3CQX | pdb_00003cqx

Chaperone Complex

PDB DOI: https://doi.org/10.2210/pdb3CQX/pdb

Classification: CHAPERONE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-04-03 Released: 2008-11-25
Deposition Author(s): Xu, Z., Nix, J.C., Misra, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.256 (Depositor)
R-Value Work:
0.222 (Depositor), 0.215 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural basis of nucleotide exchange and client binding by the Hsp70 cochaperone Bag2

Xu, Z., Page, R.C., Gomes, M.M., Kohli, E., Nix, J.C., Herr, A.B., Patterson, C., Misra, S.

(2008) Nat Struct Mol Biol 15: 1309-1317

PubMed: 19029896 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.1518
Primary Citation Related Structures:
3CQX, 3D0T

PubMed Abstract:
Cochaperones are essential for Hsp70- and Hsc70-mediated folding of proteins and include nucleotide-exchange factors (NEFs) that assist protein folding by accelerating ADP-ATP exchange on Hsp70. The cochaperone Bag2 binds misfolded Hsp70 clients and also acts as an NEF, but the molecular basis for its function is unclear. We show that, rather than being a member of the Bag domain family, Bag2 contains a new type of Hsp70 NEF domain, which we call the 'brand new bag' (BNB) domain. Free and Hsc70-bound crystal structures of Bag2-BNB show its dimeric structure, in which a flanking linker helix and loop bind to Hsc70 to promote nucleotide exchange. NMR analysis demonstrates that the client binding sites and Hsc70-interaction sites of the Bag2-BNB overlap, and that Hsc70 can displace clients from Bag2-BNB, indicating a distinct mechanism for the regulation of Hsp70-mediated protein folding by Bag2.

Organizational Affiliation

Department of Molecular Cardiology, Lerner Research Institute, NB50, 9500 Euclid Avenue, The Cleveland Clinic, Cleveland, Ohio 44195, USA.

Macromolecule Content

Total Structure Weight: 104.58 kDa
Atom Count: 7,385
Modeled Residue Count: 918
Deposited Residue Count: 948
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock cognate 71 kDa protein	A, B	386	Mus musculus	Mutation(s): 0 Gene Names: Hspa8, Hsc70, Hsc73 EC: 3.6.4.10
UniProt
Find proteins for P63017 (Mus musculus) Explore P63017 Go to UniProtKB: P63017
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63017
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BAG family molecular chaperone regulator 2	C, D	88	Mus musculus	Mutation(s): 0 Gene Names: Bag2
UniProt & NIH Common Fund Data Resources
Find proteins for Q91YN9 (Mus musculus) Explore Q91YN9 Go to UniProtKB: Q91YN9
IMPC: MGI:1891254
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q91YN9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], L [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain M [auth D] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain M [auth D] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A], K [auth A], M [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.256 (Depositor)
R-Value Work: 0.222 (Depositor), 0.215 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.846	α = 90
b = 105.808	β = 90
c = 210.683	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-11-25

Deposition Author(s):

Xu, Z.

Nix, J.C.

Misra, S.

Revision History (Full details and data files)

Version 1.0: 2008-11-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description