8RQ5

Cryo-EM structure of the light-driven sodium-pumping rhodopsin KR2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

EasyGrid: A versatile platform for automated cryo-EM sample preparation and quality control

Gemin, O.Armijo, V.Papp, G.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium pumping rhodopsin
A, B, C, D, E
280Dokdonia eikastaMutation(s): 0 
Gene Names: NaR
UniProt
Find proteins for N0DKS8 (Dokdonia eikasta)
Explore N0DKS8 
Go to UniProtKB:  N0DKS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupN0DKS8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
F [auth A],
GB [auth D],
MA [auth C],
RA [auth C],
X [auth B]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
RET (Subject of Investigation/LOI)
Query on RET

Download Ideal Coordinates CCD File 
AC [auth E],
H [auth A],
HB [auth D],
OA [auth C],
Y [auth B]
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
LFA
Query on LFA

Download Ideal Coordinates CCD File 
AB [auth C]
BA [auth B]
BB [auth C]
CA [auth B]
CB [auth C]
AB [auth C],
BA [auth B],
BB [auth C],
CA [auth B],
CB [auth C],
CC [auth E],
DA [auth B],
DB [auth C],
DC [auth E],
EA [auth B],
FA [auth B],
FB [auth D],
FC [auth E],
G [auth A],
GA [auth B],
GC [auth E],
HA [auth B],
HC [auth E],
IA [auth B],
IC [auth E],
JA [auth B],
JB [auth D],
JC [auth E],
K [auth A],
KA [auth B],
KB [auth D],
KC [auth E],
L [auth A],
LA [auth B],
LB [auth D],
LC [auth E],
M [auth A],
MB [auth D],
N [auth A],
NA [auth C],
NB [auth D],
O [auth A],
OB [auth D],
P [auth A],
PB [auth D],
Q [auth A],
QA [auth C],
QB [auth D],
R [auth A],
RB [auth D],
S [auth A],
SA [auth C],
SB [auth D],
T [auth A],
TA [auth C],
TB [auth D],
U [auth A],
UA [auth C],
UB [auth D],
VA [auth C],
VB [auth D],
W [auth B],
WA [auth C],
WB [auth E],
XA [auth C],
XB [auth E],
YA [auth C],
YB [auth E],
Z [auth B],
ZA [auth C],
ZB [auth E]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
OLA
Query on OLA

Download Ideal Coordinates CCD File 
EB [auth D],
EC [auth E],
J [auth A],
V [auth B]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
AA [auth B],
BC [auth E],
I [auth A],
IB [auth D],
PA [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUNDGermany847543

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release