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- PDB-7tbi: Composite structure of the S. cerevisiae nuclear pore complex (NPC) -

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Entry
Database: PDB / ID: 7tbi
TitleComposite structure of the S. cerevisiae nuclear pore complex (NPC)
Components
  • (Nic96 R2) x 2
  • (Nsp1) x 2
  • (Nup145N/Nup100/Nup116 ...) x 3
  • (Nup84) x 2
  • Dyn2
  • Nic96 R1
  • Nic96 SOL
  • Nup116 CTD
  • Nup120
  • Nup133
  • Nup145C
  • Nup157/Nup170
  • Nup159
  • Nup188
  • Nup192
  • Nup49
  • Nup53/Nup59 R1
  • Nup53/Nup59 R2
  • Nup53/Nup59 R3
  • Nup57
  • Nup82
  • Nup85
  • Sec13
  • Seh1
KeywordsTRANSPORT PROTEIN / nuclear pore complex / nucleocytoplasmic transport / alpha-helical solenoid / nuclear pore
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 25 Å
AuthorsPetrovic, S. / Samanta, D. / Perriches, T. / Bley, C.J. / Thierbach, K. / Brown, B. / Nie, S. / Mobbs, G.W. / Stevens, T.A. / Liu, X. ...Petrovic, S. / Samanta, D. / Perriches, T. / Bley, C.J. / Thierbach, K. / Brown, B. / Nie, S. / Mobbs, G.W. / Stevens, T.A. / Liu, X. / Tomaleri, G.P. / Schaus, L. / Hoelz, A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117360 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111461 United States
Howard Hughes Medical Institute (HHMI)55108534 United States
Heritage Medical Research Institute United States
CitationJournal: Nature / Year: 2020
Title: In-cell architecture of the nuclear pore and snapshots of its turnover.
Authors: Matteo Allegretti / Christian E Zimmerli / Vasileios Rantos / Florian Wilfling / Paolo Ronchi / Herman K H Fung / Chia-Wei Lee / Wim Hagen / Beata Turoňová / Kai Karius / Mandy Börmel / ...Authors: Matteo Allegretti / Christian E Zimmerli / Vasileios Rantos / Florian Wilfling / Paolo Ronchi / Herman K H Fung / Chia-Wei Lee / Wim Hagen / Beata Turoňová / Kai Karius / Mandy Börmel / Xiaojie Zhang / Christoph W Müller / Yannick Schwab / Julia Mahamid / Boris Pfander / Jan Kosinski / Martin Beck /
Abstract: Nuclear pore complexes (NPCs) fuse the inner and outer membranes of the nuclear envelope. They comprise hundreds of nucleoporins (Nups) that assemble into multiple subcomplexes and form large central ...Nuclear pore complexes (NPCs) fuse the inner and outer membranes of the nuclear envelope. They comprise hundreds of nucleoporins (Nups) that assemble into multiple subcomplexes and form large central channels for nucleocytoplasmic exchange. How this architecture facilitates messenger RNA export, NPC biogenesis and turnover remains poorly understood. Here we combine in situ structural biology and integrative modelling with correlative light and electron microscopy and molecular perturbation to structurally analyse NPCs in intact Saccharomyces cerevisiae cells within the context of nuclear envelope remodelling. We find an in situ conformation and configuration of the Nup subcomplexes that was unexpected from the results of previous in vitro analyses. The configuration of the Nup159 complex appears critical to spatially accommodate its function as an mRNA export platform, and as a mediator of NPC turnover. The omega-shaped nuclear envelope herniae that accumulate in nup116Δ cells conceal partially assembled NPCs lacking multiple subcomplexes, including the Nup159 complex. Under conditions of starvation, herniae of a second type are formed that cytoplasmically expose NPCs. These results point to a model of NPC turnover in which NPC-containing vesicles bud off from the nuclear envelope before degradation by the autophagy machinery. Our study emphasizes the importance of investigating the structure-function relationship of macromolecular complexes in their cellular context.
History
DepositionDec 22, 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.title / _citation_author.identifier_ORCID
Remark 0THIS ENTRY 7TBI REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN EMD-10198, DETERMINED BY M. ...THIS ENTRY 7TBI REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN EMD-10198, DETERMINED BY M.Beck,M.Allegretti

