1I8F - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF A HEPTAMERIC ARCHAEAL SM PROTEIN: IMPLICATIONS FOR THE EUKARYOTIC SNRNP CORE

Authors :   C. Mura, D. Cascio, M. R. Sawaya, D. Eisenberg

Date :   14 Mar 01 (Deposition) - 16 May 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym./Biol. Unit : A,B,C,D,E,F,G

Keywords :   Beta Barrel-Like Smap Monomers Form 35-Stranded Beta-Sheet In The Heptamer, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Mura, D. Cascio, M. R. Sawaya, D. S. Eisenberg
The Crystal Structure Of A Heptameric Archaeal Sm Protein: Implications For The Eukaryotic Snrnp Core.
Proc. Natl. Acad. Sci. Usa V. 98 5532 2001
PubMed-ID: 11331747 | Reference-DOI: 10.1073/PNAS.091102298

Molecule 1 - PUTATIVE SNRNP SM-LIKE PROTEIN
	Chains	:	A, B, C, D, E, F, G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PYROBACULUM AEROPHILUM
	Organism Taxid	:	13773

		1	2	3	4	5	6	7
Asymmetric/Biological Unit	:	A	B	C	D	E	F	G

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 5)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:27 , GLU A:33 , TYR B:61 , ARG B:63	BINDING SITE FOR RESIDUE GOL A 1001
2	AC2	SOFTWARE	LEU F:12 , ASN G:46 , ARG G:69 , GLU G:71	BINDING SITE FOR RESIDUE GOL G 1002
3	AC3	SOFTWARE	ILE A:56 , TYR A:61 , ARG A:63 , LYS G:27 , GLU G:33	BINDING SITE FOR RESIDUE GOL G 1003
4	AC4	SOFTWARE	LYS D:27 , GLU D:33 , TYR E:61 , ARG E:63	BINDING SITE FOR RESIDUE GOL D 1004
5	AC5	SOFTWARE	LEU C:25 , ARG C:35 , SER C:77 , PRO C:78 , VAL C:79 , PRO C:80 , LYS D:62 , ARG D:63	BINDING SITE FOR RESIDUE GOL C 1005

(no "SS Bond" information available for 1I8F)

(no "Cis Peptide Bond" information available for 1I8F)

(no "SAP(SNP)/Variant" information available for 1I8F)

(no "PROSITE Motif" information available for 1I8F)

(no "Exon" information available for 1I8F)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:71
 aligned with Q8ZYG5_PYRAE | Q8ZYG5 from UniProtKB/TrEMBL  Length:80

    Alignment length:71
                                    19        29        39        49        59        69        79 
          Q8ZYG5_PYRAE   10 ATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
               SCOP domains d1i8fa_ A: Archaeal homoheptameric Sm protein                           SCOP domains
               CATH domains 1i8fA00 A:10-80  [code=2.30.30.100, no name defined]                    CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  1i8f A 10 ATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
                                    19        29        39        49        59        69        79

Chain B from PDB  Type:PROTEIN  Length:72
 aligned with Q8ZYG5_PYRAE | Q8ZYG5 from UniProtKB/TrEMBL  Length:80

    Alignment length:72
                                    18        28        38        48        58        68        78  
          Q8ZYG5_PYRAE    9 FATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
               SCOP domains d1i8fb_ B: Archaeal homoheptameric Sm protein                            SCOP domains
               CATH domains 1i8fB00 B:9-80  [code=2.30.30.100, no name defined]                      CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhh..eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                  1i8f B  9 FATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
                                    18        28        38        48        58        68        78

Chain C from PDB  Type:PROTEIN  Length:68
 aligned with Q8ZYG5_PYRAE | Q8ZYG5 from UniProtKB/TrEMBL  Length:80

    Alignment length:68
                                                                                             80 
                                    23        33        43        53        63        73      | 
          Q8ZYG5_PYRAE   14 ATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP-  -
               SCOP domains d1i8fc_ C: Archaeal homoheptameric Sm protein                        SCOP domains
               CATH domains 1i8fC00 C:14-81  [code=2.30.30.100, no name defined]                 CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  1i8f C 14 ATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVPG 81
                                    23        33        43        53        63        73

