: 13616).
Symmetry type: POINT
RefinementHighest resolution: 23 Å
Refinement stepCycle: LAST / Highest resolution: 23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms95884 0 0 0 95884

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