2EUL - JenaLib

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Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Biological Unit 7 (Jmol Viewer)

Title :   STRUCTURE OF THE TRANSCRIPTION FACTOR GFH1.

Authors :   J. Symersky, A. Perederina, M. N. Vassylyeva, V. Svetlov, I. Artsimovi D. G. Vassylyev, Riken Structural Genomics/Proteomics Initiati

Date :   28 Oct 05 (Deposition) - 15 Nov 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A,B,C,D  (1x)
Biol. Unit 4: A (1x),B (1x),C (1x),D (1x)
Biol. Unit 5: A (1x),B (1x),C (1x),D (1x)
Biol. Unit 6: A (1x),B (1x),C (1x),D (1x)
Biol. Unit 7: A (1x),B (1x),C (1x),D (1x)

Keywords :   Gfh1, Transcription Factor, Rna Polymerase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Symersky, A. Perederina, M. N. Vassylyeva, V. Svetlov, I. Artsimovitch, D. G. Vassylyev
Regulation Through The Rna Polymerase Secondary Channel: Structural And Functional Variability Of The Coiled-Coil Transcription Factors.
J. Biol. Chem. V. 281 1309 2006
PubMed-ID: 16298991 | Reference-DOI: 10.1074/JBC.C500405200

Molecule 1 - ANTI-CLEAVAGE ANTI-GREA TRANSCRIPTION FACTOR GFH1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PVS26
	Expression System Strain	:	BL21(LAMBDADE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GFHI
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 25)

No.	Name	Count	Type	Full Name
1	ZN	25	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

Biological Unit 5 (0, 0)

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

Biological Unit 6 (0, 0)

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

Biological Unit 7 (0, 0)

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

Asymmetric Unit (25, 25)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:49 , HOH A:426 , HOH A:449 , HIS D:132	BINDING SITE FOR RESIDUE ZN A 401
02	AC2	SOFTWARE	ASP A:63 , GLU A:66 , ZN A:416 , ASP B:67	BINDING SITE FOR RESIDUE ZN A 402
03	AC3	SOFTWARE	GLU A:109 , HOH A:463 , GLU D:24	BINDING SITE FOR RESIDUE ZN A 403
04	AC4	SOFTWARE	GLU A:20 , GLU A:24 , HOH A:434 , ALA B:2	BINDING SITE FOR RESIDUE ZN A 404
05	AC5	SOFTWARE	ZN A:413 , ASP B:63 , ZN B:414 , HOH B:524	BINDING SITE FOR RESIDUE ZN B 405
06	AC6	SOFTWARE	ASP A:45 , HOH A:439 , ASP C:45	BINDING SITE FOR RESIDUE ZN C 406
07	AC7	SOFTWARE	ARG B:14 , HIS B:132 , GLU C:49 , HOH C:510	BINDING SITE FOR RESIDUE ZN C 407
08	AC8	SOFTWARE	ARG C:23 , GLU C:66 , ZN C:423 , HOH C:426 , ASP D:67	BINDING SITE FOR RESIDUE ZN C 408
09	AC9	SOFTWARE	GLU B:24 , GLN B:27 , LEU C:85 , GLU C:109	BINDING SITE FOR RESIDUE ZN C 409
10	BC1	SOFTWARE	ARG A:21 , HOH A:499 , GLU C:20 , GLU C:24 , ALA D:2	BINDING SITE FOR RESIDUE ZN C 400
11	BC2	SOFTWARE	MET C:1 , ASP C:67 , ZN C:421 , ASP D:63	BINDING SITE FOR RESIDUE ZN C 411
12	BC3	SOFTWARE	HOH C:483 , ASP D:114 , LYS D:118	BINDING SITE FOR RESIDUE ZN C 412
13	BC4	SOFTWARE	ASP A:67 , HOH A:425 , ARG B:23 , GLU B:66 , ZN B:405	BINDING SITE FOR RESIDUE ZN A 413
14	BC5	SOFTWARE	ASP B:63 , ZN B:405 , HOH B:459	BINDING SITE FOR RESIDUE ZN B 414
15	BC6	SOFTWARE	ASP C:63 , ASP D:63 , ZN D:422	BINDING SITE FOR RESIDUE ZN C 415
16	BC7	SOFTWARE	ARG A:23 , GLU A:66 , ZN A:402 , ASP B:67 , ARG B:71	BINDING SITE FOR RESIDUE ZN A 416
17	BC8	SOFTWARE	ASP A:63 , GLU A:66 , ASP B:63 , GLU B:66	BINDING SITE FOR RESIDUE ZN A 417
18	BC9	SOFTWARE	GLU D:54 , ARG D:57	BINDING SITE FOR RESIDUE ZN D 418
19	CC1	SOFTWARE	HIS A:132 , ASP A:136 , HOH A:483	BINDING SITE FOR RESIDUE ZN A 419
20	CC2	SOFTWARE	GLU B:54 , HOH B:440	BINDING SITE FOR RESIDUE ZN B 420
21	CC3	SOFTWARE	ASP C:67 , ZN C:411 , ILE D:62 , GLU D:66 , HOH D:470	BINDING SITE FOR RESIDUE ZN C 421
22	CC4	SOFTWARE	ZN C:415 , ASP D:63 , HOH D:510	BINDING SITE FOR RESIDUE ZN D 422
23	CC5	SOFTWARE	ASP C:63 , ZN C:408	BINDING SITE FOR RESIDUE ZN C 423
24	CC6	SOFTWARE	PRO A:143 , ASP B:114	BINDING SITE FOR RESIDUE ZN A 424
25	CC7	SOFTWARE	HIS C:132	BINDING SITE FOR RESIDUE ZN C 425

