4ZDR | pdb_00004zdr

Crystal structure of 14-3-3[zeta]-LKB1 fusion protein

PDB DOI: https://doi.org/10.2210/pdb4ZDR/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-04-18 Released: 2015-09-09
Deposition Author(s): Ding, S., Shi, Z.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.245 (Depositor), 0.252 (DCC)
R-Value Work:
0.191 (Depositor), 0.204 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of the 14-3-3 zeta-LKB1 fusion protein provides insight into a novel ligand-binding mode of 14-3-3.

Ding, S., Zhou, R., Zhu, Y.

(2015) Acta Crystallogr F Struct Biol Commun 71: 1114-1119

PubMed: 26323294 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X15012595
Primary Citation Related Structures:
4ZDR

PubMed Abstract:
The 14-3-3 proteins are a family of highly conserved proteins that play key roles in many cellular processes. The tumour suppressor LKB1 regulates cell polarity, cell growth and energy metabolism. 14-3-3 proteins bind to LKB1 and suppress its functions. Previously, preliminary crystallographic data for the 14-3-3ζ-LKB1 fusion protein have been reported. Here, the crystal structure of this fusion protein was solved and a novel potential binding mode of 14-3-3 to its ligands was found.

Organizational Affiliation

Department of General Dentistry, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai 200011, People's Republic of China.

Macromolecule Content

Total Structure Weight: 61.43 kDa
Atom Count: 3,754
Modeled Residue Count: 484
Deposited Residue Count: 532
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein zeta/delta,GGSGGS linker,Serine/threonine-protein kinase STK11	A, B	266	Homo sapiens, synthetic construct	Mutation(s): 1 Gene Names: YWHAZ, STK11, LKB1, PJS EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P63104 (Homo sapiens) Explore P63104 Go to UniProtKB: P63104
PHAROS: P63104 GTEx: ENSG00000164924
Find proteins for Q15831 (Homo sapiens) Explore Q15831 Go to UniProtKB: Q15831
PHAROS: Q15831 GTEx: ENSG00000118046
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q15831 P63104
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	C [auth A], D [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B]
TME Query on TME Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] L [auth B] F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B]	PROPANE C₃ H₈ ATUOYWHBWRKTHZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.245 (Depositor), 0.252 (DCC)
R-Value Work: 0.191 (Depositor), 0.204 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.262	α = 90
b = 130.262	β = 90
c = 264.96	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-09-09

Deposition Author(s):

Ding, S.

Shi, Z.B.

Revision History (Full details and data files)

Version 1.0: 2015-09-09
Type: Initial release
Version 1.1: 2020-01-01
Changes: Database references, Derived calculations
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description