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- PDB-7tbl: Composite structure of the human nuclear pore complex (NPC) cytop... -

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Entry
Database: PDB / ID: 7tbl
TitleComposite structure of the human nuclear pore complex (NPC) cytoplasmic face generated with a 12A cryo-ET map of the purified HeLa cell NPC
Components
  • (NUP155) x 3
  • (NUP93 R2) x 2
  • DDX19
  • ELYS
  • GLE1
  • NUP107 CTD
  • NUP107 NTD
  • NUP133
  • NUP160
  • NUP188
  • NUP205
  • NUP214 CCS1
  • NUP214 CCS2
  • NUP214 NTD
  • NUP358
  • NUP37
  • NUP42
  • NUP43
  • NUP53 R1
  • NUP53 R2
  • NUP53 R3
  • NUP53 RRM
  • NUP54
  • NUP54 Ferrodoxin-like domain
  • NUP58
  • NUP62
  • NUP62 CCS1
  • NUP62 CCS2
  • NUP75
  • NUP88 CCS1
  • NUP88 CCS2
  • NUP88 NTD
  • NUP93 R1
  • NUP93 SOL
  • NUP96
  • NUP98 APD
  • NUP98 R1
  • NUP98 R2
  • NUP98 R3
  • SEC13
  • SEH1
KeywordsTRANSPORT PROTEIN / nuclear pore complex / nucleocytoplasmic transport / alpha-helical solenoid / nuclear pore
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 23 Å
AuthorsBley, C.J. / Nie, S. / Mobbs, G.W. / Petrovic, S. / Gres, A.T. / Liu, X. / Mukherjee, S. / Harvey, S. / Huber, F.M. / Lin, D.H. ...Bley, C.J. / Nie, S. / Mobbs, G.W. / Petrovic, S. / Gres, A.T. / Liu, X. / Mukherjee, S. / Harvey, S. / Huber, F.M. / Lin, D.H. / Brown, B. / Tang, A.W. / Rundlet, E.J. / Correia, A.R. / Chen, S. / Regmi, S.G. / Stevens, T.A. / Jette, C.A. / Dasso, M. / Patke, A. / Palazzo, A.F. / Kossiakoff, A.A. / 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: Science / Year: 2022
Title: AI-based structure prediction empowers integrative structural analysis of human nuclear pores
Authors: Mosalaganti, S. / Obarska-Kosinska, A. / Siggel, M. / Taniguchi, R. / Turonova, B. / Zimmerli, C.E. / Buczak, K. / Schmidt, F.H. / Margiotta, E. / Mackmull, M.-T. / Hagen, W.J.H. / Hummer, G. ...Authors: Mosalaganti, S. / Obarska-Kosinska, A. / Siggel, M. / Taniguchi, R. / Turonova, B. / Zimmerli, C.E. / Buczak, K. / Schmidt, F.H. / Margiotta, E. / Mackmull, M.-T. / Hagen, W.J.H. / Hummer, G. / Kosinski, J. / Beck, M.
History
DepositionDec 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 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
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Remark 0THIS ENTRY 7TBL REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN EMD-14322, DETERMINED BY S. ...THIS ENTRY 7TBL REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN EMD-14322, DETERMINED BY S.Mosalaganti,A.Obarska-Kosinska,M.Siggel,R.Taniguchi,B.Turonova, C.E.Zimmerli,K.Buczak,F.H.Schmidt,E.Margiotta,M.T.Mackmull,W.J.H.Hagen,G.Hummer,J.Kosinski,M.Beck