(no "SS Bond" information available for 2EUL)

(no "Cis Peptide Bond" information available for 2EUL)

(no "SAP(SNP)/Variant" information available for 2EUL)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GREAB_2	PS00830	Prokaryotic transcription elongation factors signature 2.	GFH1_THET8	120-136	4	A:120-136 B:120-136 C:120-136 D:120-136

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GREAB_2	PS00830	Prokaryotic transcription elongation factors signature 2.	GFH1_THET8	120-136	2	A:120-136 B:120-136 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GREAB_2	PS00830	Prokaryotic transcription elongation factors signature 2.	GFH1_THET8	120-136	2	- - C:120-136 D:120-136

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GREAB_2	PS00830	Prokaryotic transcription elongation factors signature 2.	GFH1_THET8	120-136	4	A:120-136 B:120-136 C:120-136 D:120-136

Biological Unit 4 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GREAB_2	PS00830	Prokaryotic transcription elongation factors signature 2.	GFH1_THET8	120-136	4	A:120-136 B:120-136 C:120-136 D:120-136

Biological Unit 5 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GREAB_2	PS00830	Prokaryotic transcription elongation factors signature 2.	GFH1_THET8	120-136	4	A:120-136 B:120-136 C:120-136 D:120-136

Biological Unit 6 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GREAB_2	PS00830	Prokaryotic transcription elongation factors signature 2.	GFH1_THET8	120-136	4	A:120-136 B:120-136 C:120-136 D:120-136

Biological Unit 7 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GREAB_2	PS00830	Prokaryotic transcription elongation factors signature 2.	GFH1_THET8	120-136	4	A:120-136 B:120-136 C:120-136 D:120-136

(no "Exon" information available for 2EUL)

