1LNX - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE P.AEROPHILUM SMAP1 HEPTAMER IN A NEW CRYSTAL FORM (C2221)

Authors :   C. Mura, A. Kozhukhovsky, D. Eisenberg

Date :   04 May 02 (Deposition) - 25 Mar 03 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym. Unit : A,B,C,D,E,F,G
Biol. Unit 1: A,B,C,D,E,F,G  (1x)
Biol. Unit 2: A,B,C,D,E,F,G  (2x)

Keywords :   Beta Barrel-Like Structure (Ob Fold); Homoheptameric, Rna Binding Protein, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Mura, A. Kozhukhovsky, M. Gingery, M. Phillips, D. Eisenberg
The Oligomerization And Ligand-Binding Properties Of Sm-Lik Archaeal Proteins (Smaps)
Protein Sci. V. 12 832 2003
PubMed-ID: 12649441 | Reference-DOI: 10.1110/PS.0224703
(for further references see the PDB file header)

Molecule 1 - SMALL NUCLEAR RIBONUCLEOPROTEIN HOMOLOG (SM-LIKE)
	Chains	:	A, B, C, D, E, F, G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-22B(+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	SMAP1, GPA2549
	Organism Scientific	:	PYROBACULUM AEROPHILUM
	Organism Taxid	:	13773
	Synonym	:	SM-LIKE ARCHAEAL PROTEIN SMAP1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 19)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	GOL	10	Ligand/Ion	GLYCEROL
3	URI	7	Ligand/Ion	URIDINE

Biological Unit 1 (3, 19)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	GOL	10	Ligand/Ion	GLYCEROL
3	URI	7	Ligand/Ion	URIDINE

Biological Unit 2 (3, 38)

No.	Name	Count	Type	Full Name
1	ACY	4	Ligand/Ion	ACETIC ACID
2	GOL	20	Ligand/Ion	GLYCEROL
3	URI	14	Ligand/Ion	URIDINE

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN B:43 , URI B:8004 , GLY F:13 , PHE F:41 , GLN F:43 , VAL F:45 , ASN G:46 , HOH G:8215	BINDING SITE FOR RESIDUE URI F 8001
02	AC2	SOFTWARE	ASP A:42 , GLN A:43 , ASN A:46 , URI A:8003 , HOH A:8241 , LEU G:12 , GLY G:13 , LEU G:16 , PHE G:41 , ASP G:42 , GLN G:43 , HOH G:8234	BINDING SITE FOR RESIDUE URI G 8002
03	AC3	SOFTWARE	GLY A:13 , LEU A:16 , VAL A:45 , HOH A:8217 , HOH A:8241 , HOH B:8240 , GLN G:43 , URI G:8002	BINDING SITE FOR RESIDUE URI A 8003
04	AC4	SOFTWARE	GLY B:13 , LEU B:16 , PHE B:41 , ASP B:42 , GLN B:43 , HOH B:8206 , GLN F:43 , URI F:8001 , HOH F:8213	BINDING SITE FOR RESIDUE URI B 8004
05	AC5	SOFTWARE	GLY C:13 , LEU C:16 , ASP C:42 , GLN C:43 , ASN D:46 , VAL D:67 , HOH D:8230 , HOH D:8265 , GLN E:43 , URI E:8007	BINDING SITE FOR RESIDUE URI D 8005
06	AC6	SOFTWARE	GLY D:13 , LEU D:16 , GLN D:43 , VAL D:45 , HOH D:8238 , HOH D:8259 , HOH D:8261 , ASN E:46 , VAL E:67	BINDING SITE FOR RESIDUE URI D 8006
07	AC7	SOFTWARE	GLN C:43 , HOH C:8248 , URI D:8005 , HOH D:8265 , GLY E:13 , LEU E:16 , GLN E:17 , PHE E:41 , VAL E:45 , HOH E:8221 , HOH E:8244	BINDING SITE FOR RESIDUE URI E 8007
08	AC8	SOFTWARE	ARG D:35 , GLY D:58 , VAL D:60	BINDING SITE FOR RESIDUE ACY D 8101
09	AC9	SOFTWARE	ARG A:29 , ARG B:29 , ARG C:29 , ARG D:29 , ARG E:29 , ARG F:29	BINDING SITE FOR RESIDUE ACY C 8102
10	BC1	SOFTWARE	GLU A:54 , ILE A:56 , TYR A:61 , ARG A:63 , LYS G:27 , GLU G:33	BINDING SITE FOR RESIDUE GOL G 8201
11	BC2	SOFTWARE	LYS B:27 , GLU B:33 , ARG C:63	BINDING SITE FOR RESIDUE GOL B 8202
12	BC3	SOFTWARE	VAL F:60 , TYR F:61 , HOH F:8212	BINDING SITE FOR RESIDUE GOL F 8203
13	BC4	SOFTWARE	LYS E:27 , GLU E:33 , TYR F:61 , ARG F:63	BINDING SITE FOR RESIDUE GOL E 8204
14	BC5	SOFTWARE	ARG E:35 , GLY E:58 , VAL E:60 , LYS E:62	BINDING SITE FOR RESIDUE GOL E 8205
15	BC6	SOFTWARE	LYS F:27 , GLU F:33 , ARG G:63	BINDING SITE FOR RESIDUE GOL F 8206
16	BC7	SOFTWARE	LYS D:27 , GLU D:33 , ARG E:63	BINDING SITE FOR RESIDUE GOL D 8207
17	BC8	SOFTWARE	LYS C:27 , GLU C:33 , GLU D:54 , TYR D:61 , ARG D:63	BINDING SITE FOR RESIDUE GOL C 8208
18	BC9	SOFTWARE	LYS A:27 , GLU A:33 , HOH A:8233 , TYR B:61 , ARG B:63	BINDING SITE FOR RESIDUE GOL A 8209
19	CC1	SOFTWARE	GLN E:23 , ARG E:35 , GLY E:36 , ILE E:37 , ASP E:51	BINDING SITE FOR RESIDUE GOL E 8210

