1FXK | pdb_00001fxk

CRYSTAL STRUCTURE OF ARCHAEAL PREFOLDIN (GIMC).

PDB DOI: https://doi.org/10.2210/pdb1FXK/pdb

Classification: CHAPERONE
Organism(s): Methanothermobacter thermautotrophicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2000-09-26 Released: 2000-12-06
Deposition Author(s): Siegert, R., Scheufler, C., Moarefi, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.266 (Depositor), 0.266 (DCC)
R-Value Work:
0.218 (Depositor), 0.218 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of the molecular chaperone prefoldin: unique interaction of multiple coiled coil tentacles with unfolded proteins.

Siegert, R., Leroux, M.R., Scheufler, C., Hartl, F.U., Moarefi, I.

(2000) Cell 103: 621-632

PubMed: 11106732 Search on PubMed
DOI: https://doi.org/10.1016/s0092-8674(00)00165-3
Primary Citation Related Structures:
1FXK

PubMed Abstract:
Prefoldin (GimC) is a hexameric molecular chaperone complex built from two related classes of subunits and present in all eukaryotes and archaea. Prefoldin interacts with nascent polypeptide chains and, in vitro, can functionally substitute for the Hsp70 chaperone system in stabilizing non-native proteins for subsequent folding in the central cavity of a chaperonin. Here, we present the crystal structure and characterization of the prefoldin hexamer from the archaeum Methanobacterium thermoautotrophicum. Prefoldin has the appearance of a jellyfish: its body consists of a double beta barrel assembly with six long tentacle-like coiled coils protruding from it. The distal regions of the coiled coils expose hydrophobic patches and are required for multivalent binding of nonnative proteins.

Organizational Affiliation

Max-Planck Institut für Biochemie, Am Klopferspitz 18a, D82152 Martinsried, Germany.

Macromolecule Content

Total Structure Weight: 39.89 kDa
Atom Count: 3,087
Modeled Residue Count: 349
Deposited Residue Count: 349
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PREFOLDIN	A	107	Methanothermobacter thermautotrophicus	Mutation(s): 0
UniProt
Find proteins for O26774 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26774 Go to UniProtKB: O26774
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O26774
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PREFOLDIN	B	109	Methanothermobacter thermautotrophicus	Mutation(s): 0
UniProt
Find proteins for O26774 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26774 Go to UniProtKB: O26774
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O26774
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PREFOLDIN)	C	133	Methanothermobacter thermautotrophicus	Mutation(s): 0
UniProt
Find proteins for O27646 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O27646 Go to UniProtKB: O27646
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O27646
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.266 (Depositor), 0.266 (DCC)
R-Value Work: 0.218 (Depositor), 0.218 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.85	α = 90
b = 90.69	β = 90
c = 78.86	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2000-12-06

Deposition Author(s):

Siegert, R.

Scheufler, C.

Moarefi, I.

Revision History (Full details and data files)

Version 1.0: 2000-12-06
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary