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 9ZXX | pdb_00009zxx

Ca2+ bound destabilized open state Connexin-46


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9ZXX

This is version 1.1 of the entry. See complete history. 

Literature

Calcium induced N-terminal gating and pore collapse in connexin-46/50 gap junctions.

Flores, J.A., O'Neill, S.E., Jarodsky, J.M., Haddad, B.G., Reichow, S.L.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-77891-5
  • Primary Citation Related Structures: 
    9ZXX, 9ZY3, 9ZY5, 9ZY7

  • PubMed Abstract: 

    Gap junctions facilitate electrical and metabolic coupling essential for tissue function. Under ischemic conditions (e.g., heart attack or stroke), elevated intracellular calcium (Ca² + ) uncouples these communication pathways to limit the spread of cytotoxic signals, yet the structural basis of this protective response remains unclear. Here, using single-particle cryo-EM, we define the Ca² + -dependent gating mechanism of native connexin-46/50 (Cx46/50) gap junction channels. Ca 2+ binding promotes an ensemble of N-terminal (NT) domain conformations spanning destabilized and fully gated states. These conformational changes are coupled to coordinated subunit rearrangements that asymmetrically collapse the pore and enable steric occlusion by the NT domains. Comparison with recently resolved low-pH gating structures reveals that distinct physiological stimuli converge on a common NT-centered gating mechanism involving coupled NT displacement and TM2 hinge motion. Long-timescale molecular dynamics simulations identify multiple Ca 2+ interaction sites along the permeation pathway and suggest that transient inter-subunit Ca 2+ coordination can promote NT destabilization and displacement. Together, these findings support a model in which distributed Ca 2+ interactions reshape the energetic landscape of the channel to favor NT-mediated pore closure, unifying previous models of gap junction regulation and providing a mechanistic basis for Ca 2+ -dependent uncoupling during cellular stress.


  • Organizational Affiliation: 
    • Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA.

Macromolecule Content 

  • Total Structure Weight: 657.78 kDa 
  • Atom Count: 20,772 
  • Modeled Residue Count: 2,280 
  • Deposited Residue Count: 4,956 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Gap junction alpha-3 protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
413Ovis ariesMutation(s): 1 
UniProt
Find proteins for Q9TU17 (Ovis aries)
Explore Q9TU17 
Go to UniProtKB:  Q9TU17
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9TU17
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MC3

Query on MC3



Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth C]
AC [auth D]
AD [auth F]
AE [auth G]
AA [auth A],
AB [auth C],
AC [auth D],
AD [auth F],
AE [auth G],
AF [auth I],
AH [auth L],
BA [auth A],
BB [auth C],
BC [auth D],
BE [auth G],
BF [auth I],
BG [auth K],
BH [auth L],
CA [auth A],
CB [auth C],
CD [auth F],
CF [auth I],
CG [auth K],
CH [auth L],
DA [auth A],
DB [auth C],
DC [auth E],
DD [auth F],
DE [auth H],
DF [auth I],
DG [auth K],
DH [auth L],
EB [auth C],
EC [auth E],
ED [auth F],
EE [auth H],
EF [auth I],
EG [auth K],
EH [auth L],
FA [auth B],
FB [auth C],
FC [auth E],
FD [auth F],
FE [auth H],
FF [auth I],
FG [auth K],
FH [auth L],
GA [auth B],
GB [auth C],
GC [auth E],
GD [auth F],
GE [auth H],
GF [auth I],
GG [auth K],
GH [auth L],
HA [auth B],
HB [auth C],
HC [auth E],
HD [auth F],
HE [auth H],
HF [auth I],
HG [auth K],
HH [auth L],
IA [auth B],
IB [auth C],
IC [auth E],
ID [auth F],
IE [auth H],
IF [auth I],
IG [auth K],
JA [auth B],
JB [auth C],
JC [auth E],
JD [auth F],
JE [auth H],
JG [auth K],
KA [auth B],
KB [auth C],
KC [auth E],
KE [auth H],
KF [auth J],
KG [auth K],
LA [auth B],
LC [auth E],
LD [auth G],
LE [auth H],
LF [auth J],
LG [auth K],
MA [auth B],
MB [auth D],
MC [auth E],
MD [auth G],
ME [auth H],
MF [auth J],
MG [auth K],
N [auth A],
NA [auth B],
NB [auth D],
NC [auth E],
ND [auth G],
NE [auth H],
NF [auth J],
NG [auth K],
O [auth A],
OA [auth B],
OB [auth D],
OC [auth E],
OD [auth G],
OE [auth H],
OF [auth J],
OG [auth K],
P [auth A],
PA [auth B],
PB [auth D],
PC [auth E],
PD [auth G],
PE [auth H],
PF [auth J],
PG [auth K],
Q [auth A],
QA [auth B],
QB [auth D],
QC [auth E],
QD [auth G],
QE [auth H],
QF [auth J],
QG [auth K],
R [auth A],
RA [auth B],
RB [auth D],
RC [auth E],
RD [auth G],
RE [auth H],
RF [auth J],
RG [auth L],
S [auth A],
SA [auth B],
SB [auth D],
SC [auth E],
SD [auth G],
SF [auth J],
SG [auth L],
T [auth A],
TA [auth B],
TB [auth D],
TC [auth F],
TD [auth G],
TE [auth I],
TF [auth J],
TG [auth L],
U [auth A],
UB [auth D],
UC [auth F],
UD [auth G],
UE [auth I],
UF [auth J],
UG [auth L],
V [auth A],
VA [auth C],
VB [auth D],
VC [auth F],
VD [auth G],
VE [auth I],
VF [auth J],
VG [auth L],
W [auth A],
WA [auth C],
WB [auth D],
WC [auth F],
WD [auth G],
WE [auth I],
WF [auth J],
WG [auth L],
X [auth A],
XA [auth C],
XB [auth D],
XC [auth F],
XD [auth G],
XE [auth I],
XF [auth J],
XG [auth L],
Y [auth A],
YA [auth C],
YB [auth D],
YC [auth F],
YD [auth G],
YE [auth I],
YF [auth J],
YG [auth L],
Z [auth A],
ZA [auth C],
ZB [auth D],
ZC [auth F],
ZD [auth G],
ZE [auth I],
ZF [auth J]
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
C36 H72 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
AG [auth K]
BD [auth F]
CC [auth E]
CE [auth H]
EA [auth B]
AG [auth K],
BD [auth F],
CC [auth E],
CE [auth H],
EA [auth B],
JF [auth J],
KD [auth G],
LB [auth D],
M [auth A],
SE [auth I],
UA [auth C],
ZG [auth L]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesR35GM124779
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesF31EY030409

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-07
    Type: Initial release
  • Version 1.1: 2026-11-04
    Changes: Data collection, Database references