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Assembly

Deposited unit
A2: Nup157/Nup170
A3: Nup157/Nup170
A4: Nup157/Nup170
B1: Nup53/Nup59 R3
B2: Nup53/Nup59 R3
B3: Nup53/Nup59 R3
B4: Nup53/Nup59 R3
C2: Nup145N/Nup100/Nup116 R3
C3: Nup145N/Nup100/Nup116 R3
D1: Nic96 SOL
D2: Nic96 SOL
D3: Nic96 SOL
D4: Nic96 SOL
E1: Nup53/Nup59 R2
E2: Nup53/Nup59 R2
E3: Nup53/Nup59 R2
E4: Nup53/Nup59 R2
F1: Nup188
F2: Nup188
G1: Nic96 R2
G2: Nic96 R2
H1: Nup145N/Nup100/Nup116 R2
H2: Nup145N/Nup100/Nup116 R2
I1: Nup192
I2: Nup192
J1: Nic96 R2
J2: Nic96 R2
K1: Nup145N/Nup100/Nup116 R1
K2: Nup145N/Nup100/Nup116 R1
L1: Nup53/Nup59 R1
L2: Nup53/Nup59 R1
M1: Nsp1
M2: Nsp1
M3: Nsp1
M4: Nsp1
N1: Nup57
N2: Nup57
N3: Nup57
N4: Nup57
O1: Nup49
O2: Nup49
O3: Nup49
O4: Nup49
P1: Nic96 R1
P2: Nic96 R1
P3: Nic96 R1
P4: Nic96 R1
Q1: Nup133
Q2: Nup133
R1: Nup84
R2: Nup84
S1: Nup145C
S2: Nup145C
T1: Sec13
T2: Sec13
U1: Seh1
U2: Seh1
V1: Nup85
V2: Nup85
W1: Nup120
W2: Nup120
X1: Nsp1
X2: Nsp1
Y1: Nup159
Y2: Nup159
Z1: Nup82
Z2: Nup82
a1: Nup116 CTD
a2: Nup116 CTD
b1: Dyn2
b2: Dyn2
C1: Nup145N/Nup100/Nup116 R3
C4: Nup145N/Nup100/Nup116 R3
A1: Nup157/Nup170


Theoretical massNumber of molelcules
Total (without water)3,515,67474
Polymers3,515,67474
Non-polymers00
Water00
1
A2: Nup157/Nup170
A3: Nup157/Nup170
A4: Nup157/Nup170
B1: Nup53/Nup59 R3
B2: Nup53/Nup59 R3
B3: Nup53/Nup59 R3
B4: Nup53/Nup59 R3
C2: Nup145N/Nup100/Nup116 R3
C3: Nup145N/Nup100/Nup116 R3
D1: Nic96 SOL
D2: Nic96 SOL
D3: Nic96 SOL
D4: Nic96 SOL
E1: Nup53/Nup59 R2
E2: Nup53/Nup59 R2
E3: Nup53/Nup59 R2
E4: Nup53/Nup59 R2
F1: Nup188
F2: Nup188
G1: Nic96 R2
G2: Nic96 R2
H1: Nup145N/Nup100/Nup116 R2
H2: Nup145N/Nup100/Nup116 R2
I1: Nup192
I2: Nup192
J1: Nic96 R2
J2: Nic96 R2
K1: Nup145N/Nup100/Nup116 R1
K2: Nup145N/Nup100/Nup116 R1
L1: Nup53/Nup59 R1
L2: Nup53/Nup59 R1
M1: Nsp1
M2: Nsp1
M3: Nsp1
M4: Nsp1
N1: Nup57
N2: Nup57
N3: Nup57
N4: Nup57
O1: Nup49
O2: Nup49
O3: Nup49
O4: Nup49
P1: Nic96 R1
P2: Nic96 R1
P3: Nic96 R1
P4: Nic96 R1
Q1: Nup133
Q2: Nup133
R1: Nup84
R2: Nup84
S1: Nup145C
S2: Nup145C
T1: Sec13
T2: Sec13
U1: Seh1
U2: Seh1
V1: Nup85
V2: Nup85
W1: Nup120
W2: Nup120
X1: Nsp1
X2: Nsp1
Y1: Nup159
Y2: Nup159
Z1: Nup82
Z2: Nup82
a1: Nup116 CTD
a2: Nup116 CTD
b1: Dyn2
b2: Dyn2
C1: Nup145N/Nup100/Nup116 R3
C4: Nup145N/Nup100/Nup116 R3
A1: Nup157/Nup170
x 8