Chain D from PDB  Type:PROTEIN  Length:73
 aligned with Q8ZYG5_PYRAE | Q8ZYG5 from UniProtKB/TrEMBL  Length:80

    Alignment length:73
                                                                                                  80 
                                    18        28        38        48        58        68        78 | 
          Q8ZYG5_PYRAE    9 FATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP-  -
               SCOP domains d1i8fd_ D: Archaeal homoheptameric Sm protein                             SCOP domains
               CATH domains 1i8fD00 D:9-81  [code=2.30.30.100, no name defined]                       CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  1i8f D  9 FATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVPG 81
                                    18        28        38        48        58        68        78

Chain E from PDB  Type:PROTEIN  Length:70
 aligned with Q8ZYG5_PYRAE | Q8ZYG5 from UniProtKB/TrEMBL  Length:80

    Alignment length:70
                                    20        30        40        50        60        70        80
          Q8ZYG5_PYRAE   11 TLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
               SCOP domains d1i8fe_ E: Archaeal homoheptameric Sm protein                          SCOP domains
               CATH domains 1i8fE00 E:11-80  [code=2.30.30.100, no name defined]                   CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  1i8f E 11 TLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
                                    20        30        40        50        60        70        80

Chain F from PDB  Type:PROTEIN  Length:77
 aligned with Q8ZYG5_PYRAE | Q8ZYG5 from UniProtKB/TrEMBL  Length:80

    Alignment length:77
                                                                                                      80 
                                    14        24        34        44        54        64        74     | 
          Q8ZYG5_PYRAE    5 ISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP-  -
               SCOP domains d1i8ff_ F: Archaeal homoheptameric Sm protein                                 SCOP domains
               CATH domains 1i8fF00 F:5-81  [code=2.30.30.100, no name defined]                           CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh...eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                  1i8f F  5 ISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVPG 81
                                    14        24        34        44        54        64        74

Chain G from PDB  Type:PROTEIN  Length:68
 aligned with Q8ZYG5_PYRAE | Q8ZYG5 from UniProtKB/TrEMBL  Length:80

    Alignment length:68
                                    22        32        42        52        62        72        
          Q8ZYG5_PYRAE   13 GATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
               SCOP domains d1i8fg_ G: Archaeal homoheptameric Sm protein                        SCOP domains
               CATH domains 1i8fG00 G:13-80  [code=2.30.30.100, no name defined]                 CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh...eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  1i8f G 13 GATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
                                    22        32        42        52        62        72

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Sm-like fold (103)

Superfamily: Sm-like ribonucleoproteins (95)

Family: Sm motif of small nuclear ribonucleoproteins, SNRNP (31)

Protein domain: Archaeal homoheptameric Sm protein (13)

Pyrobaculum aerophilum [TaxId: 13773] (2)

1a	d1i8fa_	A:
1b	d1i8fb_	B:
1c	d1i8fc_	C:
1d	d1i8fd_	D:
1e	d1i8fe_	E:
1f	d1i8ff_	F:
1g	d1i8fg_	G:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: [code=2.30.30.100, no name defined] (40)

Pyrobaculum aerophilum. Organism_taxid: 13773. (1)

1a	1i8fC00	C:14-81
1b	1i8fG00	G:13-80
1c	1i8fE00	E:11-80
1d	1i8fA00	A:10-80
1e	1i8fB00	B:9-80
1f	1i8fD00	D:9-81
1g	1i8fF00	F:5-81

(no "Pfam Domain" information available for 1I8F)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D,E,F,G (Q8ZYG5_PYRAE | Q8ZYG5)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
	GO:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
cellular component
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0019013	viral nucleocapsid	The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1i8f)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1i8f
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	Q8ZYG5_PYRAE \| Q8ZYG5
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	Q8ZYG5_PYRAE \| Q8ZYG5
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q8ZYG5_PYRAE \| Q8ZYG5	:	1lnx

1b34	CRYSTAL STRUCTURE OF THE HUMAN SM D1D2 HETERODIMER
1d3b	CRYSTAL STRUCTURE OF THE HUMAN SM D3B HETERODIMER

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 7)

CATH Domains (1, 7)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File