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A1: NUP155
A2: NUP155
A3: NUP155
A4: NUP155
A5: NUP155
A6: NUP155
B1: NUP53 R3
B2: NUP53 R3
B3: NUP53 R3
B4: NUP53 R3
B5: NUP53 R3
B6: NUP53 R3
C1: NUP98 R3
C2: NUP98 R3
C3: NUP98 R3
C4: NUP98 R3
C5: NUP98 R3
C6: NUP98 R3
D1: NUP93 SOL
D2: NUP93 SOL
D3: NUP93 SOL
D4: NUP93 SOL
D5: NUP93 SOL
D6: NUP93 SOL
D7: NUP93 SOL
E1: NUP53 R2
E2: NUP53 R2
E3: NUP53 R2
E4: NUP53 R2
E5: NUP53 R2
E6: NUP53 R2
E7: NUP53 R2
F1: NUP188
F2: NUP188
G1: NUP93 R2
G2: NUP93 R2
H1: NUP98 R2
H2: NUP98 R2
I1: NUP205
I2: NUP205
I3: NUP205
I4: NUP205
I5: NUP205
J1: NUP93 R2
J2: NUP93 R2
J3: NUP93 R2
J4: NUP93 R2
J5: NUP93 R2
K1: NUP98 R1
K2: NUP98 R1
K3: NUP98 R1
K4: NUP98 R1
K5: NUP98 R1
L1: NUP53 R1
L2: NUP53 R1
L3: NUP53 R1
L4: NUP53 R1
L5: NUP53 R1
M1: NUP62
M2: NUP62
M3: NUP62
M4: NUP62
N1: NUP58
N2: NUP58
N3: NUP58
N4: NUP58
O1: NUP54
O2: NUP54
O3: NUP54
O4: NUP54
P1: NUP54 Ferrodoxin-like domain
P2: NUP54 Ferrodoxin-like domain
P3: NUP54 Ferrodoxin-like domain
P4: NUP54 Ferrodoxin-like domain
Q1: NUP53 RRM
Q2: NUP53 RRM
Q3: NUP53 RRM
Q4: NUP53 RRM
R1: NUP93 R1
R2: NUP93 R1
R3: NUP93 R1
R4: NUP93 R1
S1: NUP133
S2: NUP133
S3: NUP133
S4: NUP133
T1: NUP107 CTD
T2: NUP107 CTD
T3: NUP107 CTD
T4: NUP107 CTD
U1: NUP107 NTD
U2: NUP107 NTD
U3: NUP107 NTD
U4: NUP107 NTD
V1: NUP96
V2: NUP96
V3: NUP96
V4: NUP96
W1: SEC13
W2: SEC13
W3: SEC13
W4: SEC13
X1: NUP75
X2: NUP75
X3: NUP75
X4: NUP75
Y1: SEH1
Y2: SEH1
Y3: SEH1
Y4: SEH1
Z1: NUP160
Z2: NUP160
Z3: NUP160
Z4: NUP160
a1: NUP43
a2: NUP43
a3: NUP43
a4: NUP43
b1: NUP37
b2: NUP37
b3: NUP37
b4: NUP37
c1: NUP358
c2: NUP358
c3: NUP358
c4: NUP358
c5: NUP358
d1: ELYS
d2: ELYS
e: GLE1
f: NUP42
g: NUP214 NTD
h: DDX19
i: NUP88 NTD
j: NUP98 APD
k1: NUP62 CCS1
k2: NUP62 CCS2
l1: NUP214 CCS1
l2: NUP214 CCS2
m1: NUP88 CCS1
m2: NUP88 CCS2


