8RMK

Cryo-EM structure of human CALHM2 in complex with synthetic nanobody SbC2

PDB DOI: https://doi.org/10.2210/pdb8RMK/pdb
EM Map EMD-19362: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Homo sapiens, Escherichia coli MC1061
Mutation(s): No

Deposited: 2024-01-08 Released: 2024-06-19
Deposition Author(s): Drozdzyk, K., Dutzler, R.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.07 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

Structural features of heteromeric channels composed of CALHM2 and CALHM4 paralogs

Drozdzyk, K., Peter, M., Dutzler, R.

To be published.

Macromolecule Content

Total Structure Weight: 599.78 kDa
Atom Count: 36,113
Modelled Residue Count: 4,521
Deposited Residue Count: 5,335
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium homeostasis modulator protein 2	A C [auth B] D [auth C] E [auth D] F [auth E] A, C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth I], K [auth J], L [auth K]	331	Homo sapiens	Mutation(s): 0 Gene Names: CALHM2, FAM26B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HA72 (Homo sapiens) Explore Q9HA72 Go to UniProtKB: Q9HA72
PHAROS: Q9HA72 GTEx: ENSG00000138172
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HA72
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic nanobody SbC2	B [auth L] M N O P B [auth L], M, N, O, P, Q, R, S, T, U, V	154	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLC (Subject of Investigation/LOI) Query on PLC Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth F] SDF format, chain CA [auth G] SDF format, chain DA [auth H] SDF format, chain EA [auth I] SDF format, chain FA [auth J] SDF format, chain GA [auth K] SDF format, chain W [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain EA [auth I] MOL2 format, chain FA [auth J] MOL2 format, chain GA [auth K] MOL2 format, chain W [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth D]	AA [auth E] BA [auth F] CA [auth G] DA [auth H] EA [auth I] AA [auth E], BA [auth F], CA [auth G], DA [auth H], EA [auth I], FA [auth J], GA [auth K], W [auth A], X [auth B], Y [auth C], Z [auth D]	DIUNDECYL PHOSPHATIDYL CHOLINE C₃₂ H₆₅ N O₈ P IJFVSSZAOYLHEE-SSEXGKCCSA-O		Interactions Focus chain AA [auth E] Focus chain BA [auth F] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain GA [auth K] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth F] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain GA [auth K] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth D]