  • defined by author
  • Evidence: electron microscopy
  • 28.1 MDa, 592 polymers
Theoretical massNumber of molelcules
Total (without water)28,125,394592
Polymers28,125,394592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation7

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Components

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Protein , 22 types, 52 molecules A2A3A4A1D1D2D3D4F1F2G1G2I1I2J1J2M1M2M3M4N1N2N3N4O1O2O3O4Q1Q2...

#1: Protein
Nup157/Nup170


Mass: 146062.359 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Composite structure of the Chaetomium thermophilum Nup170 ortholog generated by superposition of fragment crystal structures (PDB IDs 5HB0, 5HB1, and 5HAX). To remain faithful to ...Details: Composite structure of the Chaetomium thermophilum Nup170 ortholog generated by superposition of fragment crystal structures (PDB IDs 5HB0, 5HB1, and 5HAX). To remain faithful to experimentally determined structures, we opted to interpret the in situ cryo-ET map of the S. cerevisiae NPC with C. thermophilum crystal structures.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#4: Protein
Nic96 SOL


Mass: 81199.477 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of the Chaetomium thermophilum Nic96 SOL ortholog component of the the Nic96-Nup53 heterodimer crystal structure (PDB ID 5HB3). To remain faithful to experimentally ...Details: Crystal structure of the Chaetomium thermophilum Nic96 SOL ortholog component of the the Nic96-Nup53 heterodimer crystal structure (PDB ID 5HB3). To remain faithful to experimentally determined structures, we opted to interpret the in situ cryo-ET map of the S. cerevisiae NPC with C. thermophilum crystal structures.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#6: Protein Nup188


Mass: 203076.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Single particle cryo-EM structure of the Chaetomium thermophilum Nup188 ortholog component of the the Nup188-Nic96-Nup145N heterotrimer structure (PDB ID 7MVZ). To remain faithful to ...Details: Single particle cryo-EM structure of the Chaetomium thermophilum Nup188 ortholog component of the the Nup188-Nic96-Nup145N heterotrimer structure (PDB ID 7MVZ). To remain faithful to experimentally determined structures, we opted to interpret the in situ cryo-ET map of the S. cerevisiae NPC with C. thermophilum single particle cryo-EM structures.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#7: Protein Nic96 R2


Mass: 6230.862 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Single particle cryo-EM structure of the Chaetomium thermophilum Nic96 R2 ortholog component of the the Nup188-Nic96-Nup145N heterotrimer structure (PDB ID 7MVZ). To remain faithful to ...Details: Single particle cryo-EM structure of the Chaetomium thermophilum Nic96 R2 ortholog component of the the Nup188-Nic96-Nup145N heterotrimer structure (PDB ID 7MVZ). To remain faithful to experimentally determined structures, we opted to interpret the in situ cryo-ET map of the S. cerevisiae NPC with C. thermophilum single particle cryo-EM structures.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#9: Protein Nup192


Mass: 197137.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Single particle cryo-EM structure of the Chaetomium thermophilum Nup192 ortholog component of the the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful to ...Details: Single particle cryo-EM structure of the Chaetomium thermophilum Nup192 ortholog component of the the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful to experimentally determined structures, we opted to interpret the in situ cryo-ET map of the S. cerevisiae NPC with C. thermophilum single particle cryo-EM structures.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#10: Protein Nic96 R2


Mass: 7173.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Single particle cryo-EM structure of the Chaetomium thermophilum Nic96 R2 ortholog component of the the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful ...Details: Single particle cryo-EM structure of the Chaetomium thermophilum Nic96 R2 ortholog component of the the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful to experimentally determined structures, we opted to interpret the in situ cryo-ET map of the S. cerevisiae NPC with C. thermophilum single particle cryo-EM structures.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#13: Protein
Nsp1


