Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5VRF

CryoEM Structure of the Zinc Transporter YiiP from helical crystals

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005886	cellular_component	plasma membrane
A	0006811	biological_process	monoatomic ion transport
A	0006812	biological_process	monoatomic cation transport
A	0006826	biological_process	iron ion transport
A	0006829	biological_process	zinc ion transport
A	0006882	biological_process	intracellular zinc ion homeostasis
A	0008324	molecular_function	monoatomic cation transmembrane transporter activity
A	0015086	molecular_function	cadmium ion transmembrane transporter activity
A	0015093	molecular_function	ferrous iron transmembrane transporter activity
A	0015341	molecular_function	zinc efflux antiporter activity
A	0016020	cellular_component	membrane
A	0034755	biological_process	iron ion transmembrane transport
A	0046872	molecular_function	metal ion binding
A	0055085	biological_process	transmembrane transport
A	0070574	biological_process	cadmium ion transmembrane transport
A	0071577	biological_process	zinc ion transmembrane transport
A	0098655	biological_process	monoatomic cation transmembrane transport
B	0005886	cellular_component	plasma membrane
B	0006811	biological_process	monoatomic ion transport
B	0006812	biological_process	monoatomic cation transport
B	0006826	biological_process	iron ion transport
B	0006829	biological_process	zinc ion transport
B	0006882	biological_process	intracellular zinc ion homeostasis
B	0008324	molecular_function	monoatomic cation transmembrane transporter activity
B	0015086	molecular_function	cadmium ion transmembrane transporter activity
B	0015093	molecular_function	ferrous iron transmembrane transporter activity
B	0015341	molecular_function	zinc efflux antiporter activity
B	0016020	cellular_component	membrane
B	0034755	biological_process	iron ion transmembrane transport
B	0046872	molecular_function	metal ion binding
B	0055085	biological_process	transmembrane transport
B	0070574	biological_process	cadmium ion transmembrane transport
B	0071577	biological_process	zinc ion transmembrane transport
B	0098655	biological_process	monoatomic cation transmembrane transport

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN B 301

Chain	Residue
B	ASP47
B	ASP51
B	HIS155
B	ASP159

site_id	AC2
Number of Residues	3
Details	binding site for residue ZN B 302

Chain	Residue
B	ASP70
B	HIS73
B	HIS77

site_id	AC3
Number of Residues	3
Details	binding site for residue ZN B 303

Chain	Residue
B	ASP287
A	HIS263
B	HIS285

site_id	AC4
Number of Residues	4
Details	binding site for residue ZN B 304

Chain	Residue
B	HIS234
B	ASP235
B	HIS250
B	ASP287

site_id	AC5
Number of Residues	3
Details	binding site for residue ZN A 303

Chain	Residue
A	HIS285
A	ASP287
B	HIS263

site_id	AC6
Number of Residues	4
Details	binding site for residue ZN A 301

Chain	Residue
A	ASP47
A	ASP51
A	HIS155
A	ASP159

site_id	AC7
Number of Residues	3
Details	binding site for residue ZN A 302

Chain	Residue
A	ASP70
A	HIS73
A	HIS77

site_id	AC8
Number of Residues	4
Details	binding site for residue ZN A 304

Chain	Residue
A	HIS234
A	ASP235
A	HIS250
A	ASP287

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	202
Details	Transmembrane: {"description":"Helical","evidences":[{"source":"UniProtKB","id":"P69380","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	84
Details	Topological domain: {"description":"Periplasmic","evidences":[{"source":"UniProtKB","id":"P69380","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	56
Details	Topological domain: {"description":"Cytoplasmic","evidences":[{"source":"UniProtKB","id":"P69380","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"29507252","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34254979","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"NOV-2022","submissionDatabase":"PDB data bank","title":"Characterization of individual Zn2+ binding sites of YiiP.","authors":["Lopez-Redondo M.L.","Hussein A.K.","Stokes D.L."]}},{"source":"PDB","id":"5VRF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7KZZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6E","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6I","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6J","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6K","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"29507252","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34254979","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"NOV-2022","submissionDatabase":"PDB data bank","title":"Characterization of individual Zn2+ binding sites of YiiP.","authors":["Lopez-Redondo M.L.","Hussein A.K.","Stokes D.L."]}},{"source":"PDB","id":"5VRF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7KZZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6E","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6I","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6J","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"29507252","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34254979","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"NOV-2022","submissionDatabase":"PDB data bank","title":"Characterization of individual Zn2+ binding sites of YiiP.","authors":["Lopez-Redondo M.L.","Hussein A.K.","Stokes D.L."]}},{"source":"PDB","id":"5VRF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7KZZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6E","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6F","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6J","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"29507252","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34254979","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"NOV-2022","submissionDatabase":"PDB data bank","title":"Characterization of individual Zn2+ binding sites of YiiP.","authors":["Lopez-Redondo M.L.","Hussein A.K.","Stokes D.L."]}},{"source":"PDB","id":"5VRF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7KZZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6E","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6J","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"29507252","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34254979","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"NOV-2022","submissionDatabase":"PDB data bank","title":"Characterization of individual Zn2+ binding sites of YiiP.","authors":["Lopez-Redondo M.L.","Hussein A.K.","Stokes D.L."]}},{"source":"PDB","id":"5VRF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7KZZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6E","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6I","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6K","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"29507252","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34254979","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"NOV-2022","submissionDatabase":"PDB data bank","title":"Characterization of individual Zn2+ binding sites of YiiP.","authors":["Lopez-Redondo M.L.","Hussein A.K.","Stokes D.L."]}},{"source":"PDB","id":"5VRF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7KZZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6H","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"29507252","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34254979","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5VRF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7KZZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"29507252","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34254979","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"NOV-2022","submissionDatabase":"PDB data bank","title":"Characterization of individual Zn2+ binding sites of YiiP.","authors":["Lopez-Redondo M.L.","Hussein A.K.","Stokes D.L."]}},{"source":"PDB","id":"5VRF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7KZZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6F","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6I","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6J","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"29507252","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34254979","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"NOV-2022","submissionDatabase":"PDB data bank","title":"Characterization of individual Zn2+ binding sites of YiiP.","authors":["Lopez-Redondo M.L.","Hussein A.K.","Stokes D.L."]}},{"source":"PDB","id":"5VRF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7KZZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6E","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6F","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6I","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6J","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"29507252","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34254979","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"NOV-2022","submissionDatabase":"PDB data bank","title":"Characterization of individual Zn2+ binding sites of YiiP.","authors":["Lopez-Redondo M.L.","Hussein A.K.","Stokes D.L."]}},{"source":"PDB","id":"5VRF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7KZZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6E","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6F","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8F6I","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)