{"entryType":"UniProtKB reviewed (Swiss-Prot)","primaryAccession":"P0AAS3","secondaryAccessions":["P75709","P77124","Q2MBT9"],"uniProtkbId":"YBBJ_ECOLI","entryAudit":{"firstPublicDate":"2005-10-11","lastAnnotationUpdateDate":"2026-06-10","lastSequenceUpdateDate":"2007-06-26","entryVersion":119,"sequenceVersion":2},"annotationScore":4.0,"organism":{"scientificName":"Escherichia coli (strain K12)","taxonId":83333,"lineage":["Bacteria","Pseudomonadati","Pseudomonadota","Gammaproteobacteria","Enterobacterales","Enterobacteriaceae","Escherichia"]},"proteinExistence":"1: Evidence at protein level","proteinDescription":{"recommendedName":{"fullName":{"evidences":[{"evidenceCode":"ECO:0000305"}],"value":"Inner membrane protein YbbJ"}}},"genes":[{"geneName":{"value":"ybbJ"},"orderedLocusNames":[{"value":"b0488"},{"value":"JW5065"}]}],"comments":[{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"39181124"}],"value":"Acts as a bridge to aid QmcA oligomerization and facilitates the formation of the entire QmcA-YbbJ complex"}],"commentType":"FUNCTION"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"39181124"}],"value":"Forms an heterodimer with the inner membrane protein QmcA (PubMed:39181124). The QmcA-YbbJ complex forms an intricate cage-like structure composed of 26 copies of QmcA-YbbJ heterodimers (PubMed:39181124)"}],"commentType":"SUBUNIT"},{"commentType":"SUBCELLULAR LOCATION","subcellularLocations":[{"location":{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"15919996"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"39181124"}],"value":"Cell inner membrane","id":"SL-0037"},"topology":{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"39181124"}],"value":"Multi-pass membrane protein","id":"SL-9909"}}]},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"39181124"}],"value":"The transmembrane helices of YbbJ act as adhesive elements bridging adjacent QmcA molecules, while the oligosaccharide-binding (OB) domain of YbbJ encapsulates the Band 7 (or SPFH) domain of QmcA"}],"commentType":"DOMAIN"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000305"}],"value":"Belongs to the YbbJ family"}],"commentType":"SIMILARITY"},{"commentType":"SEQUENCE CAUTION","sequenceCautionType":"Erroneous initiation","sequence":"BAE76267.1","evidences":[{"evidenceCode":"ECO:0000305"}]}],"features":[{"type":"Chain","location":{"start":{"value":1,"modifier":"EXACT"},"end":{"value":152,"modifier":"EXACT"}},"description":"Inner membrane protein YbbJ","featureId":"PRO_0000168638"},{"type":"Transmembrane","location":{"start":{"value":1,"modifier":"EXACT"},"end":{"value":21,"modifier":"EXACT"}},"description":"Helical","evidences":[{"evidenceCode":"ECO:0000255"}]},{"type":"Topological domain","location":{"start":{"value":22,"modifier":"EXACT"},"end":{"value":31,"modifier":"EXACT"}},"description":"Cytoplasmic","evidences":[{"evidenceCode":"ECO:0000305"}]},{"type":"Transmembrane","location":{"start":{"value":32,"modifier":"EXACT"},"end":{"value":52,"modifier":"EXACT"}},"description":"Helical","evidences":[{"evidenceCode":"ECO:0000255"}]},{"type":"Topological domain","location":{"start":{"value":53,"modifier":"EXACT"},"end":{"value":54,"modifier":"EXACT"}},"description":"Periplasmic","evidences":[{"evidenceCode":"ECO:0000305"}]},{"type":"Transmembrane","location":{"start":{"value":55,"modifier":"EXACT"},"end":{"value":75,"modifier":"EXACT"}},"description":"Helical","evidences":[{"evidenceCode":"ECO:0000255"}]},{"type":"Topological domain","location":{"start":{"value":76,"modifier":"EXACT"},"end":{"value":152,"modifier":"EXACT"}},"description":"Cytoplasmic","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"15919996"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"39181124"}]},{"type":"Region","location":{"start":{"value":83,"modifier":"EXACT"},"end":{"value":152,"modifier":"EXACT"}},"description":"Oligosaccharide binding (OB) fold-like domain","evidences":[{"evidenceCode":"ECO:0000305","source":"PubMed","id":"39181124"}]},{"type":"Mutagenesis","location":{"start":{"value":61,"modifier":"EXACT"},"end":{"value":61,"modifier":"EXACT"}},"description":"Cannot form the entire wild-type QmcA-YbbJ complex.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"39181124"}],"alternativeSequence":{"originalSequence":"A","alternativeSequences":["F"]}},{"type":"Mutagenesis","location":{"start":{"value":118,"modifier":"EXACT"},"end":{"value":119,"modifier":"EXACT"}},"description":"Cannot form the entire wild-type QmcA-YbbJ complex.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"39181124"}],"alternativeSequence":{"originalSequence":"DS","alternativeSequences":["AA"]}},{"type":"Mutagenesis","location":{"start":{"value":119,"modifier":"EXACT"},"end":{"value":119,"modifier":"EXACT"}},"description":"Cannot form the entire wild-type QmcA-YbbJ complex.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"39181124"}],"alternativeSequence":{"originalSequence":"S","alternativeSequences":["Y"]}},{"type":"Helix","location":{"start":{"value":9,"modifier":"EXACT"},"end":{"value":24,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"8Z5G"}]},{"type":"Turn","location":{"start":{"value":25,"modifier":"EXACT"},"end":{"value":27,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"8Z5G"}]},{"type":"Helix","location":{"start":{"value":33,"modifier":"EXACT"},"end":{"value":46,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"8Z5G"}]},{"type":"Helix","location":{"start":{"value":53,"modifier":"EXACT"},"end":{"value":55,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"8Z5G"}]},{"type":"Helix","location":{"start":{"value":56,"modifier":"EXACT"},"end":{"value":79,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"8Z5G"}]},{"type":"Turn","location":{"start":{"value":80,"modifier":"EXACT"},"end":{"value":82,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"8Z5G"}]},{"type":"Turn","location":{"start":{"value":85,"modifier":"EXACT"},"end":{"value":89,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"8Z5G"}]},{"type":"Helix","location":{"start":{"value":92,"modifier":"EXACT"},"end":{"value":95,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"8Z5G"}]},{"type":"Turn","location":{"start":{"value":96,"modifier":"EXACT"},"end":{"value":98,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"8Z5G"}]},{"type":"Beta strand","location":{"start":{"value":100,"modifier":"EXACT"},"end":{"value":102,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"8Z5G"}]},{"type":"Beta strand","location":{"start":{"value":111,"modifier":"EXACT"},"end":{"value":116,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"8Z5G"}]},{"type":"Beta strand","location":{"start":{"value":119,"modifier":"EXACT"},"end":{"value":124,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"8Z5G"}]},{"type":"Beta strand","location":{"start":{"value":134,"modifier":"EXACT"},"end":{"value":141,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"8Z5G"}]},{"type":"Beta strand","location":{"start":{"value":144,"modifier":"EXACT"},"end":{"value":149,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"8Z5G"}]}],"keywords":[{"id":"KW-0002","category":"Technical term","name":"3D-structure"},{"id":"KW-0997","category":"Cellular component","name":"Cell inner membrane"},{"id":"KW-1003","category":"Cellular component","name":"Cell membrane"},{"id":"KW-0472","category":"Cellular component","name":"Membrane"},{"id":"KW-1185","category":"Technical term","name":"Reference proteome"},{"id":"KW-0812","category":"Domain","name":"Transmembrane"},{"id":"KW-1133","category":"Domain","name":"Transmembrane helix"}],"references":[{"referenceNumber":1,"citation":{"id":"CI-B1UJ6TNQ0SAS1","citationType":"submission","authors":["Chung E.","Allen E.","Araujo R.","Aparicio A.M.","Davis K.","Duncan M.","Federspiel N.","Hyman R.","Kalman S.","Komp C.","Kurdi O.","Lew H.","Lin D.","Namath A.","Oefner P.","Roberts D.","Schramm S.","Davis R.W."],"title":"Sequence of minutes 4-25 of Escherichia coli.","publicationDate":"JAN-1997","submissionDatabase":"EMBL/GenBank/DDBJ databases"},"referencePositions":["NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]"],"referenceComments":[{"value":"K12 / MG1655 / ATCC 