Mass: 20965.451 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of the Chaetomium thermophilum Nsp1 ortholog component of the Nup49-Nup57-Nsp1-Nic96 heterotetramer structure (PDB ID 5CWS). To remain faithful to experimentally determined ...Details: Crystal structure of the Chaetomium thermophilum Nsp1 ortholog component of the Nup49-Nup57-Nsp1-Nic96 heterotetramer structure (PDB ID 5CWS). To remain faithful to experimentally determined structures, we opted to interpret the in situ cryo-ET map of the S. cerevisiae NPC with C. thermophilum crystal structures.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#14: Protein
Nup57


Mass: 24065.980 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of Chaetomium thermophilum Nup57 ortholog component of the Nup49-Nup57-Nsp1-Nic96 heterotetramer structure (PDB ID 5CWS). To remain faithful to experimentally determined ...Details: Crystal structure of Chaetomium thermophilum Nup57 ortholog component of the Nup49-Nup57-Nsp1-Nic96 heterotetramer structure (PDB ID 5CWS). To remain faithful to experimentally determined structures, we opted to interpret the in situ cryo-ET map of the S. cerevisiae NPC with C. thermophilum crystal structures.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#15: Protein
Nup49


Mass: 27988.756 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of Chaetomium thermophilum Nup49 ortholog component of the Nup49-Nup57-Nsp1-Nic96 heterotetramer structure (PDB ID 5CWS). To remain faithful to experimentally determined ...Details: Crystal structure of Chaetomium thermophilum Nup49 ortholog component of the Nup49-Nup57-Nsp1-Nic96 heterotetramer structure (PDB ID 5CWS). To remain faithful to experimentally determined structures, we opted to interpret the in situ cryo-ET map of the S. cerevisiae NPC with C. thermophilum crystal structures.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#17: Protein Nup133


Mass: 126745.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Structure of the Saccharomyces cerevisiae Nup133 component of the coat nucleoporin complex (CNC) rigid-body optimized structure (PDBDEV_00000051) generated from crystal structures of the CNC ...Details: Structure of the Saccharomyces cerevisiae Nup133 component of the coat nucleoporin complex (CNC) rigid-body optimized structure (PDBDEV_00000051) generated from crystal structures of the CNC heterohexamer (PDB ID 4XMM), Sec13-Nup145C-Nup84 heterotrimer (PDB ID 3IKO), and a homology model based on the crystal structure of the Homo sapiens NUP107-NUP133 heterodimer (PDB ID 3CQC).
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#18: Protein Nup84


Mass: 83060.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Structure of the Saccharomyces cerevisiae Nup84 component of the coat nucleoporin complex (CNC) rigid-body optimized structure (PDBDEV_00000051) generated from crystal structures of the CNC ...Details: Structure of the Saccharomyces cerevisiae Nup84 component of the coat nucleoporin complex (CNC) rigid-body optimized structure (PDBDEV_00000051) generated from crystal structures of the CNC heterohexamer (PDB ID 4XMM), Sec13-Nup145C-Nup84 heterotrimer (PDB ID 3IKO), and a homology model based on the crystal structure of the Homo sapiens NUP107-NUP133 heterodimer (PDB ID 3CQC).
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#19: Protein Nup84


Mass: 83718.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Structure of the Saccharomyces cerevisiae Nup84 component of the coat nucleoporin complex (CNC) rigid-body optimized structure (PDBDEV_00000051) generated from crystal structures of the CNC ...Details: Structure of the Saccharomyces cerevisiae Nup84 component of the coat nucleoporin complex (CNC) rigid-body optimized structure (PDBDEV_00000051) generated from crystal structures of the CNC heterohexamer (PDB ID 4XMM), Sec13-Nup145C-Nup84 heterotrimer (PDB ID 3IKO), and a homology model based on the crystal structure of the Homo sapiens NUP107-NUP133 heterodimer (PDB ID 3CQC).
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#20: Protein Nup145C


