1LWT: Intein homing endonuclease PI-SceI

Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free). Determined by X-ray diffraction at 3.2 Å resolution. Released 27 Sept 2002.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Saccharomyces cerevisiae
Chains: 3
Atoms: 5,065
Mol. weight: 74.15 kDa
Released: 27 Sept 2002

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

Secondary structure: helices and β-sheets

1LWT contains 15 α-helices and 43 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: 15 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	7-9	3	2
β-strand	10	1	3
β-strand	15-17	3	2
α-helix	18-20	3
β-strand	26-28	3	3
β-strand	34-36	3	3
β-strand	37-39	3	4
β-strand	42-45	4	1
β-strand	47-52	6	1
β-strand	72-76	5	1
α-helix	79	1
β-strand	80-82	3	5
β-strand	83-84	2	6
β-strand	85-86	2	7
β-strand	89-95	7	8
β-strand	100-113	14	8
β-strand	119-126	8	8
β-strand	129-131	3	8
α-helix	132-134	3
α-helix	137-147	11
β-strand	154-155	2	7
β-strand	158-160	3	5
α-helix	161-166	6
α-helix	169-173	5
β-strand	176-179	4	6
α-helix	188-194	7
α-helix	204-218	15
β-strand	219-220	2	9
β-strand	223-228	6	9
α-helix	233-245	13
β-strand	248-250	3	10
β-strand	253	1	9
β-strand	262-265	4	9
β-strand	266-268	3	10
α-helix	285-289	5
α-helix	290-294	5
β-strand	296-297	2	11
β-strand	300-301	2	11
α-helix	305-308	4
α-helix	312-326	15
β-strand	328-330	3	12
β-strand	332	1	13
β-strand	334	1	13
β-strand	336-341	6	12
α-helix	344-357	14
β-strand	360-362	3	12
β-strand	365-366	2	12
β-strand	380-386	7	12
α-helix	389-395	7
β-strand	417-420	4	6
β-strand	421-425	5	1
β-strand	429-432	4	1
β-strand	435-436	2	4
β-strand	443-445	3	14
β-strand	446	1	2
β-strand	450	1	6
β-strand	451-453	3	14

Molecules and chains

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

Sequence of entity 1 (B), FASTA

>1LWT_1 PI-SceI DNA substrate top strand (chains B)
CTCTATGTCGGGTGCGGAGAAAGAGGTAATGAAATGG

Sequence of entity 2 (C), FASTA

>1LWT_2 PI-SceI DNA substrate bottom strand (chains C)
GCCATTTCATTACCTCTTTCTCCGCACCCGACATAGA

Sequence of entity 3 (A), FASTA

>1LWT_3 ENDONUCLEASE PI-SCEI (chains A)
CFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSQHRAHK
SDSSREVPELLKFTCNATHELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQKKAPDGRIV
ELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDLSLLGSHVRKATYQTYA
PILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDRATFSVDSRDTSLMERVT
EYAEKLNLCAEYKDRKEPQVAKTVNLYSKVVRGNGIRNNLNTENPLWDAIVGLGFLKDGV
KNIPSFLSTDNIGTRETFLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLV
VSVNAEPAKVDMNGTKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFY
FELQELKEDDYYGITLSDDSDHQFLLANQVVVHN

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
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
1LWS 3.5 Å, Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition…
7TMM 3.5 Å, Complete V1 Complex from Saccharomyces cerevisiae

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