Theoretical massNumber of molelcules
Total (without water)6,611,248141
Polymers6,611,248141
Non-polymers00
Water00
1
A1: NUP155
A2: NUP155
A3: NUP155
A4: NUP155
A5: NUP155
A6: NUP155
B1: NUP53 R3
B2: NUP53 R3
B3: NUP53 R3
B4: NUP53 R3
B5: NUP53 R3
B6: NUP53 R3
C1: NUP98 R3
C2: NUP98 R3
C3: NUP98 R3
C4: NUP98 R3
C5: NUP98 R3
C6: NUP98 R3
D1: NUP93 SOL
D2: NUP93 SOL
D3: NUP93 SOL
D4: NUP93 SOL
D5: NUP93 SOL
D6: NUP93 SOL
D7: NUP93 SOL
E1: NUP53 R2
E2: NUP53 R2
E3: NUP53 R2
E4: NUP53 R2
E5: NUP53 R2
E6: NUP53 R2
E7: NUP53 R2
F1: NUP188
F2: NUP188
G1: NUP93 R2
G2: NUP93 R2
H1: NUP98 R2
H2: NUP98 R2
I1: NUP205
I2: NUP205
I3: NUP205
I4: NUP205
I5: NUP205
J1: NUP93 R2
J2: NUP93 R2
J3: NUP93 R2
J4: NUP93 R2
J5: NUP93 R2
K1: NUP98 R1
K2: NUP98 R1
K3: NUP98 R1
K4: NUP98 R1
K5: NUP98 R1
L1: NUP53 R1
L2: NUP53 R1
L3: NUP53 R1
L4: NUP53 R1
L5: NUP53 R1
M1: NUP62
M2: NUP62
M3: NUP62
M4: NUP62
N1: NUP58
N2: NUP58
N3: NUP58
N4: NUP58
O1: NUP54
O2: NUP54
O3: NUP54
O4: NUP54
P1: NUP54 Ferrodoxin-like domain
P2: NUP54 Ferrodoxin-like domain
P3: NUP54 Ferrodoxin-like domain
P4: NUP54 Ferrodoxin-like domain
Q1: NUP53 RRM
Q2: NUP53 RRM
Q3: NUP53 RRM
Q4: NUP53 RRM
R1: NUP93 R1
R2: NUP93 R1
R3: NUP93 R1
R4: NUP93 R1
S1: NUP133
S2: NUP133
S3: NUP133
S4: NUP133
T1: NUP107 CTD
T2: NUP107 CTD
T3: NUP107 CTD
T4: NUP107 CTD
U1: NUP107 NTD
U2: NUP107 NTD
U3: NUP107 NTD
U4: NUP107 NTD
V1: NUP96
V2: NUP96
V3: NUP96
V4: NUP96
W1: SEC13
W2: SEC13
W3: SEC13
W4: SEC13
X1: NUP75
X2: NUP75
X3: NUP75
X4: NUP75
Y1: SEH1
Y2: SEH1
Y3: SEH1
Y4: SEH1
Z1: NUP160
Z2: NUP160
Z3: NUP160
Z4: NUP160
a1: NUP43
a2: NUP43
a3: NUP43
a4: NUP43
b1: NUP37
b2: NUP37
b3: NUP37
b4: NUP37
c1: NUP358
c2: NUP358
c3: NUP358
c4: NUP358
c5: NUP358
d1: ELYS
d2: ELYS
e: GLE1
f: NUP42
g: NUP214 NTD
h: DDX19
i: NUP88 NTD
j: NUP98 APD
k1: NUP62 CCS1
k2: NUP62 CCS2
l1: NUP214 CCS1
l2: NUP214 CCS2
m1: NUP88 CCS1
m2: NUP88 CCS2
x 8


Theoretical massNumber of molelcules
Total (without water)52,889,9841128
Polymers52,889,9841128
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation7

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Components

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Protein , 33 types, 102 molecules A1A3A2A4A5A6D1D2D3D4D5D6D7F1F2G1G2I1I2I3I4I5J1J2J3J4J5M1M2M3...

#1: Protein NUP155


Mass: 146062.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Composite structure of the Chaetomium thermophilum NUP155 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 NUP155 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 cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#2: Protein NUP155


Mass: 148044.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Composite structure of the Chaetomium thermophilum NUP155 ortholog generated by superposition of fragment crystal structures (PDB IDs 5HB0, 5HAY, and 5HAX ). To remain faithful to ...Details: Composite structure of the Chaetomium thermophilum NUP155 ortholog generated by superposition of fragment crystal structures (PDB IDs 5HB0, 5HAY, and 5HAX ). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#3: Protein NUP155


