7D61

Cryo-EM Structure of human CALHM5 in the presence of EDTA

PDB DOI: https://doi.org/10.2210/pdb7D61/pdb
EM Map EMD-30587: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPMPDBTMmpstruc

Deposited: 2020-09-28 Released: 2020-12-23
Deposition Author(s): Liu, J., Guan, F.H., Wu, J., Wan, F.T., Lei, M., Ye, S.
Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structures of human calcium homeostasis modulator 5.

Liu, J., Wan, F., Jin, Q., Li, X., Bhat, E.A., Guo, J., Lei, M., Guan, F., Wu, J., Ye, S.

(2020) Cell Discov 6: 81-81

PubMed: 33298887 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-020-00228-z
Primary Citation of Related Structures:
7D60, 7D61, 7D65

Organizational Affiliation

Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.

Macromolecule Content

Total Structure Weight: 385.42 kDa
Atom Count: 26,664
Modelled Residue Count: 3,168
Deposited Residue Count: 3,168
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium homeostasis modulator protein 5	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K	288	Homo sapiens	Mutation(s): 0 Gene Names: CALHM5, C6orf188, FAM26E Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N5C1 (Homo sapiens) Explore Q8N5C1 Go to UniProtKB: Q8N5C1
PHAROS: Q8N5C1 GTEx: ENSG00000178033
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N5C1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PA8 Query on PA8 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth I] SDF format, chain BA [auth D] SDF format, chain BB [auth I] SDF format, chain CA [auth D] SDF format, chain CB [auth I] SDF format, chain DA [auth D] SDF format, chain DB [auth I] SDF format, chain EA [auth D] SDF format, chain EB [auth J] SDF format, chain FA [auth E] SDF format, chain FB [auth J] SDF format, chain GA [auth E] SDF format, chain GB [auth J] SDF format, chain HA [auth E] SDF format, chain HB [auth J] SDF format, chain IA [auth E] SDF format, chain IB [auth J] SDF format, chain JA [auth E] SDF format, chain JB [auth K] SDF format, chain KA [auth F] SDF format, chain KB [auth K] SDF format, chain L [auth A] SDF format, chain LA [auth F] SDF format, chain LB [auth K] SDF format, chain M [auth A] SDF format, chain MA [auth F] SDF format, chain MB [auth K] SDF format, chain N [auth A] SDF format, chain NA [auth F] SDF format, chain NB [auth K] SDF format, chain O [auth A] SDF format, chain OA [auth F] SDF format, chain P [auth A] SDF format, chain PA [auth G] SDF format, chain Q [auth B] SDF format, chain QA [auth G] SDF format, chain R [auth B] SDF format, chain RA [auth G] SDF format, chain S [auth B] SDF format, chain SA [auth G] SDF format, chain T [auth B] SDF format, chain TA [auth G] SDF format, chain U [auth B] SDF format, chain UA [auth H] SDF format, chain V [auth C] SDF format, chain VA [auth H] SDF format, chain W [auth C] SDF format, chain WA [auth H] SDF format, chain X [auth C] SDF format, chain XA [auth H] SDF format, chain Y [auth C] SDF format, chain YA [auth H] SDF format, chain Z [auth C] SDF format, chain ZA [auth I] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth I] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth I] MOL2 format, chain CA [auth D] MOL2 format, chain CB [auth I] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth I] MOL2 format, chain EA [auth D] MOL2 format, chain EB [auth J] MOL2 format, chain FA [auth E] MOL2 format, chain FB [auth J] MOL2 format, chain GA [auth E] MOL2 format, chain GB [auth J] MOL2 format, chain HA [auth E] MOL2 format, chain HB [auth J] MOL2 format, chain IA [auth E] MOL2 format, chain IB [auth J] MOL2 format, chain JA [auth E] MOL2 format, chain JB [auth K] MOL2 format, chain KA [auth F] MOL2 format, chain KB [auth K] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain LB [auth K] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain MB [auth K] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain NB [auth K] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth G] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth G] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth H] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth H] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth H] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth H] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth I] mmCIF format, chain AA [auth D] mmCIF format, chain AB [auth I] mmCIF format, chain BA [auth D] mmCIF format, chain BB [auth I] mmCIF format, chain CA [auth D] mmCIF format, chain CB [auth I] mmCIF format, chain DA [auth D] mmCIF format, chain DB [auth I] mmCIF format, chain EA [auth D] mmCIF format, chain EB [auth J] mmCIF format, chain FA [auth E] mmCIF format, chain FB [auth J] mmCIF format, chain GA [auth E] mmCIF format, chain GB [auth J] mmCIF format, chain HA [auth E] mmCIF format, chain HB [auth