4ODQ

Structure of SlyD delta-IF from Thermus thermophilus in complex with S3 peptide

• PDB DOI: https://doi.org/10.2210/pdb4ODQ/pdb

• Classification: ISOMERASE, CHAPERONE
• Organism(s): Thermus thermophilus, Homo sapiens, Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-01-10 Released: 2015-01-14 
• Deposition Author(s): Quistgaard, E.M., Low, C., Nordlund, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.213 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Literature

Molecular insights into substrate recognition and catalytic mechanism of the chaperone and FKBP peptidyl-prolyl isomerase SlyD.

Quistgaard, E.M., Weininger, U., Ural-Blimke, Y., Modig, K., Nordlund, P., Akke, M., Low, C.

(2016) BMC Biol 14: 82-82

• PubMed: 27664121 
• DOI: https://doi.org/10.1186/s12915-016-0300-3
• Primary Citation of Related Structures:  
  4ODK, 4ODL, 4ODM, 4ODN, 4ODO, 4ODP, 4ODQ, 4ODR


• PubMed Abstract: 
  

  Peptidyl-prolyl isomerases (PPIases) catalyze cis/trans isomerization of peptidyl-prolyl bonds, which is often rate-limiting for protein folding. SlyD is a two-domain enzyme containing both a PPIase FK506-binding protein (FKBP) domain and an insert-in-flap (IF) chaperone domain. To date, the interactions of these domains with unfolded proteins have remained rather obscure, with structural information on binding to the FKBP domain being limited to complexes involving various inhibitor compounds or a chemically modified tetrapeptide.

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Organizational Affiliation: 

Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-17177, Stockholm, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.22 kDa 
• Atom Count: 1,005 
• Modelled Residue Count: 112 
• Deposited Residue Count: 126 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase SlyD, Peptidyl-prolyl cis-trans isomerase FKBP1A chimera	A	110	Thermus thermophilus, Homo sapiens	Mutation(s): 0  Gene Names: TTHA0346, FKBP1, FKBP12, FKBP1A EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SLE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLE7  Go to UniProtKB:  Q5SLE7
Find proteins for P62942 (Homo sapiens) Explore P62942  Go to UniProtKB:  P62942
PHAROS:  P62942 GTEx:  ENSG00000088832
UniProt Groups	Q5SLE7P62942

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	B	16	Escherichia coli K-12	Mutation(s): 1
UniProt
Find proteins for P0A7V3 (Escherichia coli (strain K12)) Explore P0A7V3  Go to UniProtKB:  P0A7V3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	H [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CA	D [auth A], E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.213 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.56	α = 90
b = 93.56	β = 90
c = 93.56	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Quistgaard, E.M., Low, C., Nordlund, P.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2017-07-26
  Changes: Refinement description, Source and taxonomy
• Version 1.2: 2017-10-04
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations