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Protein

Protein lin-28 homolog B

Gene

LIN28B

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Suppressor of microRNA (miRNA) biogenesis, including that of let-7 and possibly of miR107, miR-143 and miR-200c. Binds primary let-7 transcripts (pri-let-7), including pri-let-7g and pri-let-7a-1, and sequester them in the nucleolus, away from the microprocessor complex, hence preventing their processing into mature miRNA (PubMed:22118463). Does not act on pri-miR21 (PubMed:22118463). The repression of let-7 expression is required for normal development and contributes to maintain the pluripotent state of embryonic stem cells by preventing let-7-mediated differentiation. When overexpressed, recruits ZCCHC11/TUT4 uridylyltransferase to pre-let-7 transcripts, leading to their terminal uridylation and degradation (PubMed:19703396). This activity might not be relevant in vivo, as LIN28B-mediated inhibition of let-7 miRNA maturation appears to be ZCCHC11-independent (PubMed:22118463). Interaction with target pre-miRNAs occurs via an 5'-GGAG-3' motif in the pre-miRNA terminal loop. Mediates MYC-induced let-7 repression (By similarity). When overexpressed, isoform 1 stimulates growth of the breast adenocarcinoma cell line MCF-7. Isoform 2 has no effect on cell growth.By similarity4 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi129Zinc 1By similarity1
Metal bindingi132Zinc 1By similarity1
Metal bindingi137Zinc 1By similarity1
Metal bindingi142Zinc 1By similarity1
Metal bindingi151Zinc 2By similarity1
Metal bindingi154Zinc 2By similarity1
Metal bindingi159Zinc 2By similarity1
Metal bindingi164Zinc 2By similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri127 – 144CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri149 – 166CCHC-type 2PROSITE-ProRule annotationAdd BLAST18

GO - Molecular functioni

  • DNA binding Source: InterPro
  • RNA binding Source: UniProtKB
  • zinc ion binding Source: InterPro

GO - Biological processi

  • miRNA catabolic process Source: UniProtKB
  • pre-miRNA processing Source: UniProtKB
  • regulation of transcription, DNA-templated Source: InterPro
  • RNA 3'-end processing Source: UniProtKB

Keywordsi

Molecular functionRNA-binding
Biological processRNA-mediated gene silencing
LigandMetal-binding, Zinc

Enzyme and pathway databases

SignaLinkiQ6ZN17
SIGNORiQ6ZN17

Names & Taxonomyi

Protein namesi
Recommended name:
Protein lin-28 homolog B
Short name:
Lin-28B
Gene namesi
Name:LIN28B
Synonyms:CSDD2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

EuPathDBiHostDB:ENSG00000187772.6
HGNCiHGNC:32207 LIN28B
MIMi611044 gene
neXtProtiNX_Q6ZN17

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi389421
MalaCardsiLIN28B
OpenTargetsiENSG00000187772
Orphaneti635 Neuroblastoma
PharmGKBiPA142671543

Polymorphism and mutation databases

BioMutaiLIN28B
DMDMi74758701

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002537931 – 250Protein lin-28 homolog BAdd BLAST250

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei54PhosphoserineCombined sources1
Modified residuei96PhosphoserineCombined sources1
Modified residuei105PhosphoserineCombined sources1
Modified residuei110PhosphoserineCombined sources1
Modified residuei203PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ6ZN17
MaxQBiQ6ZN17
PaxDbiQ6ZN17
PeptideAtlasiQ6ZN17
PRIDEiQ6ZN17
ProteomicsDBi67959
67960 [Q6ZN17-2]

PTM databases

iPTMnetiQ6ZN17
PhosphoSitePlusiQ6ZN17

Expressioni

Tissue specificityi

Expressed at high levels in the placenta and, at mucher lower, in testis and fetal liver (PubMed:16971064). Isoform 1 is only detected in placenta and in moderately and poorly differentiated hepatocellular carcinoma cells (at protein level). Isoform 2 is detected in fetal liver, non-tumor liver tissues, as well as well-differentiated tumor tissues (at protein level). Tends to be up-regulated in triple-negative (ER-,PR-,HER2-) breast tumors, as well as in liver, ovarian, and thyroid carcinomas (PubMed:22118463).2 Publications

Inductioni

Might be negatively regulated by the microRNA let-7b.1 Publication

Gene expression databases

BgeeiENSG00000187772 Expressed in 37 organ(s), highest expression level in placenta
CleanExiHS_LIN28B
ExpressionAtlasiQ6ZN17 baseline and differential
GenevisibleiQ6ZN17 HS

