OCA Atlas for 5IJN

5IJN

Transport Protein

date

Mar 02, 2016

title

Composite Structure Of The Inner Ring Of The Human Nuclear P Complex (32 Copies Of Nup205)

authors

J.Kosinski, S.Mosalaganti, A.Von Appen, M.Beck

compound

source

Molecule: Nuclear Pore Complex Protein Nup155
Chain: A, B, E, K, Q, W
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hela

Molecule: Nuclear Pore Complex Protein Nup93
Chain: C, I, O, U
Engineered: Yes

Molecule: Nuclear Pore Complex Protein Nup205
Chain: D, J, P, V
Engineered: Yes

Molecule: Nuclear Pore Complex Protein Nup54
Chain: F, L, R, X
Engineered: Yes

Molecule: Nuclear Pore Complex Protein Nup58
Chain: G, M, S, Y
Engineered: Yes

Molecule: Nuclear Pore Glycoprotein P62
Chain: H, N, T, Z
Synonym: 62 Kda Nucleoporin,Nucleoporin Nup62
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela
Gene: Nup62
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hela

symmetry

Space Group: P 1

R_factor

R_Free

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
1.000	1.000	1.000	90.00	90.00	90.00

method

Electron Microscopy

resolution

21.40 Å

Gene
Ontology

Chain	Function	Process	Component
C, O, I, U		intracellular transport of v...
F, L, X, R		intracellular transport of v...
K, E, Q, A, W, B		intracellular transport of v...
S, Y, M, G		intracellular transport of v...
T, N, Z, H		intracellular transport of v...
V, J, P, D		intracellular transport of v...

Primary reference

Molecular architecture of the inner ring scaffold of the human nuclear pore complex., Kosinski J, Mosalaganti S, von Appen A, Teimer R, DiGuilio AL, Wan W, Bui KH, Hagen WJ, Briggs JA, Glavy JS, Hurt E, Beck M, Science. 2016 Apr 15;352(6283):363-5. doi: 10.1126/science.aaf0643. PMID:27081072

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (11002 Kb) [Save to disk]

Biological Unit Coordinates (5ijn.pdb1.gz) 10033 Kb

CSU: Contacts of Structural Units for 5IJN

Retrieve 5IJN in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 5IJN from S2C, [Save to disk]

View 5IJN in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 5IJN

Cartoon representation from PDB Cartoon

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Crystal Contacts, from CryCo at Weizmann Institute

Fold representative 5ijn from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5ijn_U] [5ijn_M] [5ijn_P] [5ijn_L] [5ijn_V] [5ijn_S] [5ijn_I] [5ijn_T] [5ijn_H] [5ijn_E] [5ijn_F] [5ijn_X] [5ijn_W] [5ijn_R] [5ijn_J] [5ijn_B] [5ijn_C] [5ijn_K] [5ijn_N] [5ijn_D] [5ijn_Q] [5ijn] [5ijn_Y] [5ijn_Z] [5ijn_G] [5ijn_O] [5ijn_A]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Other resources with information on 5IJN

Community annotation for 5IJN at PDBWiki (http://pdbwiki.org)

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