Mass: 148637.641 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Composite structure of the Chaetomium thermophilum NUP155 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 NUP155 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 cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#6: Protein
NUP93 SOL


Mass: 74012.406 Da / Num. of mol.: 7 / Source method: isolated from a natural source
Details: Crystal structure of the Homo sapiens NUP93 SOL component of the NUP93-NUP53 heterodimer crystal structure (PDB ID 7MW1) used to interpret the cryo-ET map of the Homo sapiens NPC.
Source: (natural) Homo sapiens (human)
#8: Protein NUP188


Mass: 204007.312 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 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 Nup188-Nic96-Nup145N heterotrimer structure (PDB ID 7MVZ). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog single particle cryo-EM structures.
Source: (natural) Homo sapiens (human)
#9: Protein NUP93 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 NUP93 R2 ortholog component of the Nup188-Nic96-Nup145N heterotrimer structure (PDB ID 7MVZ). To remain faithful to ...Details: Single particle cryo-EM structure of the Chaetomium thermophilum NUP93 R2 ortholog component of the Nup188-Nic96-Nup145N heterotrimer structure (PDB ID 7MVZ). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog single particle cryo-EM structures.
Source: (natural) Homo sapiens (human)
#11: Protein
NUP205


Mass: 197137.406 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Details: Single particle cryo-EM structure of the Chaetomium thermophilum NUP205 ortholog component of the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful to ...Details: Single particle cryo-EM structure of the Chaetomium thermophilum NUP205 ortholog component of the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog single particle cryo-EM structures.
Source: (natural) Homo sapiens (human)
#12: Protein
NUP93 R2


Mass: 7173.938 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Details: Single particle cryo-EM structure of the Chaetomium thermophilum NUP93 R2 ortholog component of the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful to ...Details: Single particle cryo-EM structure of the Chaetomium thermophilum NUP93 R2 ortholog component of the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog single particle cryo-EM structures.
Source: (natural) Homo sapiens (human)
#15: Protein
NUP62


Mass: 20965.451 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of the Chaetomium thermophilum NUP62 ortholog component of the Nup49-Nup57-Nsp1-Nic96 heterotetramer structure (PDB ID 5CWS). To remain faithful to experimentally ...Details: Crystal structure of the Chaetomium thermophilum NUP62 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 cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#16: Protein
NUP58


Mass: 24065.980 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of the Chaetomium thermophilum NUP58 ortholog component of the Nup49-Nup57-Nsp1-Nic96 heterotetramer structure (PDB ID 5CWS). To remain faithful to experimentally ...Details: Crystal structure of the Chaetomium thermophilum NUP58 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 cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#17: Protein
NUP54


Mass: 27988.756 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of the Chaetomium thermophilum NUP54 ortholog component of the Nup49-Nup57-Nsp1-Nic96 heterotetramer structure (PDB ID 5CWS). To remain faithful to experimentally ...Details: Crystal structure of the Chaetomium thermophilum NUP54 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 cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#18: Protein
NUP54 Ferrodoxin-like domain


Mass: 12745.392 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of Xenopus laevis NUP54 Ferrodoxin-like domain ortholog (PDB ID 5C2U). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of ...Details: Crystal structure of Xenopus laevis NUP54 Ferrodoxin-like domain ortholog (PDB ID 5C2U). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#19: Protein
NUP53 RRM


Mass: 9693.498 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of Homo sapiens NUP53 RRM (PDB ID 4LIR) used to interpret the cryo-ET map of the Homo sapiens NPC.
Source: (natural) Homo sapiens (human)
#21: Protein
NUP133


Mass: 129108.461 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structures of Homo sapiens NUP133 component of the NUP107-NUP133 heterodimer structure (PDB ID 3CQC) and NUP133 NTD (PDB ID 1XKS) used to interpret the cryo-ET map of the Homo sapiens NPC.
Source: (natural) Homo sapiens (human)
#22: Protein
NUP107 CTD