Organism-specific databases

HPAiHPA036630
HPA061745

Interactioni

Protein-protein interaction databases

BioGridi133142, 79 interactors
IntActiQ6ZN17, 6 interactors
STRINGi9606.ENSP00000344401

Structurei

Secondary structure

1250
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ6ZN17
SMRiQ6ZN17
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini29 – 102CSDAdd BLAST74

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi112 – 125Bipartite nuclear localization signal1 PublicationAdd BLAST14
Motifi239 – 250Nucleolar localization signal1 PublicationAdd BLAST12

Domaini

The tandem zinc fingers, also referred as zinc knuckle domain (ZKD), mediate specific binding to the GGAG/GGUG motif while the CSD shows only limited pyrimidine-rich sequence specificity. Both domains bind single-stranded nucleic acids.

Sequence similaritiesi

Belongs to the lin-28 family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri127 – 144CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri149 – 166CCHC-type 2PROSITE-ProRule annotationAdd BLAST18

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG3070 Eukaryota
COG1278 LUCA
GeneTreeiENSGT00930000150863
HOGENOMiHOG000047091
HOVERGENiHBG081922
InParanoidiQ6ZN17
KOiK18754
OrthoDBiEOG091G0RTY
PhylomeDBiQ6ZN17
TreeFamiTF316240

Family and domain databases

CDDicd04458 CSP_CDS, 1 hit
InterProiView protein in InterPro
IPR011129 CSD
IPR002059 CSP_DNA-bd
IPR012340 NA-bd_OB-fold
IPR001878 Znf_CCHC
IPR036875 Znf_CCHC_sf
PfamiView protein in Pfam
PF00313 CSD, 1 hit
PF00098 zf-CCHC, 2 hits
PRINTSiPR00050 COLDSHOCK
SMARTiView protein in SMART
SM00357 CSP, 1 hit
SM00343 ZnF_C2HC, 2 hits
SUPFAMiSSF50249 SSF50249, 1 hit
SSF57756 SSF57756, 1 hit
PROSITEiView protein in PROSITE
PS51857 CSD_2, 1 hit
PS50158 ZF_CCHC, 1 hit

Sequences (2+)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 2 described isoforms and 2 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q6ZN17-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MAEGGASKGG GEEPGKLPEP AEEESQVLRG TGHCKWFNVR MGFGFISMIN
60 70 80 90 100
REGSPLDIPV DVFVHQSKLF MEGFRSLKEG EPVEFTFKKS SKGLESIRVT
110 120 130 140 150
GPGGSPCLGS ERRPKGKTLQ KRKPKGDRCY NCGGLDHHAK ECSLPPQPKK
160 170 180 190 200
CHYCQSIMHM VANCPHKNVA QPPASSQGRQ EAESQPCTST LPREVGGGHG
210 220 230 240 250
CTSPPFPQEA RAEISERSGR SPQEASSTKS SIAPEEQSKK GPSVQKRKKT
Length:250
Mass (Da):27,084
Last modified:July 5, 2004 - v1
Checksum:iDEF2920C5F1D0BBD
GO
Isoform 2 (identifier: Q6ZN17-2) [UniParc]FASTAAdd to basket
Also known as: LIN28BS

The sequence of this isoform differs from the canonical sequence as follows:
     1-70: Missing.

Note: No experimental confirmation available.
Show »
Length:180
Mass (Da):19,511
Checksum:i26526F59F88068F7
GO

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A1B0GVD3A0A1B0GVD3_HUMAN
Protein lin-28 homolog B
LIN28B
258Annotation score:
A0A1B0GTK2A0A1B0GTK2_HUMAN
Protein lin-28 homolog B
LIN28B
209Annotation score:

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0272071 – 70Missing in isoform 2. CuratedAdd BLAST70

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ127228 mRNA Translation: AAZ38897.1
AK131411 mRNA Translation: BAD18558.1
AL135911 Genomic DNA No translation available.
Z95329 Genomic DNA No translation available.
CH471051 Genomic DNA Translation: EAW48434.1
BC127712 mRNA Translation: AAI27713.1
BC127713 mRNA Translation: AAI27714.1
BC137526 mRNA Translation: AAI37527.1
BC137527 mRNA Translation: AAI37528.1
BC141960 mRNA Translation: AAI41961.1
CCDSiCCDS34504.1 [Q6ZN17-1]
RefSeqiNP_001004317.1, NM_001004317.3 [Q6ZN17-1]
UniGeneiHs.23616