Mass: 71195.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Structure of the Saccharomyces cerevisiae Nup145C component of the coat nucleoporin complex (CNC) rigid-body optimized structure (PDBDEV_00000051) generated from crystal structures of the ...Details: Structure of the Saccharomyces cerevisiae Nup145C component of the coat nucleoporin complex (CNC) rigid-body optimized structure (PDBDEV_00000051) generated from crystal structures of the CNC heterohexamer (PDB ID 4XMM), Sec13-Nup145C-Nup84 heterotrimer (PDB ID 3IKO), and a homology model based on the crystal structure of the Homo sapiens NUP107-NUP133 heterodimer (PDB ID 3CQC).
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#21: Protein Sec13


Mass: 31889.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Structure of the Saccharomyces cerevisiae Sec13 component of the coat nucleoporin complex (CNC) rigid-body optimized structure (PDBDEV_00000051) generated from crystal structures of the CNC ...Details: Structure of the Saccharomyces cerevisiae Sec13 component of the coat nucleoporin complex (CNC) rigid-body optimized structure (PDBDEV_00000051) generated from crystal structures of the CNC heterohexamer (PDB ID 4XMM), Sec13-Nup145C-Nup84 heterotrimer (PDB ID 3IKO), and a homology model based on the crystal structure of the Homo sapiens NUP107-NUP133 heterodimer (PDB ID 3CQC).
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#22: Protein Seh1


Mass: 38843.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Structure of the Saccharomyces cerevisiae Seh1 component of the coat nucleoporin complex (CNC) rigid-body optimized structure (PDBDEV_00000051) generated from crystal structures of the CNC ...Details: Structure of the Saccharomyces cerevisiae Seh1 component of the coat nucleoporin complex (CNC) rigid-body optimized structure (PDBDEV_00000051) generated from crystal structures of the CNC heterohexamer (PDB ID 4XMM), Sec13-Nup145C-Nup84 heterotrimer (PDB ID 3IKO), and a homology model based on the crystal structure of the Homo sapiens NUP107-NUP133 heterodimer (PDB ID 3CQC).
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#23: Protein Nup85


Mass: 79734.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Structure of the Saccharomyces cerevisiae Nup85 component of the coat nucleoporin complex (CNC) rigid-body optimized structure (PDBDEV_00000051) generated from crystal structures of the CNC ...Details: Structure of the Saccharomyces cerevisiae Nup85 component of the coat nucleoporin complex (CNC) rigid-body optimized structure (PDBDEV_00000051) generated from crystal structures of the CNC heterohexamer (PDB ID 4XMM), Sec13-Nup145C-Nup84 heterotrimer (PDB ID 3IKO), and a homology model based on the crystal structure of the Homo sapiens NUP107-NUP133 heterodimer (PDB ID 3CQC).
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#24: Protein Nup120


Mass: 120560.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Structure of the Saccharomyces cerevisiae Nup120 component of the coat nucleoporin complex (CNC) rigid-body optimized structure (PDBDEV_00000051) generated from crystal structures of the CNC ...Details: Structure of the Saccharomyces cerevisiae Nup120 component of the coat nucleoporin complex (CNC) rigid-body optimized structure (PDBDEV_00000051) generated from crystal structures of the CNC heterohexamer (PDB ID 4XMM), Sec13-Nup145C-Nup84 heterotrimer (PDB ID 3IKO), and a homology model based on the crystal structure of the Homo sapiens NUP107-NUP133 heterodimer (PDB ID 3CQC).
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#25: Protein Nsp1


Mass: 21209.047 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Model of Nsp1 component of the Saccharomyces cerevisiae cytoplasmic filament complex (PDBDEV_00000010 and PDBDEV_00000051) based on crystal structure of the S. cerevisiae Nup82-Nup159-Nup116 ...Details: Model of Nsp1 component of the Saccharomyces cerevisiae cytoplasmic filament complex (PDBDEV_00000010 and PDBDEV_00000051) based on crystal structure of the S. cerevisiae Nup82-Nup159-Nup116 heterotrimer (PDB ID 3PBP), S. cerevisiae Dyn2-Nup159 heterodimer (PDB ID 4DS1), and the Chaetomium thermophilum Nup49-Nup57-Nsp1-Nic96 heterotetramer (PDB ID 5CWS).
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#26: Protein Nup159