Mass: 30176.793 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of Homo sapiens NUP107 component of the NUP107-NUP133 heterodimer structure (PDB ID 3CQC) used to interpret the cryo-ET map of the Homo sapiens NPC.
Source: (natural) Homo sapiens (human)
#23: Protein
NUP107 NTD


Mass: 50170.684 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of the Saccharomyces cerevisiae NUP107 ortholog component of the coat nucleoporin complex (CNC) hexamer structure (PDB ID 4XMM). To remain faithful to experimentally ...Details: Crystal structure of the Saccharomyces cerevisiae NUP107 ortholog component of the coat nucleoporin complex (CNC) hexamer structure (PDB ID 4XMM). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#24: Protein
NUP96


Mass: 71195.070 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of the Saccharomyces cerevisiae NUP96 ortholog component of the coat nucleoporin complex (CNC) hexamer structure (PDB ID 4XMM). To remain faithful to experimentally ...Details: Crystal structure of the Saccharomyces cerevisiae NUP96 ortholog component of the coat nucleoporin complex (CNC) hexamer structure (PDB ID 4XMM). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#25: Protein
SEC13


Mass: 31889.578 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of the Saccharomyces cerevisiae SEC13 ortholog component of the coat nucleoporin complex (CNC) hexamer structure (PDB ID 4XMM). To remain faithful to experimentally ...Details: Crystal structure of the Saccharomyces cerevisiae SEC13 ortholog component of the coat nucleoporin complex (CNC) hexamer structure (PDB ID 4XMM). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#26: Protein
NUP75


Mass: 84972.438 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of the Saccharomyces cerevisiae NUP75 ortholog component of the coat nucleoporin complex (CNC) hexamer structure (PDB ID 4XMM). To remain faithful to experimentally ...Details: Crystal structure of the Saccharomyces cerevisiae NUP75 ortholog component of the coat nucleoporin complex (CNC) hexamer structure (PDB ID 4XMM). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#27: Protein
SEH1


Mass: 39170.758 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of the Saccharomyces cerevisiae SEH1 ortholog component of the coat nucleoporin complex (CNC) hexamer structure (PDB ID 4XMM). To remain faithful to experimentally ...Details: Crystal structure of the Saccharomyces cerevisiae SEH1 ortholog component of the coat nucleoporin complex (CNC) hexamer structure (PDB ID 4XMM). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#28: Protein
NUP160


Mass: 120560.328 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of the Saccharomyces cerevisiae NUP160 ortholog component of the coat nucleoporin complex (CNC) hexamer structure (PDB ID 4XMM). To remain faithful to experimentally ...Details: Crystal structure of the Saccharomyces cerevisiae NUP160 ortholog component of the coat nucleoporin complex (CNC) hexamer structure (PDB ID 4XMM). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#29: Protein
NUP43


Mass: 42195.652 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of Homo sapiens NUP43 (PDB ID 4I79) used to interpret the cryo-ET map of the Homo sapiens NPC.
Source: (natural) Homo sapiens (human)
#30: Protein
NUP37


Mass: 42807.066 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of the Schizosaccharomyces pombe NUP37 ortholog (PDB ID 4FHN). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo ...Details: Crystal structure of the Schizosaccharomyces pombe NUP37 ortholog (PDB ID 4FHN). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#31: Protein
NUP358


Mass: 85947.266 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Details: Crystal structure of Homo sapiens NUP358 NTD (PDB ID 7MNL) used to interpret the cryo-ET map of the Homo sapiens NPC.
Source: (natural) Homo sapiens (human)
#32: Protein ELYS


Mass: 54375.723 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Crystal structure of the Mus musculus ELYS NTD ortholog (PDB ID 4I0O). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens ...Details: Crystal structure of the Mus musculus ELYS NTD ortholog (PDB ID 4I0O). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#33: Protein GLE1


Mass: 36243.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Crystal structure of the Homo sapiens GLE1 CTD component of the GLE1-NUP42 heterodimer structure (PDB ID 6B4F) used to interpret the cryo-ET map of the Homo sapiens NPC.
Source: (natural) Homo sapiens (human)
#35: Protein NUP214 NTD