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:156
 aligned with GFH1_THET8 | Q5SJG6 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      
           GFH1_THET8     1 MAREVKLTKAGYERLMQQLERERERLQEATKILQELMESSDDYDDSGLEAAKQEKARIEARIDSLEDILSRAVILEEGSGEVIGLGSVVELEDPLSGERLSVQVVSPAEANVLDTPMKISDASPMGKALLGHRVGDVLSLDTPKGRREFRVVAIHG 156
               SCOP domains d2eula1 A:1-77 GreA transcript cleavage protein, N-terminal domain           d2eula2 A:78-156 GreA transcript cleavage factor, C-terminal domain             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhheee.............eeeeee....eeeeeeee............eee..hhhhhhhh......eeee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------GREAB_2          -------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2eul A   1 MAREVKLTKAGYERLMQQLERERERLQEATKILQELMESSDDYDDSGLEAAKQEKARIEARIDSLEDILSRAVILEEGSGEVIGLGSVVELEDPLSGERLSVQVVSPAEANVLDTPMKISDASPMGKALLGHRVGDVLSLDTPKGRREFRVVAIHG 156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:156
 aligned with GFH1_THET8 | Q5SJG6 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      
           GFH1_THET8     1 MAREVKLTKAGYERLMQQLERERERLQEATKILQELMESSDDYDDSGLEAAKQEKARIEARIDSLEDILSRAVILEEGSGEVIGLGSVVELEDPLSGERLSVQVVSPAEANVLDTPMKISDASPMGKALLGHRVGDVLSLDTPKGRREFRVVAIHG 156
               SCOP domains d2eulb1 B:1-77 GreA transcript cleavage protein, N-terminal domain           d2eulb2 B:78-156 GreA transcript cleavage factor, C-terminal domain             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhheee.............eeeeee....eeeeeeee............eee..hhhhhhhh......eeee......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------GREAB_2          -------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2eul B   1 MAREVKLTKAGYERLMQQLERERERLQEATKILQELMESSDDYDDSGLEAAKQEKARIEARIDSLEDILSRAVILEEGSGEVIGLGSVVELEDPLSGERLSVQVVSPAEANVLDTPMKISDASPMGKALLGHRVGDVLSLDTPKGRREFRVVAIHG 156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:156
 aligned with GFH1_THET8 | Q5SJG6 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      
           GFH1_THET8     1 MAREVKLTKAGYERLMQQLERERERLQEATKILQELMESSDDYDDSGLEAAKQEKARIEARIDSLEDILSRAVILEEGSGEVIGLGSVVELEDPLSGERLSVQVVSPAEANVLDTPMKISDASPMGKALLGHRVGDVLSLDTPKGRREFRVVAIHG 156
               SCOP domains d2eulc1 C:1-77 GreA transcript cleavage protein, N-terminal domain           d2eulc2 C:78-156 GreA transcript cleavage factor, C-terminal domain             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhheee.............eeeeee....eeeeeeee............eee..hhhhhhhh......eeee......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------GREAB_2          -------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2eul C   1 MAREVKLTKAGYERLMQQLERERERLQEATKILQELMESSDDYDDSGLEAAKQEKARIEARIDSLEDILSRAVILEEGSGEVIGLGSVVELEDPLSGERLSVQVVSPAEANVLDTPMKISDASPMGKALLGHRVGDVLSLDTPKGRREFRVVAIHG 156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain D from PDB  Type:PROTEIN  Length:156
 aligned with GFH1_THET8 | Q5SJG6 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      
           GFH1_THET8     1 MAREVKLTKAGYERLMQQLERERERLQEATKILQELMESSDDYDDSGLEAAKQEKARIEARIDSLEDILSRAVILEEGSGEVIGLGSVVELEDPLSGERLSVQVVSPAEANVLDTPMKISDASPMGKALLGHRVGDVLSLDTPKGRREFRVVAIHG 156
               SCOP domains d2euld1 D:1-77 GreA transcript cleavage protein, N-terminal domain           d2euld2 D:78-156 GreA transcript cleavage factor, C-terminal domain             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhheee.............eeeeee....eeeeeee.............ee...hhhhhhhh......eeee......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------GREAB_2          -------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2eul D   1 MAREVKLTKAGYERLMQQLERERERLQEATKILQELMESSDDYDDSGLEAAKQEKARIEARIDSLEDILSRAVILEEGSGEVIGLGSVVELEDPLSGERLSVQVVSPAEANVLDTPMKISDASPMGKALLGHRVGDVLSLDTPKGRREFRVVAIHG 156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "CATH Domain" information available for 2EUL)

(no "Pfam Domain" information available for 2EUL)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (GFH1_THET8 | Q5SJG6)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0070063	RNA polymerase binding	Interacting selectively and non-covalently with an RNA polymerase molecule or complex.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0032784	regulation of DNA-templated transcription, elongation	Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase.
	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.

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	GFH1_THET8 \| Q5SJG6	:	3aoh 3aoi 4wqt

1grj	CRYSTAL STRUCTURE OF TRANSCRIPTION CLEAVAGE FACTOR GREA FROM E. COLI
1tjl	CRYSTAL STRUCTURE OF TRANSCRIPTION FACTOR DKSA FROM E. COLI

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 25)

Sites (25, 25)

SS Bonds (0, 0)

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