1LWS: Intein homing endonuclease PI-SceI

Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence. Determined by X-ray diffraction at 3.5 Å resolution. Released 27 Sept 2002.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Saccharomyces cerevisiae
Chains: 3
Atoms: 4,756
Mol. weight: 74.23 kDa
Ligands: CA
Released: 27 Sept 2002

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

Secondary structure: helices and β-sheets

1LWS contains 19 α-helices and 40 β-strands across 1 chain. 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: 19 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
α-helix	6	1
β-strand	7-8	2	2
β-strand	10	1	3
β-strand	16-17	2	2
α-helix	18-20	3
α-helix	21-22	2
β-strand	26-28	3	3
β-strand	29	1	4
β-strand	34-36	3	3
β-strand	37-39	3	5
β-strand	42-52	11	1
α-helix	58-61	4
β-strand	63	1	6
β-strand	65	1	6
α-helix	67-69	3
β-strand	72-76	5	1
α-helix	79	1
β-strand	80-86	7	7
β-strand	89-90	2	8
β-strand	105-113	9	8
β-strand	119-126	8	8
α-helix	137-147	11
β-strand	154-160	7	7
α-helix	161-164	4
α-helix	170-174	5
β-strand	176	1	7
β-strand	177-179	3	9
β-strand	186	1	10
α-helix	190-194	5
α-helix	204-217	14
β-strand	225-229	5	11
α-helix	233-246	14
β-strand	249	1	12
β-strand	261-265	5	11
β-strand	267	1	12
α-helix	287-290	4
β-strand	296-297	2	13
β-strand	300-301	2	13
α-helix	306-309	4
β-strand	310	1	10
α-helix	312-325	14
β-strand	327-330	4	14
β-strand	336-339	4	14
α-helix	344-356	13
β-strand	360-366	7	14
β-strand	370-371	2	15
β-strand	375-376	2	15
β-strand	380-386	7	14
α-helix	389-395	7
α-helix	406-408	3
α-helix	415-416	2
β-strand	417-419	3	9
β-strand	421-432	12	1
β-strand	435-436	2	5
β-strand	443-445	3	4
β-strand	446	1	2
β-strand	450	1	9
β-strand	451-453	3	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
PI-SceI DNA recognition region top strand	B	DNA	37
PI-SceI DNA recognition region bottom strand	C	DNA	37
Endonuclease pi-scei	A	protein	454	Saccharomyces cerevisiae	P17255 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>1LWS_1 PI-SceI DNA recognition region top strand (chains B)
CTCTATGTCGGGTGCGGAGAAAGAGGTAATGAAATGG

Sequence of entity 2 (C), FASTA

>1LWS_2 PI-SceI DNA recognition region bottom strand (chains C)
GCCATTTCATTACCTCTTTCTCCGCACCCGACATAGA

Sequence of entity 3 (A), FASTA

>1LWS_3 ENDONUCLEASE PI-SCEI (chains A)
CFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSQHRAHK
SDSSREVPELLKFTCNATHELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQKKAPDGRIV
ELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDLSLLGSHVRKATYQTYA
PILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDRATFSVDSRDTSLMERVT
EYAEKLNLCAEYKDRKEPQVAKTVNLYSKVVRGNGIRNNLNTENPLWDAIVGLGFLKDGV
KNIPSFLSTDNIGTRETFLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLV
VSVNAEPAKVDMNGTKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFY
FELQELKEDDYYGITLSDDSDHQFLLANQVVVHN

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

Primary citation

Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence. Moure, C.M., Gimble, F.S., Quiocho, F.A. Nat Struct Biol (2002) 9:764-770. DOI 10.1038/nsb840 · PubMed

Other PDB entries of the same protein (UniProt P17255 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1GPP 1.35 Å, Crystal structure of the S.cerevisiae Homing Endonuclease PI-SceI Domain I
1DFA 2.0 Å, Crystal structure of pi-scei in C2 space group
1EF0 2.1 Å, Crystal structure of pi-scei miniprecursor
1JVA 2.1 Å, Crystal structure of the VMA1-derived endonuclease bearing the N and C extein propeptides
1VDE 2.4 Å, Pi-scei, a homing endonuclease with protein splicing activity
9COP 2.7 Å, Yeast RAVE bound to V-ATPase V1 complex
1UM2 2.9 Å, Crystal Structure of the Vma1-Derived Endonuclease with the Ligated Extein Segment
1LWT 3.2 Å, Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA…
7TMO 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 1
7TMP 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 2
7TMQ 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 3
7TMM 3.5 Å, Complete V1 Complex from Saccharomyces cerevisiae

Browse structure collections

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