Mass: 46809.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Crystal structure of the Homo sapiens NUP214 NTD component of the NUP214-DDX19 heterodimer structure (PDB ID 3FMO) used to interpret the cryo-ET map of the Homo sapiens NPC.
Source: (natural) Homo sapiens (human)
#36: Protein DDX19


Mass: 26180.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Crystal structure of the Homo sapiens DDX19 component of the NUP214-DDX19 heterodimer structure (PDB ID 3FMO) used to interpret the cryo-ET map of the Homo sapiens NPC.
Source: (natural) Homo sapiens (human)
#37: Protein NUP88 NTD


Mass: 53462.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Crystal structure of Homo sapiens NUP88 NTD component of the NUP88-NUP98 heterodimer structure (PDB ID 7MNI) used to interpret the cryo-ET map of the Homo sapiens NPC.
Source: (natural) Homo sapiens (human)
#38: Protein NUP98 APD


Mass: 16969.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Crystal structure of Homo sapiens NUP98 APD component of the NUP88-NUP98 heterodimer structure (PDB ID 7MNI) used to interpret the cryo-ET map of the Homo sapiens NPC.
Source: (natural) Homo sapiens (human)
#39: Protein NUP62 CCS1


Mass: 10260.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Crystal structure of Xenopus laevis NUP62 CCS1 ortholog component of the channel nucleoporin heterotrimer (CNT; NUP62-NUP54-NUP58) structure (PDB ID 5C3L). To remain faithful to ...Details: Crystal structure of Xenopus laevis NUP62 CCS1 ortholog component of the channel nucleoporin heterotrimer (CNT; NUP62-NUP54-NUP58) structure (PDB ID 5C3L). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#41: Protein NUP214 CCS1


Mass: 7847.665 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Poly-alanine model of the NUP214 CCS1 based on the Xenopus laevis and Chaetomium thermophilum channel nucleoporin heterotrimer (CNT; NUP62-NUP54-NUP58) crystal structures (PDB ID 5C3L and 5CWS).
Source: (natural) Homo sapiens (human)
#43: Protein NUP88 CCS1


Mass: 7507.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Poly-alanine model of the NUP88 CCS1 based on the Xenopus laevis and Chaetomium thermophilum channel nucleoporin heterotrimer (CNT; NUP62-NUP54-NUP58) crystal structures (PDB ID 5C3L and 5CWS).
Source: (natural) Homo sapiens (human)

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Protein/peptide , 11 types, 39 molecules B1B2B3B4B5B6C1C2C3C4C5C6E1E2E3E4E5E6E7H1H2K1K2K3K4K5L1L2L3L4...

#4: Protein/peptide
NUP53 R3


Mass: 1612.008 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: Crystal structure of the Chaetomium thermophilum NUP53 R3 ortholog component of the Nup170-Nup53 heterodimer structure (PDB ID 5HAX). To remain faithful to experimentally determined ...Details: Crystal structure of the Chaetomium thermophilum NUP53 R3 ortholog component of the Nup170-Nup53 heterodimer structure (PDB ID 5HAX). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#5: Protein/peptide
NUP98 R3


Mass: 2258.661 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: Crystal structure of the Chaetomium thermophilum NUP98 R3 ortholog component of the Nup170-Nup145N heterodimer structure (PDB ID 5HB0). To remain faithful to experimentally determined ...Details: Crystal structure of the Chaetomium thermophilum NUP98 R3 ortholog component of the Nup170-Nup145N heterodimer structure (PDB ID 5HB0). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#7: Protein/peptide
NUP53 R2


