5W3S

Cryo-electron microscopy structure of a TRPML3 ion channel

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000421	cellular_component	autophagosome membrane
A	0005253	molecular_function	monoatomic anion channel activity
A	0005261	molecular_function	monoatomic cation channel activity
A	0005267	molecular_function	potassium channel activity
A	0005272	molecular_function	sodium channel activity
A	0005764	cellular_component	lysosome
A	0005765	cellular_component	lysosomal membrane
A	0005768	cellular_component	endosome
A	0005886	cellular_component	plasma membrane
A	0008289	molecular_function	lipid binding
A	0008324	molecular_function	monoatomic cation transmembrane transporter activity
A	0016020	cellular_component	membrane
A	0019722	biological_process	calcium-mediated signaling
A	0031901	cellular_component	early endosome membrane
A	0031902	cellular_component	late endosome membrane
A	0034220	biological_process	monoatomic ion transmembrane transport
A	0035725	biological_process	sodium ion transmembrane transport
A	0042802	molecular_function	identical protein binding
A	0042995	cellular_component	cell projection
A	0051289	biological_process	protein homotetramerization
A	0060171	cellular_component	stereocilium membrane
A	0071805	biological_process	potassium ion transmembrane transport
A	0072345	molecular_function	NAADP-sensitive calcium-release channel activity
A	0080025	molecular_function	phosphatidylinositol-3,5-bisphosphate binding
A	0097682	molecular_function	intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity
A	0098655	biological_process	monoatomic cation transmembrane transport
A	0098656	biological_process	monoatomic anion transmembrane transport
B	0000421	cellular_component	autophagosome membrane
B	0005253	molecular_function	monoatomic anion channel activity
B	0005261	molecular_function	monoatomic cation channel activity
B	0005267	molecular_function	potassium channel activity
B	0005272	molecular_function	sodium channel activity
B	0005764	cellular_component	lysosome
B	0005765	cellular_component	lysosomal membrane
B	0005768	cellular_component	endosome
B	0005886	cellular_component	plasma membrane
B	0008289	molecular_function	lipid binding
B	0008324	molecular_function	monoatomic cation transmembrane transporter activity
B	0016020	cellular_component	membrane
B	0019722	biological_process	calcium-mediated signaling
B	0031901	cellular_component	early endosome membrane
B	0031902	cellular_component	late endosome membrane
B	0034220	biological_process	monoatomic ion transmembrane transport
B	0035725	biological_process	sodium ion transmembrane transport
B	0042802	molecular_function	identical protein binding
B	0042995	cellular_component	cell projection
B	0051289	biological_process	protein homotetramerization
B	0060171	cellular_component	stereocilium membrane
B	0071805	biological_process	potassium ion transmembrane transport
B	0072345	molecular_function	NAADP-sensitive calcium-release channel activity
B	0080025	molecular_function	phosphatidylinositol-3,5-bisphosphate binding
B	0097682	molecular_function	intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity
B	0098655	biological_process	monoatomic cation transmembrane transport
B	0098656	biological_process	monoatomic anion transmembrane transport
C	0000421	cellular_component	autophagosome membrane
C	0005253	molecular_function	monoatomic anion channel activity
C	0005261	molecular_function	monoatomic cation channel activity
C	0005267	molecular_function	potassium channel activity
C	0005272	molecular_function	sodium channel activity
C	0005764	cellular_component	lysosome
C	0005765	cellular_component	lysosomal membrane
C	0005768	cellular_component	endosome
C	0005886	cellular_component	plasma membrane
C	0008289	molecular_function	lipid binding
C	0008324	molecular_function	monoatomic cation transmembrane transporter activity
C	0016020	cellular_component	membrane
C	0019722	biological_process	calcium-mediated signaling
C	0031901	cellular_component	early endosome membrane
C	0031902	cellular_component	late endosome membrane
C	0034220	biological_process	monoatomic ion transmembrane transport
C	0035725	biological_process	sodium ion transmembrane transport
C	0042802	molecular_function	identical protein binding
C	0042995	cellular_component	cell projection
C	0051289	biological_process	protein homotetramerization
C	0060171	cellular_component	stereocilium membrane
C	0071805	biological_process	potassium ion transmembrane transport
C	0072345	molecular_function	NAADP-sensitive calcium-release channel activity
C	0080025	molecular_function	phosphatidylinositol-3,5-bisphosphate binding
C	0097682	molecular_function	intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity
C	0098655	biological_process	monoatomic cation transmembrane transport
C	0098656	biological_process	monoatomic anion transmembrane transport
D	0000421	cellular_component	autophagosome membrane
D	0005253	molecular_function	monoatomic anion channel activity
D	0005261	molecular_function	monoatomic cation channel activity
D	0005267	molecular_function	potassium channel activity
D	0005272	molecular_function	sodium channel activity
D	0005764	cellular_component	lysosome
D	0005765	cellular_component	lysosomal membrane
D	0005768	cellular_component	endosome
D	0005886	cellular_component	plasma membrane
D	0008289	molecular_function	lipid binding
D	0008324	molecular_function	monoatomic cation transmembrane transporter activity
D	0016020	cellular_component	membrane
D	0019722	biological_process	calcium-mediated signaling
D	0031901	cellular_component	early endosome membrane
D	0031902	cellular_component	late endosome membrane
D	0034220	biological_process	monoatomic ion transmembrane transport
D	0035725	biological_process	sodium ion transmembrane transport
D	0042802	molecular_function	identical protein binding
D	0042995	cellular_component	cell projection
D	0051289	biological_process	protein homotetramerization
D	0060171	cellular_component	stereocilium membrane
D	0071805	biological_process	potassium ion transmembrane transport
D	0072345	molecular_function	NAADP-sensitive calcium-release channel activity
D	0080025	molecular_function	phosphatidylinositol-3,5-bisphosphate binding
D	0097682	molecular_function	intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity
D	0098655	biological_process	monoatomic cation transmembrane transport
D	0098656	biological_process	monoatomic anion transmembrane transport

