1EFA | PD0118 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE LAC REPRESSOR DIMER BOUND TO OPERATOR AND THE ANTI-INDUCER ONPF

Authors :   C. E. Bell, M. Lewis

Date :   07 Feb 00 (Deposition) - 06 Mar 00 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Protein-Dna Complex, Helix-Turn-Helix, Gene Regulation, Molecular Switch, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. E. Bell, M. Lewis
A Closer View Of The Conformation Of The Lac Repressor Boun To Operator.
Nat. Struct. Biol. V. 7 209 2000
PubMed-ID: 10700279 | Reference-DOI: 10.1038/78907
(for further references see the PDB file header)

*Molecule 1 - DNA (5'- D(GPAPAPTTPGPTPGPAPGPCPGPCPTPCPAPCPAPAPTPT)-3')**
	Chains	:	D, E
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - LAC REPRESSOR
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 1-333
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	NPF	3	Ligand/Ion	ORTHONITROPHENYL-BETA-D-FUCOPYRANOSIDE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NPF	2	Ligand/Ion	ORTHONITROPHENYL-BETA-D-FUCOPYRANOSIDE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	NPF	1	Ligand/Ion	ORTHONITROPHENYL-BETA-D-FUCOPYRANOSIDE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:75 , ILE A:79 , ASN A:125 , LEU A:148 , ASP A:149 , PHE A:161 , SER A:193 , ARG A:197 , ASN A:246 , ASP A:274 , PHE A:293 , HOH A:908	BINDING SITE FOR RESIDUE NPF A 901
2	AC2	SOFTWARE	ALA B:75 , ILE B:79 , LEU B:148 , ASP B:149 , PHE B:161 , SER B:193 , ARG B:197 , ASN B:246 , ASP B:274 , PHE B:293 , HOH B:916	BINDING SITE FOR RESIDUE NPF B 902
3	AC3	SOFTWARE	ALA C:75 , ILE C:79 , LEU C:148 , ASP C:149 , PHE C:161 , SER C:193 , ARG C:197 , ASN C:246 , ASP C:274 , PHE C:293 , HOH C:911 , HOH C:912	BINDING SITE FOR RESIDUE NPF C 903

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

Asymmetric Unit

No.	Residues
1	Ile A:283	-	Pro A:284
2	Ile B:283	-	Pro B:284
3	Ile C:283	-	Pro C:284

Asymmetric Unit (1, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LACI_ECOLI_001 *	Y	282	D	LACI_ECOLI	---	---	A/B/C	Y	282	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LACI_ECOLI_001 *	Y	282	D	LACI_ECOLI	---	---	A/B	Y	282	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LACI_ECOLI_001 *	Y	282	D	LACI_ECOLI	---	---	C	Y	282	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LACI_2	PS50932	LacI-type HTH domain profile.	LACI_ECOLI	4-58	2	A:4-58 B:4-58
2	HTH_LACI_1	PS00356	LacI-type HTH domain signature.	LACI_ECOLI	6-24	2	A:6-24 B:6-24

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LACI_2	PS50932	LacI-type HTH domain profile.	LACI_ECOLI	4-58	2	A:4-58 B:4-58
2	HTH_LACI_1	PS00356	LacI-type HTH domain signature.	LACI_ECOLI	6-24	2	A:6-24 B:6-24

Biological Unit 2 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LACI_2	PS50932	LacI-type HTH domain profile.	LACI_ECOLI	4-58	0	- -
2	HTH_LACI_1	PS00356	LacI-type HTH domain signature.	LACI_ECOLI	6-24	0	- -

(no "Exon" information available for 1EFA)

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:328
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:328
                                    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        
           LACI_ECOLI     2 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTT 329
               SCOP domains d1efaa1 A:2-60 Lac repressor (LacR), N-terminal domain     d1efaa2 A:61-329 Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                                SCOP domains
               CATH domains 1efaA01 A:2-60 lambda repressor-like DNA-binding domains   1efaA02 A:61-160,A:293-318  [code=3.40.50.2300, no name defined]                                    1efaA03 A:161-292,A:319-329  [code=3.40.50.2300, no name defined]                                                                   1efaA02 A:61-160,A:293-3181efaA03     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh...hhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh....eee..........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhh.........eeeeee.hhhhhhh.....eee.hhhhhhhhhhhhhhhhhh......eeee..eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D----------------------------------------------- SAPs(SNPs)
                PROSITE (1) --HTH_LACI_2  PDB: A:4-58 UniProt: 4-58                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----HTH_LACI_1         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1efa A   2 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKTAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTT 329
                                    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

Chain B from PDB  Type:PROTEIN  Length:330
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:330
                                    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
           LACI_ECOLI     2 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLA 331
               SCOP domains d1efab1 B:2-60 Lac repressor (LacR), N-terminal domain     d1efab2 B:61-331 Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                                  SCOP domains
               CATH domains 1efaB01 B:2-59 lambda repressor-like DNA-binding domains  1efaB02 B:60-160,B:291-317  [code=3.40.50.2300, no name defined]                                     1efaB03 B:161-290,B:318-331  [code=3.40.50.2300, no name defined]                                                                 1efaB02 B:60-160,B:291-317 1efaB03        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhh...hhhhhhhhhh......hhhhhhhhhhhhhh....hhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh....eee..........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhh.........eeeeee..hhhhhh....eeee.hhhhhhhhhhhhhhhhhh......eeee..eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --HTH_LACI_2  PDB: B:4-58 UniProt: 4-58                  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----HTH_LACI_1         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1efa B   2 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKTAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLA 331
                                    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

Chain C from PDB  Type:PROTEIN  Length:286
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:286
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325      
           LACI_ECOLI    46 NYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLA 331
               SCOP domains d1efac1 C:46-60d1efac2 C:61-331 Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------1efaC01 C:62-161,C:291-320  [code=3.40.50.2300, no name defined]                                    1efaC02 C:162-290,C:321-331  [code=3.40.50.2300, no name defined]                                                                1efaC01 C:62-161,C:291-320    1efaC02     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh....eee..........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhh.........eeeeee..hhhhhh....eeee.hhhhhhhhhhhhhhhhhh......eeee..eee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_LACI_2   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1efa C  46 NYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKTAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLA 331
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325

Chain D from PDB  Type:DNA  Length:17
                                                 
                 1efa D   5 TGTGAGCGCTCACAATT  21
                                    14

Chain E from PDB  Type:DNA  Length:17
                                                 
                 1efa E   2 AATTGTGAGCGCTCACA  18
                                    11

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.2300, no name defined] (308)

[unclassified] (27)

1a	1efaC02	C:162-290,C:321-331
1b	1efaA02	A:61-160,A:293-318
1c	1efaA03	A:161-292,A:319-329
1d	1efaB03	B:161-290,B:318-331
1e	1efaC01	C:62-161,C:291-320
1f	1efaB02	B:60-160,B:291-317

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: 434 Repressor (Amino-terminal Domain) (116)

Homologous Superfamily: lambda repressor-like DNA-binding domains (100)

[unclassified] (45)

2a	1efaA01	A:2-60
2b	1efaB01	B:2-59

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (LACI_ECOLI | P03023)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000986	bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0001141	transcriptional repressor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to stop, prevent, or reduce the frequency, rate or extent of transcription from a bacterial-type RNA polymerase promoter.
biological process
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	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.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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		Ile A:283 - Pro A:284	[ RasMol ]
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		Ile C:283 - Pro C:284	[ RasMol ]

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	1efa
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Description

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