3LPE - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SPT4/5NGN HETERODIMER COMPLEX FROM METHANOCOCCUS JANNASCHII

Authors :   A. Hirtreiter, G. E. Damsma, A. C. M. Cheung, D. Klose, D. Grohmann, E. Vo A. C. R. Martin, P. Cramer, F. Werner

Date :   05 Feb 10 (Deposition) - 09 Mar 10 (Release) - 28 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E,F  (1x)
Biol. Unit 4: G,H  (1x)

Keywords :   Transcription Regulation, Spt4, Spt5, Nusg, Archaea, Evolution, Dna- Directed Rna Polymerase, Metal-Binding, Nucleotidyltransferase, Transcription, Transferase, Zinc-Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Hirtreiter, G. E. Damsma, A. C. Cheung, D. Klose, D. Grohmann, E. Vojnic, A. C. Martin, P. Cramer, F. Werner
Spt4/5 Stimulates Transcription Elongation Through The Rna Polymerase Clamp Coiled-Coil Motif.
Nucleic Acids Res. V. 38 4040 2010
PubMed-ID: 20197319 | Reference-DOI: 10.1093/NAR/GKQ135

Molecule 1 - PUTATIVE TRANSCRIPTION ANTITERMINATION PROTEIN NUSG
	Chains	:	A, C, E, G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2TK
	Expression System Strain	:	BL21 (ROSETTA 2) NOVAGEN
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	NGN DOMAIN
	Gene	:	MJ0372
	Organism Common	:	METHANOCOCCUS JANNASCHII
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Synonym	:	TRANSCRIPTION ELONGATION FACTOR SPT5 NGN

Molecule 2 - DNA-DIRECTED RNA POLYMERASE SUBUNIT E''
	Chains	:	B, D, F, H
	EC Number	:	2.7.7.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2TK
	Expression System Strain	:	BL21 (ROSETTA 2) NOVAGEN
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RPOE2, MJ0396
	Organism Common	:	METHANOCOCCUS JANNASCHII
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Synonym	:	TRANSCRIPTION ELONGATION FACTOR SPT4

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F
Biological Unit 4 (1x)	:							G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS B:4 , CYS B:7 , CYS B:16 , CYS B:19	BINDING SITE FOR RESIDUE ZN B 60
2	AC2	SOFTWARE	CYS D:4 , CYS D:7 , CYS D:16 , CYS D:19 , HOH D:225	BINDING SITE FOR RESIDUE ZN D 60
3	AC3	SOFTWARE	CYS F:4 , CYS F:7 , CYS F:16 , CYS F:19	BINDING SITE FOR RESIDUE ZN F 60
4	AC4	SOFTWARE	CYS H:4 , CYS H:7 , CYS H:16 , CYS H:19 , HOH H:316	BINDING SITE FOR RESIDUE ZN H 60

(no "SS Bond" information available for 3LPE)

(no "Cis Peptide Bond" information available for 3LPE)

(no "SAP(SNP)/Variant" information available for 3LPE)

(no "PROSITE Motif" information available for 3LPE)

(no "Exon" information available for 3LPE)

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:84
 aligned with SPT5_METJA | Q57818 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:84
                              1                                                                                 
                              |      8        18        28        38        48        58        68        78    
            SPT5_METJA    - --MIFAVRTMVGQEKNIAGLMASRAEKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVPGTIAIEEIEPLLTP 82
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhh...eeeeee......eeeeee.hhhhhhhhhh....eeee.....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  3lpe A -1 AHMIFAVRTMVGQEKNIAGLMASRAEKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVPGTIAIEEIEPLLTP 82
                                     8        18        28        38        48        58        68        78

Chain B from PDB  Type:PROTEIN  Length:59
 aligned with SPT4_METJA | Q57839 from UniProtKB/Swiss-Prot  Length:59

    Alignment length:59
                                    10        20        30        40        50         
            SPT4_METJA    1 MRACLKCKYLTNDEICPICHSPTSENWIGLLIVINPEKSEIAKKAGIDIKGKYALSVKE 59
               SCOP domains d3lpeb_ B: automated matches                                SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....ee...........ee..ee.eeee.....hhhhhhh.....eee..ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                  3lpe B  1 MRACLKCKYLTNDEICPICHSPTSENWIGLLIVINPEKSEIAKKAGIDIKGKYALSVKE 59
                                    10        20        30        40        50

Chain C from PDB  Type:PROTEIN  Length:84
 aligned with SPT5_METJA | Q57818 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:84
                              1                                                                                 
                              |      8        18        28        38        48        58        68        78    
            SPT5_METJA    - --MIFAVRTMVGQEKNIAGLMASRAEKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVPGTIAIEEIEPLLTP 82
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhhh..eeeeee......eeeeee.hhhhhhhhhh....eeee.....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  3lpe C -1 AHMIFAVRTMVGQEKNIAGLMASRAEKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVPGTIAIEEIEPLLTP 82
                                     8        18        28        38        48        58        68        78