47076","type":"STRAIN"}]},{"referenceNumber":2,"citation":{"id":"9278503","citationType":"journal article","authors":["Blattner F.R.","Plunkett G. III","Bloch C.A.","Perna N.T.","Burland V.","Riley M.","Collado-Vides J.","Glasner J.D.","Rode C.K.","Mayhew G.F.","Gregor J.","Davis N.W.","Kirkpatrick H.A.","Goeden M.A.","Rose D.J.","Mau B.","Shao Y."],"citationCrossReferences":[{"database":"PubMed","id":"9278503"},{"database":"DOI","id":"10.1126/science.277.5331.1453"}],"title":"The complete genome sequence of Escherichia coli K-12.","publicationDate":"1997","journal":"Science","firstPage":"1453","lastPage":"1462","volume":"277"},"referencePositions":["NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]"],"referenceComments":[{"value":"K12 / MG1655 / ATCC 47076","type":"STRAIN"}]},{"referenceNumber":3,"citation":{"id":"16738553","citationType":"journal article","authors":["Hayashi K.","Morooka N.","Yamamoto Y.","Fujita K.","Isono K.","Choi S.","Ohtsubo E.","Baba T.","Wanner B.L.","Mori H.","Horiuchi T."],"citationCrossReferences":[{"database":"PubMed","id":"16738553"},{"database":"DOI","id":"10.1038/msb4100049"}],"title":"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110.","publicationDate":"2006","journal":"Mol. Syst. Biol.","firstPage":"E1","lastPage":"E5","volume":"2"},"referencePositions":["NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]"],"referenceComments":[{"value":"K12 / W3110 / ATCC 27325 / DSM 5911","type":"STRAIN"}]},{"referenceNumber":4,"citation":{"id":"15919996","citationType":"journal article","authors":["Daley D.O.","Rapp M.","Granseth E.","Melen K.","Drew D.","von Heijne G."],"citationCrossReferences":[{"database":"PubMed","id":"15919996"},{"database":"DOI","id":"10.1126/science.1109730"}],"title":"Global topology analysis of the Escherichia coli inner membrane proteome.","publicationDate":"2005","journal":"Science","firstPage":"1321","lastPage":"1323","volume":"308"},"referencePositions":["TOPOLOGY [LARGE SCALE ANALYSIS]","SUBCELLULAR LOCATION"],"referenceComments":[{"value":"K12 / MG1655 / ATCC 47076","type":"STRAIN"}]},{"referenceNumber":5,"citation":{"id":"39181124","citationType":"journal article","authors":["Tan K.A.","Qiao Z.","Lim Z.Z.E.","Yeo J.Y.","Yong Y.","Do P.H.","Ero R.","Gao Y.G."],"citationCrossReferences":[{"database":"PubMed","id":"39181124"},{"database":"DOI","id":"10.1016/j.str.2024.07.022"}],"title":"Cryo-EM structure of the SPFH-NfeD family protein complex QmcA-YbbJ.","publicationDate":"2024","journal":"Structure","firstPage":"1603","lastPage":"1610.e3","volume":"32"},"referencePositions":["STRUCTURE BY ELECTRON MICROSCOPY (2.90 ANGSTROMS) OF THE QMCA-YBBJ COMPLEX","FUNCTION","INTERACTION WITH QMCA","SUBUNIT","SUBCELLULAR LOCATION","DOMAIN","MUTAGENESIS OF ALA-61; 118-ASP-SER-119 AND SER-119"],"evidences":[{"evidenceCode":"ECO:0007744","source":"PDB","id":"8Z5G"}]}],"uniProtKBCrossReferences":[{"database":"EMBL","id":"U82664","properties":[{"key":"ProteinId","value":"AAB40242.1"},{"key":"Status","value":"-"},{"key":"MoleculeType","value":"Genomic_DNA"}]},{"database":"EMBL","id":"U00096","properties":[{"key":"ProteinId","value":"AAC73590.2"},{"key":"Status","value":"-"},{"key":"MoleculeType","value":"Genomic_DNA"}]},{"database":"EMBL","id":"AP009048","properties":[{"key":"ProteinId","value":"BAE76267.1"},{"key":"Status","value":"ALT_INIT"},{"key":"MoleculeType","value":"Genomic_DNA"}]},{"database":"PIR","id":"G64779","properties":[{"key":"EntryName","value":"G64779"}]},{"database":"RefSeq","id":"NP_415021.2","properties":[{"key":"NucleotideSequenceId","value":"NC_000913.3"}]},{"database":"RefSeq","id":"WP_000970323.1","properties":[{"key":"NucleotideSequenceId","value":"NZ_CP009789.1"}]},{"database":"PDB","id":"8Z5G","properties":[{"key":"Method","value":"EM"},{"key":"Resolution","value":"2.90 