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1  structure 135  species 0  interactions 232  sequences 2  architectures

Family: SLBP_RNA_bind (PF15247)

Summary: Histone RNA hairpin-binding protein RNA-binding domain

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SLBP Edit Wikipedia article

Stem-loop binding protein
Crystal structure of the histone mRNA stem-loop, human stem-loop binding protein and 3′hExo ternary complex.png
Available structures
PDB Ortholog search: PDBe, RCSB
Symbols SLBP ; HBP
External IDs OMIM602422 MGI108402 HomoloGene31389 GeneCards: SLBP Gene
RNA expression pattern
PBB GE SLBP 206052 s at tn.png
More reference expression data
Species Human Mouse
Entrez 7884 20492
Ensembl ENSG00000163950 ENSMUSG00000004642
UniProt Q14493 P97440
RefSeq (mRNA) NM_006527 NM_001289724
RefSeq (protein) NP_006518 NP_001276653
Location (UCSC) Chr 4:
1.69 – 1.71 Mb
Chr 5:
33.63 – 33.65 Mb
PubMed search [1] [2]

Histone RNA hairpin-binding protein or stem-loop binding protein (SLBP) is a protein that in humans is encoded by the SLBP gene.[1][2][3]

Species distribution

SLBP has been cloned from humans, C. elegans, D. melanogaster, X. laevis, and sea urchins. The full length human protein has 270 amino acids (31 kDa) with a centrally located RNA binding domain (RBD). The 75 amino acid RBD is well conserved across species, however the remainder of SLBP is highly divergent in most organisms and not homologous to any other protein in the eukaryotic genomes.


This gene encodes a protein that binds to the histone 3' UTR stem-loop structure in replication-dependent histone mRNAs. Histone mRNAs do not contain introns or polyadenylation signals, and are processed by a single endonucleolytic cleavage event downstream of the stem-loop. The stem-loop structure is essential for efficient processing of the histone pre-mRNA but this structure also controls the transport, translation and stability of histone mRNAs. SLBP expression is regulated during S-phase of the cell cycle, increasing more than 10-fold during the latter part of G1.

All SLBP proteins are capable of forming a highly stable complex with histone stem-loop RNA. Complex formation with the histone mRNA stem-loop is achieved by a novel three-helix bundle fold. SLBP proteins also recognize the tetraloop structure of the histone hairpin, the base of the stem, and the 5' flanking region. The crystal structure of human SLBP in complex with the stem-loop RNA as well as the exonuclease Eri1 reveals that the Arg181 residue of SLBP specifically interacts with the second guanine base in the RNA stem.[4]The rest of the protein is intrinsically disordered in fruit-flies as well as in humans. A unique feature of the SLBP RBD is that it is phosphorylated in its RNA binding domain at the Thr171 residue. The SLBP RBD also undergoes proline isomerization about this sequence and is a substrate for the prolyl isomerase Pin1. The N-terminal domain of human SLBP is required for translation activation of histone mRNAs via its interaction with SLIP1. SLBP also interacts with the CBP80 associated protein CTIF to facilitate rapid degradation of histone mRNAs. SLBP is a phosphoprotein and besides T171, it is also phosphorylated at Ser7, Ser20, Ser23, Thr60, Thr61 in mammalian cells. The phosphorylation at Thr60 is mediated by CK2 and Thr61 is by Cyclin A/Cdk1.[3]


  1. ^ Martin F, Schaller A, Eglite S, Schumperli D, Muller B (Mar 1997). "The gene for histone RNA hairpin binding protein is located on human chromosome 4 and encodes a novel type of RNA binding protein". EMBO J 16 (4): 769–78. doi:10.1093/emboj/16.4.769. PMC 1169678. PMID 9049306. 
  2. ^ McCombie WR, Martin-Gallardo A, Gocayne JD, FitzGerald M, Dubnick M, Kelley JM, Castilla L, Liu LI, Wallace S, Trapp S (August 1992). "Expressed genes, Alu repeats and polymorphisms in cosmids sequenced from chromosome 4p16.3". Nat. Genet. 1 (5): 348–53. doi:10.1038/ng0892-348. PMID 1338771. 
  3. ^ a b "Entrez Gene: SLBP stem-loop (histone) binding protein". 
  4. ^ Dazhi Tan, William F. Marzluff, Zbigniew Dominski, Liang Tong (Jan 2013). "Structure of Histone mRNA Stem-Loop, Human Stem-Loop Binding Protein, and 3′hExo Ternary Complex". Science 339 (6117): 318–321. doi:10.1126/science.1228705. PMC 3552377. PMID 23329046. 

Further reading

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Histone RNA hairpin-binding protein RNA-binding domain Provide feedback

This family represents the RNA-binding domain of histone RNA hairpin-binding protein [1].

Literature references

  1. Wang ZF, Whitfield ML, Ingledue TC 3rd, Dominski Z, Marzluff WF;, Genes Dev. 1996;10:3028-3040.: The protein that binds the 3' end of histone mRNA: a novel RNA-binding protein required for histone pre-mRNA processing. PUBMED:8957003 EPMC:8957003

External database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

Domain organisation

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We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Curation and family details

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This family is new in this Pfam release.

Seed source: Jackhmmer:Q14493
Previous IDs: none
Type: Family
Author: Eberhardt RY, Coggill P, Hetherington K
Number in seed: 52
Number in full: 232
Average length of the domain: 76.20 aa
Average identity of full alignment: 47 %
Average coverage of the sequence by the domain: 23.06 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 37.2 39.8
Noise cut-off 26.9 24.3
Model length: 73
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the SLBP_RNA_bind domain has been found. There are 1 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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