Chain D from PDB  Type:PROTEIN  Length:59
 aligned with SPT4_METJA | Q57839 from UniProtKB/Swiss-Prot  Length:59

    Alignment length:59
                                    10        20        30        40        50         
            SPT4_METJA    1 MRACLKCKYLTNDEICPICHSPTSENWIGLLIVINPEKSEIAKKAGIDIKGKYALSVKE 59
               SCOP domains d3lped_ D: automated matches                                SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....ee...........ee..ee.eeee.....hhhhhhh.....eee..ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                  3lpe D  1 MRACLKCKYLTNDEICPICHSPTSENWIGLLIVINPEKSEIAKKAGIDIKGKYALSVKE 59
                                    10        20        30        40        50

Chain E from PDB  Type:PROTEIN  Length:84
 aligned with SPT5_METJA | Q57818 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:84
                              1                                                                                 
                              |      8        18        28        38        48        58        68        78    
            SPT5_METJA    - --MIFAVRTMVGQEKNIAGLMASRAEKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVPGTIAIEEIEPLLTP 82
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhh...eeeeee......eeeeee.hhhhhhhhhh....eeee.....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  3lpe E -1 AHMIFAVRTMVGQEKNIAGLMASRAEKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVPGTIAIEEIEPLLTP 82
                                     8        18        28        38        48        58        68        78

Chain F from PDB  Type:PROTEIN  Length:59
 aligned with SPT4_METJA | Q57839 from UniProtKB/Swiss-Prot  Length:59

    Alignment length:59
                                    10        20        30        40        50         
            SPT4_METJA    1 MRACLKCKYLTNDEICPICHSPTSENWIGLLIVINPEKSEIAKKAGIDIKGKYALSVKE 59
               SCOP domains d3lpef_ F: automated matches                                SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....ee...........ee..ee.eeee.....hhhhhhh.....eee..ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                  3lpe F  1 MRACLKCKYLTNDEICPICHSPTSENWIGLLIVINPEKSEIAKKAGIDIKGKYALSVKE 59
                                    10        20        30        40        50

Chain G from PDB  Type:PROTEIN  Length:84
 aligned with SPT5_METJA | Q57818 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:84
                              1                                                                                 
                              |      8        18        28        38        48        58        68        78    
            SPT5_METJA    - --MIFAVRTMVGQEKNIAGLMASRAEKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVPGTIAIEEIEPLLTP 82
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhh...eeeeee......eeeeee.hhhhhhhhhh....eeee.....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  3lpe G -1 AHMIFAVRTMVGQEKNIAGLMASRAEKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVPGTIAIEEIEPLLTP 82
                                     8        18        28        38        48        58        68        78

Chain H from PDB  Type:PROTEIN  Length:59
 aligned with SPT4_METJA | Q57839 from UniProtKB/Swiss-Prot  Length:59

    Alignment length:59
                                    10        20        30        40        50         
            SPT4_METJA    1 MRACLKCKYLTNDEICPICHSPTSENWIGLLIVINPEKSEIAKKAGIDIKGKYALSVKE 59
               SCOP domains d3lpeh_ H: automated matches                                SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....ee...........ee..ee.eeee.....hhhhhhh.....eee..ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                  3lpe H  1 MRACLKCKYLTNDEICPICHSPTSENWIGLLIVINPEKSEIAKKAGIDIKGKYALSVKE 59
                                    10        20        30        40        50

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: Small proteins (3458)

Fold: Rubredoxin-like (572)

Superfamily: RNA polymerase subunits (39)

Family: automated matches (1)

Protein domain: automated matches (1)

Methanocaldococcus jannaschii [TaxId: 2190] (1)

1a	d3lpeb_	B:
1b	d3lped_	D:
1c	d3lpef_	F:
1d	d3lpeh_	H:

(no "CATH Domain" information available for 3LPE)

(no "Pfam Domain" information available for 3LPE)

Asymmetric Unit(hide GO term definitions)

Chain A,C,E,G (SPT5_METJA | Q57818)

molecular function
	GO:0003735	structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.
	GO:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	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: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.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Chain B,D,F,H (SPT4_METJA | Q57839)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3lpe)

Biological Units
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		Biological Unit 4	[ Jena3D ]

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	3lpe
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Access by UniProt ID/Accession number
	SPT4_METJA \| Q57839
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	SPT5_METJA \| Q57818
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	2.7.7.6
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	SPT4_METJA \| Q57839
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	SPT5_METJA \| Q57818
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	SPT4_METJA \| Q57839	:	4zn1 4zn3
	SPT5_METJA \| Q57818	:	3ewg 4zn1 4zn3

1ryq	MOLECULAR REPLACEMENT SEARCH MODEL
3ewg	MOLECULAR REPLACEMENT SEARCH MODEL

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Gene Ontology (10, 12)

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