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- PDB-7tbk: Composite structure of the dilated human nuclear pore complex (NP... -

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Entry
Database: PDB / ID: 7tbk
TitleComposite structure of the dilated human nuclear pore complex (NPC) symmetric core generated with a 37A in situ cryo-ET map of CD4+ T cell NPC
Components
  • (NUP155Nucleoporin 155) x 3
  • (NUP54 Ferrodoxin-like ...) x 2
  • (NUP93 R2) x 2
  • NUP107 CTD
  • NUP107 NTD
  • NUP133Nuclear pore complex protein Nup133
  • NUP160Nucleoporin 160
  • NUP188Nucleoporin 188
  • NUP205Nucleoporin 205
  • NUP37Nucleoporin 37
  • NUP43Nucleoporin 43
  • NUP53 R1
  • NUP53 R2
  • NUP53 R3
  • NUP54Nucleoporin 54
  • NUP58
  • NUP62Nuclear pore glycoprotein p62
  • NUP75
  • NUP93 R1
  • NUP93 SOL
  • NUP96
  • 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: 37 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: Cell / Year: 2021
Title: Cone-shaped HIV-1 capsids are transported through intact nuclear pores.
Authors: Vojtech Zila / Erica Margiotta / Beata Turoňová / Thorsten G Müller / Christian E Zimmerli / Simone Mattei / Matteo Allegretti / Kathleen Börner / Jona Rada / Barbara Müller / Marina ...Authors: Vojtech Zila / Erica Margiotta / Beata Turoňová / Thorsten G Müller / Christian E Zimmerli / Simone Mattei / Matteo Allegretti / Kathleen Börner / Jona Rada / Barbara Müller / Marina Lusic / Hans-Georg Kräusslich / Martin Beck /
Abstract: Human immunodeficiency virus (HIV-1) remains a major health threat. Viral capsid uncoating and nuclear import of the viral genome are critical for productive infection. The size of the HIV-1 capsid ...Human immunodeficiency virus (HIV-1) remains a major health threat. Viral capsid uncoating and nuclear import of the viral genome are critical for productive infection. The size of the HIV-1 capsid is generally believed to exceed the diameter of the nuclear pore complex (NPC), indicating that capsid uncoating has to occur prior to nuclear import. Here, we combined correlative light and electron microscopy with subtomogram averaging to capture the structural status of reverse transcription-competent HIV-1 complexes in infected T cells. We demonstrated that the diameter of the NPC in cellulo is sufficient for the import of apparently intact, cone-shaped capsids. Subsequent to nuclear import, we detected disrupted and empty capsid fragments, indicating that uncoating of the replication complex occurs by breaking the capsid open, and not by disassembly into individual subunits. Our data directly visualize a key step in HIV-1 replication and enhance our mechanistic understanding of the viral life cycle.
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 7TBK REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN EMD-11967, DETERMINED BY E. ...THIS ENTRY 7TBK REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN EMD-11967, DETERMINED BY E.Margiotta,M.Beck

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: NUP54 Ferrodoxin-like domain
Q2: NUP54 Ferrodoxin-like domain
Q3: NUP54 Ferrodoxin-like domain
Q4: NUP54 Ferrodoxin-like domain
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


Theoretical massNumber of molelcules
Total (without water)5,829,999122
Polymers5,829,999122
Non-polymers00
Water0
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: NUP54 Ferrodoxin-like domain
Q2: NUP54 Ferrodoxin-like domain
Q3: NUP54 Ferrodoxin-like domain
Q4: NUP54 Ferrodoxin-like domain
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
x 8


  • defined by author
  • Evidence: electron microscopy
  • 46.6 MDa, 976 polymers
Theoretical massNumber of molelcules
Total (without water)46,639,990976
Polymers46,639,990976
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation7

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Components

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Protein , 21 types, 79 molecules A1A3A2A4A5A6D1D2D3D4D5D6D7F1F2G1G2I1I2I3I4I5J1J2J3J4J5M1M2M3...

#1: Protein NUP155 / Nucleoporin 155


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 / Nucleoporin 155


Mass: 148044.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Composite structure of Chaetomium thermophilum NUP155 ortholog generated by superposition of crystal structures (PDB IDs 5HB0, 5HAY, and 5HAX ). To remain faithful to experimentally ...Details: Composite structure of Chaetomium thermophilum NUP155 ortholog generated by superposition of 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 / Nucleoporin 155


Mass: 148335.266 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)
#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 / Nucleoporin 188


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 / Nucleoporin 205


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 / Nuclear pore glycoprotein p62


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 / Nucleoporin 54


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)
#21: Protein
NUP133 / Nuclear pore complex 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: 79734.820 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: 38843.422 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 / Nucleoporin 160


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 / Nucleoporin 43


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 / Nucleoporin 37


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)

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Protein/peptide , 7 types, 35 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)

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NUP54 Ferrodoxin-like ... , 2 types, 8 molecules P1P2P3P4Q1Q2Q3Q4

#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
NUP54 Ferrodoxin-like domain


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)

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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

ComponentName: Nuclear pore complex from human CD4+ T cells.Nuclear pore
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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 FIELDBright-field microscopy / Nominal defocus max: 4500 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 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 792 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 99 / Num. of volumes extracted: 792
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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