Mass: 38939.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Model of Nup159 component of the Saccharomyces cerevisiae cytoplasmic filament complex (PDBDEV_00000010 and PDBDEV_00000051) based on crystal structure of the S. cerevisiae Nup82-Nup159- ...Details: Model of Nup159 component of the Saccharomyces cerevisiae cytoplasmic filament complex (PDBDEV_00000010 and PDBDEV_00000051) based on crystal structure of the S. cerevisiae Nup82-Nup159-Nup116 heterotrimer (PDB ID 3PBP), S. cerevisiae Dyn2-Nup159 heterodimer (PDB ID 4DS1), and the Chaetomium thermophilum Nup49-Nup57-Nsp1-Nic96 heterotetramer (PDB ID 5CWS).
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#27: Protein Nup82


Mass: 82174.047 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Model of Nup82 component of the Saccharomyces cerevisiae cytoplasmic filament complex (PDBDEV_00000010 and PDBDEV_00000051) based on crystal structure of the S. cerevisiae Nup82-Nup159- ...Details: Model of Nup82 component of the Saccharomyces cerevisiae cytoplasmic filament complex (PDBDEV_00000010 and PDBDEV_00000051) based on crystal structure of the S. cerevisiae Nup82-Nup159-Nup116 heterotrimer (PDB ID 3PBP), S. cerevisiae Dyn2-Nup159 heterodimer (PDB ID 4DS1), and the Chaetomium thermophilum Nup49-Nup57-Nsp1-Nic96 heterotetramer (PDB ID 5CWS).
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#28: Protein Nup116 CTD


Mass: 16602.947 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Crystal structure of Saccharomyces cerevisiae Nup116 CTD component of the Nup82-Nup159-Nup116 heterotrimer structure (PDB ID 3PBP) used to interpret the in situ cryo-ET map of the S. cerevisiae NPC.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#29: Protein Dyn2


Mass: 9751.221 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Model of Dyn2 component of the Saccharomyces cerevisiae cytoplasmic filament complex (PDBDEV_00000010 and PDBDEV_00000051) based on crystal structure of the S. cerevisiae Nup82-Nup159-Nup116 ...Details: Model of Dyn2 component of the Saccharomyces cerevisiae cytoplasmic filament complex (PDBDEV_00000010 and PDBDEV_00000051) based on crystal structure of the S. cerevisiae Nup82-Nup159-Nup116 heterotrimer (PDB ID 3PBP), S. cerevisiae Dyn2-Nup159 heterodimer (PDB ID 4DS1), and the Chaetomium thermophilum Nup49-Nup57-Nsp1-Nic96 heterotetramer (PDB ID 5CWS).
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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Protein/peptide , 4 types, 14 molecules B1B2B3B4E1E2E3E4L1L2P1P2P3P4

#2: Protein/peptide
Nup53/Nup59 R3


Mass: 1612.008 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of the Chaetomium thermophilum Nup53/Nup59 R3 ortholog component of the the Nup170-Nup53 heterodimer structure (PDB ID 5HAX). To remain faithful to experimentally ...Details: Crystal structure of the Chaetomium thermophilum Nup53/Nup59 R3 ortholog component of the the Nup170-Nup53 heterodimer structure (PDB ID 5HAX). To remain faithful to experimentally determined structures, we opted to interpret the in situ cryo-ET map of the S. cerevisiae NPC with C. thermophilum crystal structures.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#5: Protein/peptide
Nup53/Nup59 R2


Mass: 1949.145 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of the Chaetomium thermophilum Nup53/Nup59 R2 ortholog component of the the Nic96-Nup53 heterodimer crystal structure (PDB ID 5HB3). To remain faithful to experimentally ...Details: Crystal structure of the Chaetomium thermophilum Nup53/Nup59 R2 ortholog component of the the Nic96-Nup53 heterodimer crystal structure (PDB ID 5HB3). To remain faithful to experimentally determined structures, we opted to interpret the in situ cryo-ET map of the S. cerevisiae NPC with C. thermophilum crystal structures.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#12: Protein/peptide Nup53/Nup59 R1


