1EFA: Lac repressor dimer

Crystal structure of the lac repressor dimer bound to operator and the anti-inducer onpf. Determined by X-ray diffraction at 2.6 Å resolution. Released 6 Mar 2000.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Escherichia coli
Chains: 5
Atoms: 7,838
Mol. weight: 121.05 kDa
Ligands: NPF
Released: 6 Mar 2000

Explore 1EFA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1EFA contains 39 α-helices and 43 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 14 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
α-helix	17-24	8
α-helix	33-45	13
α-helix	51-56	6
β-strand	63-68	6	1
α-helix	74-89	16
β-strand	93-98	6	1
α-helix	104-116	13
β-strand	121-125	5	1
α-helix	130-139	10
β-strand	145-147	3	1
β-strand	158-161	4	1
α-helix	163-176	14
β-strand	182-186	5	2
α-helix	192-206	15
β-strand	214-217	4	2
α-helix	222-234	13
β-strand	241-244	4	2
α-helix	247-258	12
α-helix	262-263	2
β-strand	264	1	3
β-strand	268	1	3
β-strand	269-271	3	2
β-strand	272-274	3	4
α-helix	277-281	5
β-strand	288-290	3	4
α-helix	293-308	16
β-strand	316-319	4	1
β-strand	322-324	3	4

Chain B: 14 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
α-helix	17-24	8
α-helix	33-44	12
α-helix	51-56	6
β-strand	63-69	7	5
α-helix	74-89	16
β-strand	93-99	7	5
α-helix	104-116	13
β-strand	121-125	5	5
α-helix	130-139	10
β-strand	145-147	3	5
β-strand	158-161	4	5
α-helix	163-176	14
β-strand	182-186	5	6
α-helix	192-206	15
β-strand	214-217	4	6
α-helix	222-234	13
β-strand	241-244	4	6
α-helix	247-258	12
α-helix	262-263	2
β-strand	264	1	7
β-strand	268	1	7
β-strand	269-274	6	6
α-helix	278-281	4
β-strand	287-290	4	6
α-helix	293-308	16
β-strand	316-319	4	5
β-strand	322-324	3	6

Chain C: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	51-56	6
β-strand	63-69	7	8
α-helix	74-89	16
β-strand	93-99	7	8
α-helix	104-116	13
β-strand	121-125	5	8
α-helix	130-139	10
β-strand	145-147	3	8
β-strand	158-161	4	8
α-helix	163-176	14
β-strand	182-186	5	9
α-helix	192-206	15
β-strand	214-217	4	9
α-helix	222-234	13
β-strand	241-244	4	9
α-helix	247-258	12
α-helix	262-263	2
β-strand	264	1	10
β-strand	268	1	10
β-strand	269-274	6	9
α-helix	278-281	4
β-strand	287-290	4	9
α-helix	293-308	16
β-strand	316-319	4	8
β-strand	322-324	3	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(gpapapttpgptpgpapgpcpgpcptpcpapcpapaptp*t)-3')	D, E	DNA	21
Lac repressor	A, B, C	protein	333	Escherichia coli	P03023 (AlphaFold model)

Sequence of entity 1 (D, E), FASTA

>1EFA_1 DNA (5'-D(*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3') (chains D, E)
GAATTGTGAGCGCTCACAATT

Sequence of entity 2 (A, B, C), FASTA

>1EFA_2 LAC REPRESSOR (chains A, B, C)
MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ
SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKTAVHNLLAQRVS
GLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQ
QIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPT
AMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTS
VDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPN

Ligands and cofactors

ID	Name	Formula	Copies
NPF	2-nitrophenyl beta-D-fucopyranoside	C12 H15 N O7	3

Primary citation

A closer view of the conformation of the Lac repressor bound to operator. Bell, C.E., Lewis, M. Nat Struct Biol (2000) 7:209-214. DOI 10.1038/78907 · PubMed

Other PDB entries of the same protein (UniProt P03023 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8GOH 1.1 Å, Homotetramic Antiparallel Coiled-Coil of 23-residues LacI C-terminal tetramerization helix
1JYE 1.7 Å, Structure of a Dimeric Lac Repressor with C-terminal Deletion and K84L Substitution
2P9H 2.0 Å, High resolution structure of the Lactose Repressor bound to IPTG
3EDC 2.1 Å, Crystal Structure of a 1.6-hexanediol Bound Tetrameric Form of Escherichia coli…
1TLF 2.6 Å, Unprecedented quaternary structure of E. Coli lac repressor core tetramer: implications…
1LBI 2.7 Å, Lac repressor
4RZS 2.71 Å, Lac repressor engineered to bind sucralose, unliganded tetramer
1JYF 3.0 Å, Structure of the Dimeric Lac Repressor with an 11-residue C-terminal Deletion.
4RZT 3.1 Å, Lac repressor engineered to bind sucralose, sucralose-bound tetramer
1LBH 3.2 Å, Intact lactose operon repressor with gratuitous inducer iptg
2PAF 3.5 Å, Crystal Structure of the Lactose Repressor bound to anti-inducer ONPF in induced state
2PE5 3.5 Å, Crystal Structure of the Lac Repressor bound to ONPG in repressed state

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1EFA is part of these collections:

DNA and RNA

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