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

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

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

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

(no "Exon" information available for 1LNX)

Asymmetric 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:74
 aligned with Q8ZYG5_PYRAE | Q8ZYG5 from UniProtKB/TrEMBL  Length:80

    Alignment length:74
                                                                                                   80 
                                    17        27        37        47        57        67        77  | 
          Q8ZYG5_PYRAE    8 CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP-  -
               SCOP domains d1lnxa_ A: Archaeal homoheptameric Sm protein                              SCOP domains
               CATH domains 1lnxA00 A:8-81  [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
                  1lnx A  8 CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVPG 81
                                    17        27        37        47        57        67        77

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

    Alignment length:73
                                    17        27        37        47        57        67        77   
          Q8ZYG5_PYRAE    8 CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
               SCOP domains d1lnxb_ B: Archaeal homoheptameric Sm protein                             SCOP domains
               CATH domains 1lnxB00 B:8-80  [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
                  1lnx B  8 CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
                                    17        27        37        47        57        67        77

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

    Alignment length:73
                                    17        27        37        47        57        67        77   
          Q8ZYG5_PYRAE    8 CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
               SCOP domains d1lnxc_ C: Archaeal homoheptameric Sm protein                             SCOP domains
               CATH domains 1lnxC00 C:8-80  [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
                  1lnx C  8 CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
                                    17        27        37        47        57        67        77

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

    Alignment length:73
                                    17        27        37        47        57        67        77   
          Q8ZYG5_PYRAE    8 CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
               SCOP domains d1lnxd_ D: Archaeal homoheptameric Sm protein                             SCOP domains
               CATH domains 1lnxD00 D:8-80  [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
                  1lnx D  8 CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
                                    17        27        37        47        57        67        77

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

    Alignment length:73
                                    17        27        37        47        57        67        77   
          Q8ZYG5_PYRAE    8 CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
               SCOP domains d1lnxe_ E: Archaeal homoheptameric Sm protein                             SCOP domains
               CATH domains 1lnxE00 E:8-80  [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
                  1lnx E  8 CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
                                    17        27        37        47        57        67        77