Mass: 903.057 Da / Num. of mol.: 7 / Source method: isolated from a natural source
Details: Crystal structure of the Homo sapiens NUP53 R2 component of the NUP93-NUP53 heterodimer crystal structure (PDB ID 7MW1) used to interpret the cryo-ET map of the Homo sapiens NPC.
Source: (natural) Homo sapiens (human)
#10: Protein/peptide NUP98 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 NUP98 R2 ortholog component of the Nup188-Nic96-Nup145N heterotrimer structure (PDB ID 7MVZ). To remain faithful to ...Details: Single particle cryo-EM structure of the Chaetomium thermophilum NUP98 R2 ortholog component of the Nup188-Nic96-Nup145N heterotrimer structure (PDB ID 7MVZ). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog single particle cryo-EM structures.
Source: (natural) Homo sapiens (human)
#13: Protein/peptide
NUP98 R1


Mass: 1062.345 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Details: Single particle cryo-EM structure of the Chaetomium thermophilum NUP98 R1 ortholog component of the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful to ...Details: Single particle cryo-EM structure of the Chaetomium thermophilum NUP98 R1 ortholog component of the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog single particle cryo-EM structures.
Source: (natural) Homo sapiens (human)
#14: Protein/peptide
NUP53 R1


Mass: 222.241 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Details: Single particle cryo-EM structure of the Chaetomium thermophilum NUP53 R1 ortholog component of the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful to ...Details: Single particle cryo-EM structure of the Chaetomium thermophilum NUP53 R1 ortholog component of the Nup192-Nic96-Nup53-Nup145N heterotetramer structure (PDB ID 7MVV). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog single particle cryo-EM structures.
Source: (natural) Homo sapiens (human)
#20: Protein/peptide
NUP93 R1


Mass: 4441.164 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Crystal structure of the Chaetomium thermophilum NUP93 R1 ortholog component of the Nup49-Nup57-Nsp1-Nic96 heterotetramer structure (PDB ID 5CWS). To remain faithful to experimentally ...Details: Crystal structure of the Chaetomium thermophilum NUP93 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 cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#34: Protein/peptide NUP42


Mass: 5141.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Crystal structure of the Homo sapiens NUP42 GBM component of the GLE1-NUP42 heterodimer structure (PDB ID 6B4F) used to interpret the cryo-ET map of the Homo sapiens NPC.
Source: (natural) Homo sapiens (human)
#40: Protein/peptide NUP62 CCS2


Mass: 4416.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Crystal structure of Xenopus laevis NUP62 CCS2 ortholog component of the channel nucleoporin heterotrimer (CNT; NUP62-NUP54-NUP58) structure (PDB ID 5C3L). To remain faithful to ...Details: Crystal structure of Xenopus laevis NUP62 CCS2 ortholog component of the channel nucleoporin heterotrimer (CNT; NUP62-NUP54-NUP58) structure (PDB ID 5C3L). To remain faithful to experimentally determined structures, we opted to interpret the cryo-ET map of the Homo sapiens NPC with ortholog crystal structures.
Source: (natural) Homo sapiens (human)
#42: Protein/peptide NUP214 CCS2


Mass: 3337.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Poly-alanine model of the NUP214 CCS2 based on the Xenopus laevis and Chaetomium thermophilum channel nucleoporin heterotrimer (CNT; NUP62-NUP54-NUP58) crystal structures (PDB ID 5C3L and 5CWS).
Source: (natural) Homo sapiens (human)
#44: Protein/peptide NUP88 CCS2


Mass: 1720.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Poly-alanine model of the NUP88 CCS2 based on the Xenopus laevis and Chaetomium thermophilum channel nucleoporin heterotrimer (CNT; NUP62-NUP54-NUP58) crystal structures (PDB ID 5C3L and 5CWS).
Source: (natural) Homo sapiens (human)

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Nuclear pore complex from purified HeLa cell nuclear envelopes.
Type: COMPLEX / Entity ID: #1-#2, #4-#44 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
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: 4000 nm / Nominal defocus min: 1900 nm
Image recordingElectron dose: 4 e/Å2 / Avg electron dose per subtomogram: 110 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: 23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17368 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 170 / Num. of volumes extracted: 17368
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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