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12  structures 23  species 0  interactions 35  sequences 7  architectures

Family: bCoV_SUD_M (PF11633)

Summary: Betacoronavirus single-stranded poly(A) binding domain

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Betacoronavirus single-stranded poly(A) binding domain Provide feedback

This domain identifies non-structural protein NSP3, the product of ORF1a in group 2 coronavirus. It is found in human SARS coronavirus polyprotein 1a and 1ab, and in related coronavirus polyproteins [1]. NSP3 binds to viral RNA, nucleocapsid protein, as well as other viral proteins, and participates in polyprotein processing [2]. The domain exhibits a macrodomain fold containing the nsp3 residues 528 to 648, with a flexibly extended N-terminal tail from residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. SUD-M(527-651) binds single-stranded poly(A); the contact area with this RNA on the protein surface, and the electrophoretic mobility shift assays confirm that SUD-M has higher affinity for purine bases than for pyrimidine bases [3].

Literature references

  1. Snijder EJ, Bredenbeek PJ, Dobbe JC, Thiel V, Ziebuhr J, Poon LL, Guan Y, Rozanov M, Spaan WJ, Gorbalenya AE; , J Mol Biol. 2003;331:991-1004.: Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. PUBMED:12927536 EPMC:12927536

  2. Lei J, Kusov Y, Hilgenfeld R;, Antiviral Res. 2018;149:58-74.: Nsp3 of coronaviruses: Structures and functions of a large multi-domain protein. PUBMED:29128390 EPMC:29128390

  3. Chatterjee A, Johnson MA, Serrano P, Pedrini B, Joseph JS, Neuman BW, Saikatendu K, Buchmeier MJ, Kuhn P, Wuthrich K;, J Virol. 2009;83:1823-1836.: Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold. PUBMED:19052085 EPMC:19052085

This tab holds annotation information from the InterPro database.

InterPro entry IPR024375

This entry represents the macrodomain referred to as SUD-M (middle SUD subdomain) of the SARS-unique domain (SUD) which binds G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides) [ PUBMED:26149721 ]. It can be found in non-structural protein 3 (NSP3) of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and related coronaviruses [ PUBMED:12927536 ]. NSP3 binds to viral RNA, nucleocapsid protein, as well as other viral proteins, and participates in polyprotein processing. It is a multifunctional protein comprising up to 16 different domains and regions [ PUBMED:29128390 ]. In SARS-CoV the SUD-M (527-651) domain has been shown to bind single-stranded poly(A). It has been shown through the contact area with this RNA on the protein surface, and the electrophoretic mobility shift assays, that SUD-M has higher affinity for purine bases than for pyrimidine bases [ PUBMED:19052085 ].

SUD consists of three globular domains separated by short linker peptide segments: SUD-N, SUD-M, and SUD-C [ PUBMED:20493876 ]. Among these, SUD-N and SUD-M are macrodomains. The SUD-N domain is a related macrodomain which also binds G-quadruplexes [ PUBMED:19436709 ]. While SUD-N is specific to the NSP3 of SARS and betacoronaviruses of the sarbecovirus subgenera (B lineage), SUD-M is present in most NSP3 proteins except the NSP3 from betacoronaviruses of the embecovirus subgenera (A lineage). SUD-M, despite its name, is not specific to SARS. SUD-C adopts a frataxin-like fold, has structural similarity to DNA-binding domains of DNA-modifying enzymes, binds single-stranded RNA, and regulates the RNA binding behavior of the SUD-M macrodomain. SARS-CoV Nsp3 contains a third macrodomain (the X-domain). The X-domain may function as a module binding poly(ADP-ribose); however, SUD-N and SUD-M do not bind ADP-ribose, as the triple glycine sequence involved in its binding is not conserved in these [ PUBMED:29128390 ].

Nsp3c-N and Nsp3c-M each display a typical alpha/beta/alpha Macro domain fold, in spite of the complete absence of sequence similarities. The central beta sheet with six beta strands in the order beta1-beta6-beta5-beta2-beta4-beta3 is flanked by two (or three) helices on either side. Only the last strand, beta3, is antiparallel to the other strands. Currently, most known functions of Nsp3c-N/M are connected with RNA binding. All the residues important for binding ADP-ribose and for de-MARylation/de-PARylation activity are not conserved in Nsp3c-N/M; therefore Nsp3c-N/M cannot bind ADP-ribose. Both Nsp3c-N and Nsp3c-M domains bind unusual nucleic acid structures formed by consecutives guanosine nucleotides, where four strands of nucleic acid are forming a superhelix (so-called G-quadruplexes) [ PUBMED:19436709 , PUBMED:19052085 , PUBMED:20493876 , PUBMED:26149721 , PUBMED:29128390 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan MACRO (CL0223), which has the following description:

This superfamily includes the Macro domain as well as the amino terminal domain from peptidase M17 proteins.

The clan contains the following 8 members:

bCoV_SUD_M DUF2263 DUF2362 Macro Macro_2 PARG_cat Pdase_M17_N2 Peptidase_M17_N


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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

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

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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: pdb_2jwi
Previous IDs: Nsp3; SUD-M; bCoV_SUD-M;
Type: Domain
Sequence Ontology: SO:0000417
Author: Pollington J , Chuguransky S
Number in seed: 2
Number in full: 35
Average length of the domain: 133.7 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 2.26 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.0 24.0
Trusted cut-off 24.2 24.6
Noise cut-off 23.8 19.4
Model length: 143
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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 bCoV_SUD_M domain has been found. There are 12 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 sequence.

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