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	binding site for residue Y01 A 601

Chain	Residue
A	ALA419
A	ALA420
A	TYR423
A	SER448
B	Y01601
C	3PE601

---

site_id	AC2
Number of Residues	2
Details	binding site for residue NA A 602

Chain	Residue
C	NA603
C	NA604

---

site_id	AC3
Number of Residues	1
Details	binding site for residue 3PE A 604

Chain	Residue
B	Y01602

---

site_id	AC4
Number of Residues	6
Details	binding site for residue Y01 A 605

Chain	Residue
A	CYS50
A	ILE67
A	ILE70
A	THR74
A	TRP385
A	TYR391

---

site_id	AC5
Number of Residues	6
Details	binding site for residue Y01 A 606

Chain	Residue
A	TYR472
A	TRP475
A	TYR483
A	SER487
C	ASN445
C	Y01606

---

site_id	AC6
Number of Residues	6
Details	binding site for residue Y01 B 601

Chain	Residue
A	ASN445
A	Y01601
B	TYR472
B	TRP475
B	ILE480
B	TYR483

---

site_id	AC7
Number of Residues	6
Details	binding site for residue Y01 B 602

Chain	Residue
A	3PE604
B	ALA419
B	ALA420
B	TYR423
B	SER448
D	Y01602

---

site_id	AC8
Number of Residues	1
Details	binding site for residue 3PE B 603

Chain	Residue
D	Y01605

---

site_id	AC9
Number of Residues	7
Details	binding site for residue Y01 B 604

Chain	Residue
B	CYS50
B	ILE67
B	ILE70
B	THR74
B	TRP385
B	VAL388
B	TYR391

---

site_id	AD1
Number of Residues	1
Details	binding site for residue 3PE C 601

Chain	Residue
A	Y01601

---

site_id	AD2
Number of Residues	7
Details	binding site for residue Y01 C 602

Chain	Residue
C	CYS50
C	ILE67
C	ILE70
C	THR74
C	TRP385
C	VAL388
C	TYR391

---

site_id	AD3
Number of Residues	1
Details	binding site for residue NA C 603

Chain	Residue
A	NA602

---

site_id	AD4
Number of Residues	2
Details	binding site for residue NA C 604

Chain	Residue
A	NA602
C	NA605

---

site_id	AD5
Number of Residues	1
Details	binding site for residue NA C 605

Chain	Residue
C	NA604

---

site_id	AD6
Number of Residues	6
Details	binding site for residue Y01 C 606

Chain	Residue
A	Y01606
C	ALA419
C	ALA420
C	TYR423
C	SER448
D	3PE603

---

site_id	AD7
Number of Residues	6
Details	binding site for residue Y01 C 607

Chain	Residue
C	TYR472
C	TRP475
C	ILE480
C	TYR483
D	ASN445
D	Y01605

---

site_id	AD8
Number of Residues	7
Details	binding site for residue Y01 D 602

Chain	Residue
B	ASN445
B	Y01602
D	TYR472
D	TRP475
D	ILE480
D	TYR483
D	SER487

---