Mass: 222.241 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Single particle cryo-EM structure of the Chaetomium thermophilum Nup53/Nup59 R1 ortholog component of the the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain ...Details: Single particle cryo-EM structure of the Chaetomium thermophilum Nup53/Nup59 R1 ortholog component of the the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful to experimentally determined structures, we opted to interpret the in situ cryo-ET map of the S. cerevisiae NPC with C. thermophilum single particle cryo-EM structures.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#16: Protein/peptide
Nic96 R1


Mass: 4441.164 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of Chaetomium thermophilum Nic96 R1 ortholog component of the Nup49-Nup57-Nsp1-Nic96 heterotetramer structure (PDB ID 5CWS). To remain faithful to experimentally determined ...Details: Crystal structure of Chaetomium thermophilum Nic96 R1 ortholog component of the Nup49-Nup57-Nsp1-Nic96 heterotetramer structure (PDB ID 5CWS). To remain faithful to experimentally determined structures, we opted to interpret the in situ cryo-ET map of the S. cerevisiae NPC with C. thermophilum crystal structures.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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Nup145N/Nup100/Nup116 ... , 3 types, 8 molecules C2C3C1C4H1H2K1K2

#3: Protein/peptide
Nup145N/Nup100/Nup116 R3


Mass: 1991.335 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of the Chaetomium thermophilum Nup145N/Nup100/Nup116 R3 ortholog component of the the Nup170-Nup145N heterodimer structure (PDB ID 5HB0). To remain faithful to ...Details: Crystal structure of the Chaetomium thermophilum Nup145N/Nup100/Nup116 R3 ortholog component of the the Nup170-Nup145N heterodimer structure (PDB ID 5HB0). To remain faithful to experimentally determined structures, we opted to interpret the in situ cryo-ET map of the S. cerevisiae NPC with C. thermophilum crystal structures.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#8: Protein/peptide Nup145N/Nup100/Nup116 R2


Mass: 1348.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Single particle cryo-EM structure of the Chaetomium thermophilum Nup145N/Nup100/Nup116 R2 ortholog component of the the Nup188-Nic96-Nup145N heterotrimer structure (PDB ID 7MVZ). To remain ...Details: Single particle cryo-EM structure of the Chaetomium thermophilum Nup145N/Nup100/Nup116 R2 ortholog component of the the Nup188-Nic96-Nup145N heterotrimer structure (PDB ID 7MVZ). To remain faithful to experimentally determined structures, we opted to interpret the in situ cryo-ET map of the S. cerevisiae NPC with C. thermophilum single particle cryo-EM structures.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#11: Protein/peptide Nup145N/Nup100/Nup116 R1


Mass: 1062.345 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Single particle cryo-EM structure of the Chaetomium thermophilum Nup145N/Nup100/Nup116 R1 ortholog component of the the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To ...Details: Single particle cryo-EM structure of the Chaetomium thermophilum Nup145N/Nup100/Nup116 R1 ortholog component of the the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful to experimentally determined structures, we opted to interpret the in situ cryo-ET map of the S. cerevisiae NPC with C. thermophilum single particle cryo-EM structures.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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Details

Has ligand of interestN

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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

Component
IDNameTypeEntity IDParent-IDSource
1Nuclear pore complexCOMPLEXall0NATURAL
2Inner ringCOMPLEX#1-#161NATURAL
3Outer ringCOMPLEX#17-#241NATURAL
4Cytoplasmic filament complexCOMPLEX#26-#291NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Saccharomyces cerevisiae (brewer's yeast)4932
32Saccharomyces cerevisiae (brewer's yeast)4932
43Saccharomyces cerevisiae (brewer's yeast)4932
54Saccharomyces cerevisiae (brewer's yeast)4932
Buffer solutionpH: 7.5
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 4 e/Å2 / Avg electron dose per subtomogram: 140 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4000 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 240 / Num. of volumes extracted: 4000
Atomic model buildingDetails: Authors state that the clashes between nucleoporin structures result from docking nucleoporin structures from different species into low-resolution cryo-ET maps of intact NPCs without flexible fitting.

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