Chain F from PDB  Type:PROTEIN  Length:74
 aligned with Q8ZYG5_PYRAE | Q8ZYG5 from UniProtKB/TrEMBL  Length:80

    Alignment length:74
                                                                                                   80 
                                    17        27        37        47        57        67        77  | 
          Q8ZYG5_PYRAE    8 CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP-  -
               SCOP domains d1lnxf_ F: Archaeal homoheptameric Sm protein                              SCOP domains
               CATH domains 1lnxF00 F:8-81  [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
                  1lnx F  8 CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVPG 81
                                    17        27        37        47        57        67        77

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

    Alignment length:73
                                    17        27        37        47        57        67        77   
          Q8ZYG5_PYRAE    8 CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
               SCOP domains d1lnxg_ G: Archaeal homoheptameric Sm protein                             SCOP domains
               CATH domains 1lnxG00 G:8-80  [code=2.30.30.100, no name defined]                       CATH domains
           Pfam domains (1) ------LSM-1lnxG01 G:14-78                                              -- Pfam domains (1)
           Pfam domains (2) ------LSM-1lnxG02 G:14-78                                              -- Pfam domains (2)
           Pfam domains (3) ------LSM-1lnxG03 G:14-78                                              -- Pfam domains (3)
           Pfam domains (4) ------LSM-1lnxG04 G:14-78                                              -- Pfam domains (4)
           Pfam domains (5) ------LSM-1lnxG05 G:14-78                                              -- Pfam domains (5)
           Pfam domains (6) ------LSM-1lnxG06 G:14-78                                              -- Pfam domains (6)
           Pfam domains (7) ------LSM-1lnxG07 G:14-78                                              -- Pfam domains (7)
         Sec.struct. author ...hhhhhhhhh...eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  1lnx G  8 CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVYKRGTMVVRGENVLFISPVP 80
                                    17        27        37        47        57        67        77

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 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	d1lnxa_	A:
1b	d1lnxd_	D:
1c	d1lnxe_	E:
1d	d1lnxf_	F:
1e	d1lnxg_	G:
1f	d1lnxb_	B:
1g	d1lnxc_	C:

Asymmetric 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. (2)

1a	1lnxB00	B:8-80
1b	1lnxC00	C:8-80
1c	1lnxD00	D:8-80
1d	1lnxE00	E:8-80
1e	1lnxG00	G:8-80
1f	1lnxA00	A:8-81
1g	1lnxF00	F:8-81

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Sm-like (17)

Family: LSM (13)

Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827) (1)

1a	LSM-1lnxG01	G:14-78
1b	LSM-1lnxG02	G:14-78
1c	LSM-1lnxG03	G:14-78
1d	LSM-1lnxG04	G:14-78
1e	LSM-1lnxG05	G:14-78
1f	LSM-1lnxG06	G:14-78
1g	LSM-1lnxG07	G:14-78

Asymmetric 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.

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

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UniProtKB/TrEMBL
	Q8ZYG5_PYRAE \| Q8ZYG5	:	1i8f

1i4k	THE ARCHAEOGLOBUS FULGIDUS SM PROTEIN
1i5l	THE ARCHAEOGLOBUS FULGIDUS SM PROTEIN WITH OLIGOURIDINE BOUND
1i81	METHANOBACTERIAL HOMOLOG (MTH SMAP1) OF THIS PROTEIN
1i8f	THE SAME PROTEIN (P.AEROPHILUM SMAP1) IN A C2 LATTICE
1jbm	METHANOBACTERIAL HOMOLOG (MTH SMAP1) OF THIS PROTEIN
1jri	METHANOBACTERIAL HOMOLOG (MTH SMAP1) OF THIS PROTEIN
1loj	CRYSTAL STRUCTURE OF A METHANOBACTERIAL SM-LIKE ARCHAEAL PROTEIN BOUND TO UMP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 19)

Sites (19, 19)

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

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SCOP Domains (1, 7)

CATH Domains (1, 7)

Pfam Domains (1, 7)

Gene Ontology (4, 4)

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