Genome annotation databases

EnsembliENST00000345080; ENSP00000344401; ENSG00000187772 [Q6ZN17-1]
GeneIDi389421
KEGGihsa:389421
UCSCiuc003pqv.2 human [Q6ZN17-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Web resourcesi

Atlas of Genetics and Cytogenetics in Oncology and Haematology

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ127228 mRNA Translation: AAZ38897.1
AK131411 mRNA Translation: BAD18558.1
AL135911 Genomic DNA No translation available.
Z95329 Genomic DNA No translation available.
CH471051 Genomic DNA Translation: EAW48434.1
BC127712 mRNA Translation: AAI27713.1
BC127713 mRNA Translation: AAI27714.1
BC137526 mRNA Translation: AAI37527.1
BC137527 mRNA Translation: AAI37528.1
BC141960 mRNA Translation: AAI41961.1
CCDSiCCDS34504.1 [Q6ZN17-1]
RefSeqiNP_001004317.1, NM_001004317.3 [Q6ZN17-1]
UniGeneiHs.23616

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4A4IX-ray1.95A/B24-111[»]
ProteinModelPortaliQ6ZN17
SMRiQ6ZN17
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi133142, 79 interactors
IntActiQ6ZN17, 6 interactors
STRINGi9606.ENSP00000344401

PTM databases

iPTMnetiQ6ZN17
PhosphoSitePlusiQ6ZN17

Polymorphism and mutation databases

BioMutaiLIN28B
DMDMi74758701

Proteomic databases

EPDiQ6ZN17
MaxQBiQ6ZN17
PaxDbiQ6ZN17
PeptideAtlasiQ6ZN17
PRIDEiQ6ZN17
ProteomicsDBi67959
67960 [Q6ZN17-2]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000345080; ENSP00000344401; ENSG00000187772 [Q6ZN17-1]
GeneIDi389421
KEGGihsa:389421
UCSCiuc003pqv.2 human [Q6ZN17-1]

Organism-specific databases

CTDi389421
DisGeNETi389421
EuPathDBiHostDB:ENSG00000187772.6
GeneCardsiLIN28B
HGNCiHGNC:32207 LIN28B
HPAiHPA036630
HPA061745
MalaCardsiLIN28B
MIMi611044 gene
neXtProtiNX_Q6ZN17
OpenTargetsiENSG00000187772
Orphaneti635 Neuroblastoma
PharmGKBiPA142671543
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3070 Eukaryota
COG1278 LUCA
GeneTreeiENSGT00930000150863
HOGENOMiHOG000047091
HOVERGENiHBG081922
InParanoidiQ6ZN17
KOiK18754
OrthoDBiEOG091G0RTY
PhylomeDBiQ6ZN17
TreeFamiTF316240

Enzyme and pathway databases

SignaLinkiQ6ZN17
SIGNORiQ6ZN17

Miscellaneous databases

ChiTaRSiLIN28B human
GenomeRNAii389421
PROiPR:Q6ZN17
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000187772 Expressed in 37 organ(s), highest expression level in placenta
CleanExiHS_LIN28B
ExpressionAtlasiQ6ZN17 baseline and differential
GenevisibleiQ6ZN17 HS

Family and domain databases

CDDicd04458 CSP_CDS, 1 hit
InterProiView protein in InterPro
IPR011129 CSD
IPR002059 CSP_DNA-bd
IPR012340 NA-bd_OB-fold
IPR001878 Znf_CCHC
IPR036875 Znf_CCHC_sf
PfamiView protein in Pfam
PF00313 CSD, 1 hit
PF00098 zf-CCHC, 2 hits
PRINTSiPR00050 COLDSHOCK
SMARTiView protein in SMART
SM00357 CSP, 1 hit
SM00343 ZnF_C2HC, 2 hits
SUPFAMiSSF50249 SSF50249, 1 hit
SSF57756 SSF57756, 1 hit
PROSITEiView protein in PROSITE
PS51857 CSD_2, 1 hit
PS50158 ZF_CCHC, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiLN28B_HUMAN
AccessioniPrimary (citable) accession number: Q6ZN17
Secondary accession number(s): A1L165, B2RPN6, Q5TCM4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 17, 2006
Last sequence update: July 5, 2004
Last modified: November 7, 2018
This is version 142 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
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