1ZC8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   COORDINATES OF TMRNA, SMPB, EF-TU AND H44 FITTED INTO CRYO-EM MAP OF THE 70S RIBOSOME AND TMRNA COMPLEX

Authors :   M. Valle, R. Gillet, S. Kaur, A. Henne, V. Ramakrishnan, J. Frank

Date :   11 Apr 05 (Deposition) - 19 Apr 05 (Release) - 11 Dec 13 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   13.00

Chains :   Asym./Biol. Unit : A,B,C,F,G,H,I,J,K,Y,Z

Keywords :   Smpb, Tmrna, Ef-Tu, H44, 30S, 16S Rrna, Cryo-Em, Trans-Translation, 70S, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Valle, R. Gillet, S. Kaur, A. Henne, V. Ramakrishnan, J. Frank
Visualizing Tmrna Entry Into A Stalled Ribosome
Science V. 300 127 2003
PubMed-ID: 12677067 | Reference-DOI: 10.1126/SCIENCE.1081798
(for further references see the PDB file header)

Molecule 1 - TLD 16S RIBOSOMAL RNA
	Chains	:	A
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

Molecule 2 - H2 16S RRNA
	Chains	:	B
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

Molecule 3 - H2B D MRNA
	Chains	:	C
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

Molecule 4 - PROTEIN KINASE 4 MRNA
	Chains	:	G
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Other Details	:	PK1

Molecule 5 - H5 16S RIBOSOMAL RNA
	Chains	:	F
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

Molecule 6 - PROTEIN KINASE 2 MRNA
	Chains	:	H
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Other Details	:	PK2

Molecule 7 - PROTEIN KINASE 3
	Chains	:	I
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Other Details	:	PK3

Molecule 8 - PROTEIN KINASE 4 MRNA
	Chains	:	J
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Other Details	:	PK4

Molecule 9 - H44 16S RIBOSOMAL RNA
	Chains	:	Z
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

Molecule 10 - SSRA-BINDING PROTEIN
	Chains	:	K
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

Molecule 11 - ELONGATION FACTOR TU
	Chains	:	Y
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Synonym	:	EF-TU

		1	2	3	4	5	6	7	8	9	10	11
Asymmetric/Biological Unit	:	A	B	C	F	G	H	I	J	K	Y	Z

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1ZC8)

(no "Site" information available for 1ZC8)

(no "SS Bond" information available for 1ZC8)

(no "Cis Peptide Bond" information available for 1ZC8)

(no "SAP(SNP)/Variant" information available for 1ZC8)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SSRP	PS01317	SsrA-binding protein.	SSRP_AQUAE	28-40	1	K:27-39
2	G_TR_1	PS00301	Translational (tr)-type guanine nucleotide-binding (G) domain signature.	EFTU1_THET8	52-67	1	Y:51-66

(no "Exon" information available for 1ZC8)

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:RNA  Length:59
                                                                                            
                1zc8 A    1 GGGGCUGAUUCUGGAUUCGACGGGAUAUUUCGGACGCGGGUUCAACUCCCGCCAGCUCC  359
                                    10        20     ||330       340       350         
                                                    26|                                
                                                    327

Chain B from PDB  Type:RNA  Length:16
                                                 
                1zc8 B    1 UUGCGAAACAUGUAGG   16
                                    10

Chain C from PDB  Type:RNA  Length:31
                                                                
                1zc8 C    1 CCCAAGGUGCAUGCGCAUGUAGUACCGAGGA   31
                                    10        20        30

Chain F from PDB  Type:RNA  Length:29
                                                              
                1zc8 F    1 CUUUAGCAGCUUAAUAACCUGCUUAGAGC   29
                                    10        20

Chain G from PDB  Type:RNA  Length:30
                                                               
                1zc8 G    1 CGAGGGGCGGUUGGCCUCGUAAAAAGCCGC   30
                                    10        20        30

Chain H from PDB  Type:RNA  Length:59
                                                                                            
                1zc8 H    1 CCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAG   59
                                    10        20        30        40        50