J] mmCIF format, chain IA [auth E] mmCIF format, chain IB [auth J] mmCIF format, chain JA [auth E] mmCIF format, chain JB [auth K] mmCIF format, chain KA [auth F] mmCIF format, chain KB [auth K] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain LB [auth K] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain MB [auth K] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain NB [auth K] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth G] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth G] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth H] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth H] mmCIF format, chain W [auth C] mmCIF format, chain WA [auth H] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth H] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth H] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth I]	AA [auth D] AB [auth I] BA [auth D] BB [auth I] CA [auth D] AA [auth D], AB [auth I], BA [auth D], BB [auth I], CA [auth D], CB [auth I], DA [auth D], DB [auth I], EA [auth D], EB [auth J], FA [auth E], FB [auth J], GA [auth E], GB [auth J], HA [auth E], HB [auth J], IA [auth E], IB [auth J], JA [auth E], JB [auth K], KA [auth F], KB [auth K], L [auth A], LA [auth F], LB [auth K], M [auth A], MA [auth F], MB [auth K], N [auth A], NA [auth F], NB [auth K], O [auth A], OA [auth F], P [auth A], PA [auth G], Q [auth B], QA [auth G], R [auth B], RA [auth G], S [auth B], SA [auth G], T [auth B], TA [auth G], U [auth B], UA [auth H], V [auth C], VA [auth H], W [auth C], WA [auth H], X [auth C], XA [auth H], Y [auth C], YA [auth H], Z [auth C], ZA [auth I]	1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE C₁₉ H₃₆ O₈ P XYSBQYUENLDGMI-QGZVFWFLSA-M		Interactions Focus chain AA [auth D] Focus chain AB [auth I] Focus chain BA [auth D] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain CB [auth I] Focus chain DA [auth D] Focus chain DB [auth I] Focus chain EA [auth D] Focus chain EB [auth J] Focus chain FA [auth E] Focus chain FB [auth J] Focus chain GA [auth E] Focus chain GB [auth J] Focus chain HA [auth E] Focus chain HB [auth J] Focus chain IA [auth E] Focus chain IB [auth J] Focus chain JA [auth E] Focus chain JB [auth K] Focus chain KA [auth F] Focus chain KB [auth K] Focus chain L [auth A] Focus chain LA [auth F] Focus chain LB [auth K] Focus chain M [auth A] Focus chain MA [auth F] Focus chain MB [auth K] Focus chain N [auth A] Focus chain NA [auth F] Focus chain NB [auth K] Focus chain O [auth A] Focus chain OA [auth F] Focus chain P [auth A] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain RA [auth G] Focus chain S [auth B] Focus chain SA [auth G] Focus chain T [auth B] Focus chain TA [auth G] Focus chain U [auth B] Focus chain UA [auth H] Focus chain V [auth C] Focus chain VA [auth H] Focus chain W [auth C] Focus chain WA [auth H] Focus chain X [auth C] Focus chain XA [auth H] Focus chain Y [auth C] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth I] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth I] Focus chain BA [auth D] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain CB [auth I] Focus chain DA [auth D] Focus chain DB [auth I] Focus chain EA [auth D] Focus chain EB [auth J] Focus chain FA [auth E] Focus chain FB [auth J] Focus chain GA [auth E] Focus chain GB [auth J] Focus chain HA [auth E] Focus chain HB [auth J] Focus chain IA [auth E] Focus chain IB [auth J] Focus chain JA [auth E] Focus chain JB [auth K] Focus chain KA [auth F] Focus chain KB [auth K] Focus chain L [auth A] Focus chain LA [auth F] Focus chain LB [auth K] Focus chain M [auth A] Focus chain MA [auth F] Focus chain MB [auth K] Focus chain N [auth A] Focus chain NA [auth F] Focus chain NB [auth K] Focus chain O [auth A] Focus chain OA [auth F] Focus chain P [auth A] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain RA [auth G] Focus chain S [auth B] Focus chain SA [auth G] Focus chain T [auth B] Focus chain TA [auth G] Focus chain U [auth B] Focus chain UA [auth H] Focus chain V [auth C] Focus chain VA [auth H] Focus chain W [auth C] Focus chain WA [auth H] Focus chain X [auth C] Focus chain XA [auth H] Focus chain Y [auth C] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth I]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-12-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2016YFA0500404
Ministry of Science and Technology (MoST, China)	China	2018YFA0508100
National Natural Science Foundation of China (NSFC)	China	31525001
National Natural Science Foundation of China (NSFC)	China	31971127
National Natural Science Foundation of China (NSFC)	China	31870724
National Natural Science Foundation of China (NSFC)	China	31900041
National Natural Science Foundation of China (NSFC)	China	31525007
National Natural Science Foundation of China (NSFC)	China	31930063