A"},{"key":"Chains","value":"AA/AB/B/CA/D/EA/F/GA/H/IA/J/KA/L/MA/N/OA/P/QA/R/SA/T/UA/W/WA/Y/YA=1-152"}]},{"database":"PDBsum","id":"8Z5G","properties":[{"key":"Description","value":"-"}]},{"database":"AlphaFoldDB","id":"P0AAS3","properties":[{"key":"Description","value":"-"}]},{"database":"EMDB","id":"EMD-39773","properties":[{"key":"Description","value":"-"}]},{"database":"SMR","id":"P0AAS3","properties":[{"key":"Description","value":"-"}]},{"database":"BioGRID","id":"4261106","properties":[{"key":"Interactions","value":"7"}]},{"database":"FunCoup","id":"P0AAS3","properties":[{"key":"Number of interactors","value":"50"}]},{"database":"STRING","id":"511145.b0488","properties":[{"key":"Description","value":"-"}]},{"database":"PaxDb","id":"511145-b0488","properties":[{"key":"Description","value":"-"}]},{"database":"EnsemblBacteria","id":"AAC73590","properties":[{"key":"ProteinId","value":"AAC73590"},{"key":"GeneId","value":"b0488"}]},{"database":"GeneID","id":"93776961","properties":[{"key":"Description","value":"-"}]},{"database":"GeneID","id":"945126","properties":[{"key":"Description","value":"-"}]},{"database":"KEGG","id":"ecj:JW5065","properties":[{"key":"Description","value":"-"}]},{"database":"KEGG","id":"eco:b0488","properties":[{"key":"Description","value":"-"}]},{"database":"KEGG","id":"ecoc:C3026_02400","properties":[{"key":"Description","value":"-"}]},{"database":"PATRIC","id":"fig|1411691.4.peg.1788","properties":[{"key":"GeneDesignation","value":"-"}]},{"database":"EchoBASE","id":"EB3045","properties":[{"key":"Description","value":"-"}]},{"database":"eggNOG","id":"COG1585","properties":[{"key":"ToxonomicScope","value":"Bacteria"}]},{"database":"HOGENOM","id":"CLU_116732_4_0_6","properties":[{"key":"Description","value":"-"}]},{"database":"InParanoid","id":"P0AAS3","properties":[{"key":"Description","value":"-"}]},{"database":"OMA","id":"FWDSAFW","properties":[{"key":"Fingerprint","value":"-"}]},{"database":"OrthoDB","id":"6402862at2","properties":[{"key":"Description","value":"-"}]},{"database":"PhylomeDB","id":"P0AAS3","properties":[{"key":"Description","value":"-"}]},{"database":"BioCyc","id":"EcoCyc:G6264-MONOMER","properties":[{"key":"Description","value":"-"}]},{"database":"PRO","id":"PR:P0AAS3","properties":[{"key":"Description","value":"-"}]},{"database":"Proteomes","id":"UP000000625","properties":[{"key":"Component","value":"Chromosome"}]},{"database":"GO","id":"GO:0005886","properties":[{"key":"GoTerm","value":"C:plasma membrane"},{"key":"GoEvidenceType","value":"IDA:EcoCyc"}],"evidences":[{"evidenceCode":"ECO:0000314","source":"PubMed","id":"15919996"}]},{"database":"FunFam","id":"2.40.50.140:FF:000118","properties":[{"key":"EntryName","value":"NfeD family protein"},{"key":"MatchStatus","value":"1"}]},{"database":"Gene3D","id":"2.40.50.140","properties":[{"key":"EntryName","value":"Nucleic acid-binding proteins"},{"key":"MatchStatus","value":"1"}]},{"database":"InterPro","id":"IPR052165","properties":[{"key":"EntryName","value":"Membrane_assoc_protease"}]},{"database":"InterPro","id":"IPR012340","properties":[{"key":"EntryName","value":"NA-bd_OB-fold"}]},{"database":"InterPro","id":"IPR002810","properties":[{"key":"EntryName","value":"NfeD-like_C"}]},{"database":"PANTHER","id":"PTHR33507","properties":[{"key":"EntryName","value":"INNER MEMBRANE PROTEIN YBBJ"},{"key":"MatchStatus","value":"1"}]},{"database":"PANTHER","id":"PTHR33507:SF3","properties":[{"key":"EntryName","value":"INNER MEMBRANE PROTEIN YBBJ"},{"key":"MatchStatus","value":"1"}]},{"database":"Pfam","id":"PF01957","properties":[{"key":"EntryName","value":"NfeD"},{"key":"MatchStatus","value":"1"}]},{"database":"SUPFAM","id":"SSF141322","properties":[{"key":"EntryName","value":"NfeD domain-like"},{"key":"MatchStatus","value":"1"}]}],"sequence":{"value":"MMELMVVHPHIFWLSLGGLLLAAEMLGGNGYLLWSGVAAVITGLVVWLVPLGWEWQGVMFAILTLLAAWLWWKWLSRRVREQKHSDSHLNQRGQQLIGRRFVLESPLVNGRGHMRVGDSSWPVSASEDLGAGTHVEVIAIEGITLHIRAVSS","length":152,"molWeight":16939,"crc64":"FDD3930F4D4FE76E","md5":"22CCEB8EA8572D920B6EA0113AFE5DDB"},"extraAttributes":{"countByCommentType":{"FUNCTION":1,"SUBUNIT":1,"SUBCELLULAR LOCATION":1,"DOMAIN":1,"SIMILARITY":1,"SEQUENCE CAUTION":1},"countByFeatureType":{"Chain":1,"Transmembrane":3,"Topological domain":3,"Region":1,"Mutagenesis":3,"Helix":5,"Turn":4,"Beta strand":5},"uniParcId":"UPI0000163979"}}