Chain I from PDB  Type:RNA  Length:49
                                                                                  
                1zc8 I    1 AUCGCGUGGAAGCCCUGCCUGGGGUUGAAGCGUUAAAACUUAAUCAGGC   49
                                    10        20        30        40

Chain J from PDB  Type:RNA  Length:52
                                                                                     
                1zc8 J    1 GUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGAC   52
                                    10        20        30        40        50

Chain K from PDB  Type:PROTEIN  Length:130
 aligned with SSRP_AQUAE | O66640 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:130
                                    11        21        31        41        51        61        71        81        91       101       111       121       131
          SSRP_AQUAE      2 GKSDKIIPIAENKEAKAKYDILETYEAGIVLKGSEVKSLREKGTVSFKDSFVRIENGEAWLYNLYIAPYKHATIENHDPLRKRKLLLHKREIMRLYGKVQEKGYTIIPLKLYWKNNKVKVLIALAKGKKL  131
               SCOP domains d1zc8k1 K:1-130 Small protein B (SmpB)                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------SSRP         ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zc8 K    1 GKSDKIIPIAENKEAKAKYDILETYEAGIVLKGSEVKSLREKGTVSFKDSFVRIENGEAWLYNLYIAPYKHATIENHDPLRKRKLLLHKREIMRLYGKVQEKGYTIIPLKLYWKNNKVKVLIALAKGKKL  130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain Y from PDB  Type:PROTEIN  Length:405
 aligned with EFTU1_THET8 | Q5SHN6 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:405
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401     
         EFTU1_THET8      2 AKGEFVRTKPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEQMHRNPKTRRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRRTVVTGVEMHRKTLQEGIAGDNVGVLLRGVSREEVERGQVLAKPGSITPHTKFEASVYVLKKEEGGRHTGFFSGYRPQFYFRTTDVTGVVQLPPGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE  406
               SCOP domains --------d1zc8y3 Y:9-212 Elongation factor Tu (EF-Tu), N-terminal (G) domain                                                                                                                                         d1zc8y1 Y:213-312 Elongation factor Tu (EF-Tu), domain 2                                            d1zc8y2 Y:313-405 Elongation factor Tu (EF-Tu)                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................................................................................................................................................................................................................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------G_TR_1          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zc8 Y    1 AKGEFIRTKPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEEMHKNPKTKRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKPGSITPHTKFEASVYILKKEEGGRHTGFFTGYRPQFYFRTTDVTGVVRLPQGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE  405
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400

Chain Z from PDB  Type:RNA  Length:91
                                                                                                                            
                1zc8 Z 1406 GCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUC 1496
                                  1415      1425      1435      1445      1455      1465      1475      1485      1495

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 '\|'

(no "CATH Domain" information available for 1ZC8)

(no "Pfam Domain" information available for 1ZC8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain K (SSRP_AQUAE | O66640)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
	GO:0070929	trans-translation	A translational elongation process in which transfer of a translating ribosome from one mRNA to another RNA template takes place. Trans-translation occurs during tmRNA release of stalled ribosomes.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain Y (EFTU1_THET8 | Q5SHN6)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
	GO:0006414	translational elongation	The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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
(no "Ligands, Modified Residues, Ions" information available for 1zc8)

	Sites
(no "Sites" information available for 1zc8)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1zc8)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit 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
	1zc8
		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
	EFTU1_THET8 \| Q5SHN6
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	SSRP_AQUAE \| O66640
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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
	EFTU1_THET8 \| Q5SHN6
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	SSRP_AQUAE \| O66640
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	EFTU1_THET8 \| Q5SHN6	:	1ha3 2c78 4v5g 4v5p 4v5q 4v5r 4v5s 4v8q
	SSRP_AQUAE \| O66640	:	1k8h 1p6v 2ob7

1b23	STRUCTURE OF EF-TU
1k8h	STRUCTURE OF SMPB
1n32	STRUCTURE OF H44 RELATED ID: EMD-1122 RELATED DB: EMDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (4, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 12)

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