4PKN

Crystal structure of the football-shaped GroEL-GroES2-(ADPBeFx)14 complex containing substrate Rubisco


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.66 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Formation and structures of GroEL:GroES2 chaperonin footballs, the protein-folding functional form.

Fei, X.Ye, X.LaRonde, N.A.Lorimer, G.H.

(2014) Proc Natl Acad Sci U S A 111: 12775-12780

  • DOI: https://doi.org/10.1073/pnas.1412922111
  • Primary Citation of Related Structures:  
    4PKN, 4PKO

  • PubMed Abstract: 

    The GroE chaperonins assist substrate protein (SP) folding by cycling through several conformational states. With each cycle the SP is, in turn, captured, unfolded, briefly encapsulated (t1/2 ∼ 1 s), and released by the chaperonin complex. The protein-folding functional form is the US-football-shaped GroEL:GroES2 complex. We report structures of two such "football" complexes to ∼ 3.7-Å resolution; one is empty whereas the other contains encapsulated SP in both chambers. Although encapsulated SP is not visible on the electron density map, using calibrated FRET and order-of-addition experiments we show that owing to SP-catalyzed ADP/ATP exchange both chambers of the football complex encapsulate SP efficiently only if the binding of SP precedes that of ATP. The two rings of GroEL thus behave as a parallel processing machine, rather than functioning alternately. Compared with the bullet-shaped GroEL:GroES1 complex, the GroEL:GroES2 football complex differs conformationally at the GroEL-GroES interface and also at the interface between the two GroEL rings. We propose that the electrostatic interactions between the ε-NH(3+) of K105 of helix D in one ring with the negatively charged carboxyl oxygen of A109 at the carboxyl end of helix D of the other ring provide the structural basis for negative inter-ring cooperativity.


  • Organizational Affiliation

    Biophysics Graduate Program, Center for Biological Structure and Organization.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60 kDa chaperonin548Escherichia coliMutation(s): 0 
Gene Names: groELgroLmopABN17_41231BU34_16740ECs5124LF82_0923
UniProt
Find proteins for Q548M1 (Escherichia coli)
Explore Q548M1 
Go to UniProtKB:  Q548M1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ548M1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
10 kDa chaperonin97Escherichia coliMutation(s): 0 
Gene Names: groSgroESmopBBN17_41221BU34_16745ECs5123LF82_0924
UniProt
Find proteins for Q7BGE6 (Escherichia coli)
Explore Q7BGE6 
Go to UniProtKB:  Q7BGE6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7BGE6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
AB [auth D]
CA [auth G]
CC [auth N]
EB [auth K]
GA [auth A]
AB [auth D],
CA [auth G],
CC [auth N],
EB [auth K],
GA [auth A],
IB [auth J],
KA [auth B],
MB [auth I],
OA [auth F],
QB [auth L],
SA [auth E],
UB [auth M],
WA [auth C],
YB [auth H]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF
Query on BEF

Download Ideal Coordinates CCD File 
BB [auth D]
DA [auth G]
DC [auth N]
FB [auth K]
HA [auth A]
BB [auth D],
DA [auth G],
DC [auth N],
FB [auth K],
HA [auth A],
JB [auth J],
LA [auth B],
NB [auth I],
PA [auth F],
RB [auth L],
TA [auth E],
VB [auth M],
XA [auth C],
ZB [auth H]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
K
Query on K

Download Ideal Coordinates CCD File 
BC [auth H]
DB [auth D]
FA [auth G]
FC [auth N]
HB [auth K]
BC [auth H],
DB [auth D],
FA [auth G],
FC [auth N],
HB [auth K],
JA [auth A],
LB [auth J],
NA [auth B],
PB [auth I],
RA [auth F],
TB [auth L],
VA [auth E],
XB [auth M],
ZA [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth H]
CB [auth D]
EA [auth G]
EC [auth N]
GB [auth K]
AC [auth H],
CB [auth D],
EA [auth G],
EC [auth N],
GB [auth K],
IA [auth A],
KB [auth J],
MA [auth B],
OB [auth I],
QA [auth F],
SB [auth L],
UA [auth E],
WB [auth M],
YA [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.66 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.952α = 90
b = 173.653β = 90
c = 411.27γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
University of MarylandUnited StatesAnn.Wylie dissertation fellowship
University of MarylandUnited StatesBailey fellowship

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-09-03
    Changes: Database references
  • Version 1.2: 2014-10-01
    Changes: Database references
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy