43YG | pdb_000043yg

Cryo-EM structure of an N-terminal deletion mutant of AGAP001487 in a nanodisc

PDB DOI: https://doi.org/10.2210/pdb43YG/pdb
EM Map EMD-82387: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Anopheles gambiae
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2026-07-21 Released: 2026-11-11
Deposition Author(s): Kawaguchi, S., Hirano, H., Watanabe, M., Suzuki, S., Nishikawa, K., Fujiyoshi, Y., Oshima, A.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.76 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 43YG

This is version 1.0 of the entry. See complete history.

Literature

N-terminal integrity governs heptamer assembly and maturation in an Anopheles innexin

Kawaguchi, S., Hirano, H., Watanabe, M., Suzuki, S., Nishikawa, K., Fujiyoshi, Y., Oshima, A.

To be published.

Macromolecule Content

Total Structure Weight: 342.5 kDa
Atom Count: 20,658
Modeled Residue Count: 2,423
Deposited Residue Count: 2,597
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Innexin shaking-B	A, B, C, D, E A, B, C, D, E, F, G	371	Anopheles gambiae	Mutation(s): 0 Gene Names: shakB, AGAP001487
UniProt
Find proteins for Q7PXN1 (Anopheles gambiae) Explore Q7PXN1 Go to UniProtKB: Q7PXN1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7PXN1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LBN Query on LBN Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth G] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain LA [auth E] SDF format, chain N [auth B] SDF format, chain NA [auth F] SDF format, chain O [auth B] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain SA [auth G] SDF format, chain TA [auth G] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain VA [auth G] SDF format, chain W [auth C] SDF format, chain WA [auth G] SDF format, chain X [auth C] SDF format, chain XA [auth G] SDF format, chain Y [auth C] SDF format, chain YA [auth G] SDF format, chain Z [auth C] SDF format, chain ZA [auth G] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth G] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth G] MOL2 format, chain TA [auth G] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth G] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth G] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth G] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth G] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth G] mmCIF format, chain AA [auth C] mmCIF format, chain AB [auth G] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth G] mmCIF format, chain TA [auth G] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth G] mmCIF format, chain W [auth C] mmCIF format, chain WA [auth G] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth G] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth G] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth G]	AA [auth C] AB [auth G] BA [auth D] CA [auth D] DA [auth D] AA [auth C], AB [auth G], BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], K [auth A], KA [auth E], L [auth A], LA [auth E], N [auth B], NA [auth F], O [auth B], OA [auth F], P [auth B], PA [auth F], Q [auth B], QA [auth F], R [auth B], S [auth B], SA [auth G], TA [auth G], U [auth C], V [auth C], VA [auth G], W [auth C], WA [auth G], X [auth C], XA [auth G], Y [auth C], YA [auth G], Z [auth C], ZA [auth G]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-VYOBOKEXSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth G] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain N [auth B] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain U [auth C] Focus chain V [auth C] Focus chain VA [auth G] Focus chain W [auth C] Focus chain WA [auth G] Focus chain X [auth C] Focus chain XA [auth G] Focus chain Y [auth C] Focus chain YA [auth G] Focus chain Z [auth C] Focus chain ZA [auth G] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth G] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain N [auth B] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain U [auth C] Focus chain V [auth C] Focus chain VA [auth G] Focus chain W [auth C] Focus chain WA [auth G] Focus chain X [auth C] Focus chain XA [auth G] Focus chain Y [auth C] Focus chain YA [auth G] Focus chain Z [auth C] Focus chain ZA [auth G]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain JA [auth E] SDF format, chain M [auth B] SDF format, chain MA [auth F] SDF format, chain RA [auth G] SDF format, chain T [auth C] SDF format, chain UA [auth G] MOL2 format, chain JA [auth E] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth F] MOL2 format, chain RA [auth G] MOL2 format, chain T [auth C] MOL2 format, chain UA [auth G] mmCIF format, chain JA [auth E] mmCIF format, chain M [auth B] mmCIF format, chain MA [auth F] mmCIF format, chain RA [auth G] mmCIF format, chain T [auth C] mmCIF format, chain UA [auth G]	JA [auth E] M [auth B] MA [auth F] RA [auth G] T [auth C] JA [auth E], M [auth B], MA [auth F], RA [auth G], T [auth C], UA [auth G]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain JA [auth E] Focus chain M [auth B] Focus chain MA [auth F] Focus chain RA [auth G] Focus chain T [auth C] Focus chain UA [auth G] Interactions & Density Focus chain JA [auth E] Focus chain M [auth B] Focus chain MA [auth F] Focus chain RA [auth G] Focus chain T [auth C] Focus chain UA [auth G]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.76 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2026-11-11
Type: Initial release