5LUM | pdb_00005lum

Alpha-crystallin domain of human HSPB6 patched with its N-terminal peptide

PDB DOI: https://doi.org/10.2210/pdb5LUM/pdb

Classification: Protein/Peptide
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-09-09 Released: 2017-02-01
Deposition Author(s): Sluchanko, N.N., Beelen, S., Kulikova, A.A., Weeks, S.D., Antson, A.A., Gusev, N.B., Strelkov, S.V.
Funding Organization(s): RFBR, FWO, KULeuven grant, Wellcome Trust, Biostruct-X, European Union, European Molecular Biology Organization

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.227 (Depositor), 0.241 (DCC)
R-Value Work:
0.207 (Depositor), 0.212 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural Basis for the Interaction of a Human Small Heat Shock Protein with the 14-3-3 Universal Signaling Regulator.

Sluchanko, N.N., Beelen, S., Kulikova, A.A., Weeks, S.D., Antson, A.A., Gusev, N.B., Strelkov, S.V.

(2017) Structure 25: 305-316

PubMed: 28089448 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.str.2016.12.005
Primary Citation Related Structures:
5LTW, 5LU1, 5LU2, 5LUM

PubMed Abstract:
By interacting with hundreds of protein partners, 14-3-3 proteins coordinate vital cellular processes. Phosphorylation of the small heat shock protein, HSPB6, within its intrinsically disordered N-terminal domain activates its interaction with 14-3-3, ultimately triggering smooth muscle relaxation. After analyzing the binding of an HSPB6-derived phosphopeptide to 14-3-3 using isothermal calorimetry and X-ray crystallography, we have determined the crystal structure of the complete assembly consisting of the 14-3-3 dimer and full-length HSPB6 dimer and further characterized this complex in solution using fluorescence spectroscopy, small-angle X-ray scattering, and limited proteolysis. We show that selected intrinsically disordered regions of HSPB6 are transformed into well-defined conformations upon the interaction, whereby an unexpectedly asymmetric structure is formed. This structure provides the first atomic resolution snapshot of a human small HSP in functional state, explains how 14-3-3 proteins sequester their regulatory partners, and can inform the design of small-molecule interaction modifiers to be used as myorelaxants.

Organizational Affiliation

Laboratory of Structural Biochemistry of Proteins, A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, 119071 Moscow, Russia. Electronic address: nikolai.sluchanko@mail.ru.

Macromolecule Content

Total Structure Weight: 48.2 kDa
Atom Count: 3,416
Modeled Residue Count: 435
Deposited Residue Count: 435
Unique protein chains: 2

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein beta-6	A [auth F], C [auth G], E [auth H], G [auth I], I [auth J]	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O14558 (Homo sapiens) Explore O14558 Go to UniProtKB: O14558
PHAROS: O14558 GTEx: ENSG00000004776
Entity Groups
UniProt Group	O14558
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein beta-6	B [auth A], D [auth B], F [auth C], H [auth D], J [auth E]	78	Homo sapiens	Mutation(s): 0 Gene Names: HSPB6
UniProt & NIH Common Fund Data Resources
Find proteins for O14558 (Homo sapiens) Explore O14558 Go to UniProtKB: O14558
PHAROS: O14558 GTEx: ENSG00000004776
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O14558
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain M [auth D] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain N [auth E] MOL2 format, chain M [auth D] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain N [auth E] mmCIF format, chain M [auth D] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], M [auth D], N [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth D] Focus chain N [auth E] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth D] Focus chain N [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.227 (Depositor), 0.241 (DCC)
R-Value Work: 0.207 (Depositor), 0.212 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.687	α = 90
b = 105.687	β = 90
c = 111.95	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-02-01

Deposition Author(s):

Funding Organization	Location	Grant Number
RFBR	Russian Federation	14-04-00146, 16-04-00016
FWO	Belgium	G069708N, G093615N and WO03315N
KULeuven grant	Belgium	OT13/097
Wellcome Trust	United Kingdom	098230
Biostruct-X	Belgium	283570
European Union	Belgium	FP7/2007-2013
European Molecular Biology Organization	Belgium	ASTF#637-2014

Revision History (Full details and data files)

Version 1.0: 2017-02-01
Type: Initial release
Version 1.1: 2017-02-15
Changes: Database references
Version 1.2: 2017-09-06
Changes: Author supporting evidence
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Refinement description