9A1M | pdb_00009a1m

Integrative model of the nuclear pore complex from Schizosaccharomyces pombe

Integrative structure models are generated using different types of input information, including varied experimental data, physical principles, statistical preferences, and other prior information.

• PDB DOI: https://doi.org/10.2210/pdb9A1M/pdb

• Mutation(s): No 


• Deposited: 2021-10-20 Released: 2021-11-12 
• Deposition Author(s): Christian E. Zimmerli, Matteo Allegretti, Vasileios Rantos, Sara K. Goetz, Agnieszka Obarska-Kosinska, Ievgeniia Zagoriy, Aliaksandr Halavatyi, Gerhard Hummer, Julia Mahamid, Jan Kosinski, Martin Beck

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Integrative Structure Snapshot

• Multi-Scale: No 
• Multi-State: No 
• Ordered-State: No 
• Deposited Models: 1 
• Representative Model: 1 

Literature

Nuclear pores dilate and constrict in cellulo

Christian E. Zimmerli, Matteo Allegretti, Vasileios Rantos, Sara K. Goetz, Agnieszka Obarska-Kosinska, Ievgeniia Zagoriy, Aliaksandr Halavatyi, Gerhard Hummer, Julia Mahamid, Jan Kosinski, Martin Beck

(2021) Science 

• PubMed: 34762489 
• DOI: https://doi.org/10.1126/science.abd9776
• Primary Citation Related Structures: 
  9A1M, 9A1N, 9A1O


• PubMed Abstract: 
  

  In eukaryotic cells, nuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes and mediate nucleocytoplasmic exchange. They are made of 30 different nucleoporins and form a cylindrical architecture around an aqueous central channel. This architecture is highly dynamic in space and time. Variations in NPC diameter have been reported, but the physiological circumstances and the molecular details remain unknown. Here, we combined cryo–electron tomography with integrative structural modeling to capture a molecular movie of the respective large-scale conformational changes in cellulo. Although NPCs of exponentially growing cells adopted a dilated conformation, they reversibly constricted upon cellular energy depletion or conditions of hypertonic osmotic stress. Our data point to a model where the nuclear envelope membrane tension is linked to the conformation of the NPC.

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Organizational Affiliation: 
• Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.
Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany.
Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.
Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany.
EMBL Hamburg, 22607 Hamburg, Germany.
Advanced Light Microscopy Facility, EMBL, 69117 Heidelberg, Germany.
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.
Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.

Assembly  

Global Symmetry: Cyclic - C8  (Explore in 3D)
Global Stoichiometry: Hetero 392-mer - A32B32C32D32E32F24G24H24I24J24K24L24M16N16O16P16 Pseudo Symmetry: Cyclic - C8  (Explore in 3D)
Pseudo Stoichiometry: Hetero 392-mer - A72B32C32D32E32F32G24H24I24J24K16L16M16N8O8 

Macromolecule Content 

• Total Structure Weight: 38,218.06 kDa 
• Atom Count: 1,893,744 
• Modeled Residue Count: 293,440 
• Deposited Residue Count: 293,440 
• Unique protein chains: 16

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup107	L, L1, L10, L11, L12, L13, L14, L15, L2, L3, L4, L5, L6, L7, L8, L9	813	N/A	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup85	P, P1, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19, P2, P20, P21, P22, P23, P3, P4, P5, P6, P7, P8, P9	675	N/A	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup120	R, R1, R10, R11, R12, R13, R14, R15, R16, R17, R18, R19, R2, R20, R21, R22, R23, R3, R4, R5, R6, R7, R8, R9	1,136	N/A	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup37	S, S1, S10, S11, S12, S13, S14, S15, S16, S17, S18, S19, S2, S20, S21, S22, S23, S3, S4, S5, S6, S7, S8, S9	391	N/A	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup132	Q, Q1, Q10, Q11, Q12, Q13, Q14, Q15, Q2, Q3, Q4, Q5, Q6, Q7, Q8, Q9	1,162	N/A	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup189c	M, M1, M10, M11, M12, M13, M14, M15, M16, M17, M18, M19, M2, M20, M21, M22, M23, M3, M4, M5, M6, M7, M8, M9	844	N/A	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Seh1	O, O1, O10, O11, O12, O13, O14, O15, O16, O17, O18, O19, O2, O20, O21, O22, O23, O3, O4, O5, O6, O7, O8, O9	339	N/A	Mutation(s): 0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Sec13	N, N1, N10, N11, N12, N13, N14, N15, N16, N17, N18, N19, N2, N20, N21, N22, N23, N3, N4, N5, N6, N7, N8, N9	297	N/A	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Ely5	T, T1, T10, T11, T12, T13, T14, T15, T16, T17, T18, T19, T2, T20, T21, T22, T23, T3, T4, T5, T6, T7, T8, T9	298	N/A	Mutation(s): 0

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup184	B, B1, B10, B11, B12, B13, B14, B15, B2, B3, B4, B5, B6, B7, B8, B9	1,564	N/A	Mutation(s): 0

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup186	C, C1, C10, C11, C12, C13, C14, C15, C2, C3, C4, C5, C6, C7, C8, C9	1,647	N/A	Mutation(s): 0

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup155	D, D1, D10, D11, D12, D13, D14, D15, D16, D17, D18, D19, D2, D20, D21, D22, D23, D24, D25, D26, D27, D28, D29, D3, D30, D31, D4, D5, D6, D7, D8, D9	1,315	N/A	Mutation(s): 0

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup97	Y, Y1, Y10, Y11, Y12, Y13, Y14, Y15, Y16, Y17, Y18, Y19, Y2, Y20, Y21, Y22, Y23, Y24, Y25, Y26, Y27, Y28, Y29, Y3, Y30, Y31, Y4, Y5, Y6, Y7, Y8, Y9	851	N/A	Mutation(s): 0

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Nsp1	J, J1, J10, J11, J12, J13, J14, J15, J16, J17, J18, J19, J2, J20, J21, J22, J23, J24, J25, J26, J27, J28, J29, J3, J30, J31, J4, J5, J6, J7, J8, J9	598	N/A	Mutation(s): 0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup44	H, H1, H10, H11, H12, H13, H14, H15, H16, H17, H18, H19, H2, H20, H21, H22, H23, H24, H25, H26, H27, H28, H29, H3, H30, H31, H4, H5, H6, H7, H8, H9	403	N/A	Mutation(s): 0

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup45	I, I1, I10, I11, I12, I13, I14, I15, I16, I17, I18, I19, I2, I20, I21, I22, I23, I24, I25, I26, I27, I28, I29, I3, I30, I31, I4, I5, I6, I7, I8, I9	425	N/A	Mutation(s): 0

Experimental Data & Validation

Integrative Structure Snapshot

• Multi-Scale: No 
• Multi-State: No 
• Ordered-State: No 
• Deposited Models: 1 
• Representative Model: 1 

Structure Validation

View Full Validation Report

View Summary Validation Report

Entry History 

Deposition Data

• Released Date: 2021-11-12 
Deposition Author(s): Christian E. Zimmerli, Matteo Allegretti, Vasileios Rantos, Sara K. Goetz, Agnieszka Obarska-Kosinska, Ievgeniia Zagoriy, Aliaksandr Halavatyi, Gerhard Hummer, Julia Mahamid, Jan Kosinski, Martin Beck

Revision History  

• Version 1.0: 2021-11-12
  Type: Initial release