3KEP | pdb_00003kep

Crystal structure of the autoproteolytic domain from the nuclear pore complex component NUP145 from Saccharomyces cerevisiae

PDB DOI: https://doi.org/10.2210/pdb3KEP/pdb

Classification: PROTEIN TRANSPORT, RNA BINDING PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-10-26 Released: 2009-12-22
Deposition Author(s): Sampathkumar, P., Ozyurt, S.A., Do, J., Bain, K., Dickey, M., Gheyi, T., Sali, A., Kim, S.J., Phillips, J., Pieper, U., Fernandez-Martinez, J., Franke, J.D., Atwell, S., Thompson, D.A., Emtage, J.S., Wasserman, S., Rout, M., Sauder, J.M., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.244 (Depositor), 0.251 (DCC)
R-Value Work:
0.213 (Depositor), 0.220 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup145.

Sampathkumar, P., Ozyurt, S.A., Do, J., Bain, K.T., Dickey, M., Rodgers, L.A., Gheyi, T., Sali, A., Kim, S.J., Phillips, J., Pieper, U., Fernandez-Martinez, J., Franke, J.D., Martel, A., Tsuruta, H., Atwell, S., Thompson, D.A., Emtage, J.S., Wasserman, S.R., Rout, M.P., Sauder, J.M., Burley, S.K.

(2010) Proteins 78: 1992-1998

PubMed: 20310066 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/prot.22707
Primary Citation Related Structures:
3KEP, 3KES

Organizational Affiliation

New York SGX Research Center for Structural Genomics (NYSGXRC), Eli Lilly and Company, Lilly Biotechnology Center, San Diego, California 92121, USA. sampathkumarpa@lilly.com

Macromolecule Content

Total Structure Weight: 41.87 kDa
Atom Count: 2,626
Modeled Residue Count: 292
Deposited Residue Count: 348
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoporin NUP145	A, B	174	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: NUP145, RAT10, YGL092W EC: 3.4.21
UniProt
Find proteins for P49687 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49687 Go to UniProtKB: P49687
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49687
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.244 (Depositor), 0.251 (DCC)
R-Value Work: 0.213 (Depositor), 0.220 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.037	α = 90
b = 91.037	β = 90
c = 108.394	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing
SHELXD	phasing
SHELXE	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-12-22

Deposition Author(s):

Fernandez-Martinez, J.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-12-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-10-10
Changes: Database references
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2018-11-21
Changes: Data collection, Structure summary
Version 1.5: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.6: 2024-10-16
Changes: Data collection, Database references, Structure summary