site_id	AD9
Number of Residues	1
Details	binding site for residue 3PE D 603

Chain	Residue
C	Y01606

---

site_id	AE1
Number of Residues	7
Details	binding site for residue Y01 D 604

Chain	Residue
D	CYS50
D	ILE67
D	ILE70
D	THR74
D	TRP385
D	VAL388
D	TYR391

---

site_id	AE2
Number of Residues	7
Details	binding site for residue Y01 D 605

Chain	Residue
B	3PE603
C	Y01607
D	CYS416
D	ALA419
D	ALA420
D	TYR423
D	SER448

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	692
Details	TOPO_DOM: Cytoplasmic => ECO:0000269|PubMed:29019979

Chain	Residue	Details
A	MET1-LYS62
C	ARG305-TRP341
C	GLY393-ARG414
C	ILE498-LYS553
D	MET1-LYS62
D	ARG305-TRP341
D	GLY393-ARG414
D	ILE498-LYS553
A	ARG305-TRP341
A	GLY393-ARG414
A	ILE498-LYS553
B	MET1-LYS62
B	ARG305-TRP341
B	GLY393-ARG414
B	ILE498-LYS553
C	MET1-LYS62

---

site_id	SWS_FT_FI2
Number of Residues	484
Details	TRANSMEM: Helical => ECO:0000269|PubMed:29019979

Chain	Residue	Details
A	LEU63-SER83
B	VAL372-LEU392
B	PHE415-GLY435
B	LEU476-PHE497
C	LEU63-SER83
C	ASN284-ILE304
C	TYR342-ILE362
C	VAL372-LEU392
C	PHE415-GLY435
C	LEU476-PHE497
D	LEU63-SER83
A	ASN284-ILE304
D	ASN284-ILE304
D	TYR342-ILE362
D	VAL372-LEU392
D	PHE415-GLY435
D	LEU476-PHE497
A	TYR342-ILE362
A	VAL372-LEU392
A	PHE415-GLY435
A	LEU476-PHE497
B	LEU63-SER83
B	ASN284-ILE304
B	TYR342-ILE362

---

site_id	SWS_FT_FI3
Number of Residues	896
Details	TOPO_DOM: Extracellular => ECO:0000269|PubMed:29019979

Chain	Residue	Details
A	ASN84-HIS283
C	GLN363-ASP371
C	PRO436-SER443
C	ALA465-TRP475
D	ASN84-HIS283
D	GLN363-ASP371
D	PRO436-SER443
D	ALA465-TRP475
A	GLN363-ASP371
A	PRO436-SER443
A	ALA465-TRP475
B	ASN84-HIS283
B	GLN363-ASP371
B	PRO436-SER443
B	ALA465-TRP475
C	ASN84-HIS283

---

site_id	SWS_FT_FI4
Number of Residues	80
Details	INTRAMEM: Pore-forming => ECO:0000269|PubMed:29019979

Chain	Residue	Details
A	LEU444-PHE464
B	LEU444-PHE464
C	LEU444-PHE464
D	LEU444-PHE464

---

site_id	SWS_FT_FI5
Number of Residues	4
Details	SITE: Interaction with phosphoinositides => ECO:0000269|PubMed:29019979

Chain	Residue	Details
A	ARG305
B	ARG305
C	ARG305
D	ARG305

---

site_id	SWS_FT_FI6
Number of Residues	8
Details	CARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000255

Chain	Residue	Details
A	GLN138
A	ASN205
B	GLN138
B	ASN205
C	GLN138
C	ASN205
D	GLN138
D	ASN205

---