6PW0

Cytochrome C oxidase delta 6 mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural changes at the surface of cytochrome c oxidase alter the proton-pumping stoichiometry.

Berg, J.Liu, J.Svahn, E.Ferguson-Miller, S.Brzezinski, P.

(2019) Biochim Biophys Acta Bioenerg 1861: 148116-148116

  • DOI: https://doi.org/10.1016/j.bbabio.2019.148116
  • Primary Citation of Related Structures:  
    6PW0, 6PW1

  • PubMed Abstract: 

    Data from earlier studies showed that minor structural changes at the surface of cytochrome c oxidase, in one of the proton-input pathways (the D pathway), result in dramatically decreased activity and a lower proton-pumping stoichiometry. To further investigate how changes around the D pathway orifice influence functionality of the enzyme, here we modified the nearby C-terminal loop of subunit I of the Rhodobacter sphaeroides cytochrome c oxidase. Removal of 16 residues from this flexible surface loop resulted in a decrease in the proton-pumping stoichiometry to <50% of that of the wild-type enzyme. Replacement of the protonatable residue Glu552, part of the same loop, by an Ala, resulted in a similar decrease in the proton-pumping stoichiometry without loss of the O 2 -reduction activity or changes in the proton-uptake kinetics. The data show that minor structural changes at the orifice of the D pathway, at a distance of ~40 Å from the proton gate of cytochrome c oxidase, may alter the proton-pumping stoichiometry of the enzyme.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1
A, C
560Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Gene Names: coxIRSP_1877
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q3J5A7 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3J5A7 
Go to UniProtKB:  Q3J5A7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3J5A7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2
B, D
262Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Gene Names: coxIIRSP_1826
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q3J5G0 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3J5G0 
Go to UniProtKB:  Q3J5G0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3J5G0
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
E, F
2N/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEA (Subject of Investigation/LOI)
Query on HEA

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
KA [auth C],
LA [auth C]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
DMU
Query on DMU

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J [auth A]
K [auth A]
L [auth A]
M [auth A]
MA [auth C]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
MA [auth C],
N [auth A],
NA [auth C],
UA [auth D],
Z [auth B]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
TRD
Query on TRD

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AA [auth B]
BA [auth B]
CA [auth B]
O [auth A]
OA [auth C]
AA [auth B],
BA [auth B],
CA [auth B],
O [auth A],
OA [auth C],
P [auth A],
PA [auth C],
Q [auth A],
QA [auth C],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
VA [auth D],
WA [auth D]
TRIDECANE
C13 H28
IIYFAKIEWZDVMP-UHFFFAOYSA-N
HTH
Query on HTH

Download Ideal Coordinates CCD File 
DA [auth B],
V [auth A]
(2S,3R)-heptane-1,2,3-triol
C7 H16 O3
HXYCHJFUBNTKQR-RQJHMYQMSA-N
TRS
Query on TRS

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IA [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
CD
Query on CD

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AB [auth D],
GA [auth B],
HA [auth B],
ZA [auth D]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
EA [auth B]
FA [auth B]
RA [auth C]
W [auth A]
XA [auth D]
EA [auth B],
FA [auth B],
RA [auth C],
W [auth A],
XA [auth D],
YA [auth D]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CA
Query on CA

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TA [auth C],
Y [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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SA [auth C],
X [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
OH
Query on OH

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G [auth A],
JA [auth C]
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.905α = 90
b = 131.477β = 90
c = 176.601γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
JBluIce-EPICSdata collection
HKL-2000data scaling
PHENIXmodel building
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary