1VDE: Pi-scei

Name: PDB 1VDE: Pi-scei, a homing endonuclease with protein splicing activity
Published: 1998-04-08
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: endonuclease

Pi-scei, a homing endonuclease with protein splicing activity. Determined by X-ray diffraction at 2.4 Å resolution. Released 8 Apr 1998.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 7,116
Mol. weight: 102.01 kDa
Released: 8 Apr 1998

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

Secondary structure: helices and β-sheets

1VDE contains 32 α-helices and 72 β-strands across 2 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: 17 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	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
α-helix	29	1
β-strand	34-36	3	3
β-strand	37-39	3	4
β-strand	42-52	11	1
β-strand	57	1	5
α-helix	67	1
β-strand	68	1	5
β-strand	72-76	5	1
α-helix	79	1
β-strand	80-86	7	6
β-strand	89-90	2	7
β-strand	104-113	10	7
β-strand	119-128	10	7
α-helix	138-148	11
β-strand	154-160	7	6
α-helix	161-166	6
α-helix	169-174	6
β-strand	176-179	4	6
α-helix	188-195	8
α-helix	204-218	15
β-strand	219	1	8
β-strand	225-229	5	8
α-helix	233-245	13
β-strand	248-254	7	8
β-strand	261-268	8	8
α-helix	269	1
α-helix	285-292	8
β-strand	296-297	2	9
β-strand	300-301	2	9
α-helix	305-309	5
α-helix	312-326	15
β-strand	327-330	4	10
β-strand	332	1	11
β-strand	334	1	11
β-strand	336-341	6	10
α-helix	344-356	13
β-strand	360-366	7	10
β-strand	380-386	7	10
α-helix	388-395	8
α-helix	406-408	3
β-strand	417-419	3	6
β-strand	421-432	12	1
β-strand	435-436	2	4
β-strand	443-445	3	12
β-strand	446	1	2
β-strand	450	1	6
β-strand	451-453	3	12

Chain B: 15 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	13
β-strand	7-9	3	14
β-strand	10	1	15
β-strand	15-17	3	14
α-helix	18-20	3
β-strand	26-28	3	15
β-strand	34-36	3	15
β-strand	37-39	3	16
β-strand	42-44	3	13
β-strand	47-52	6	13
β-strand	72-76	5	13
α-helix	79	1
β-strand	80-86	7	17
β-strand	89-90	2	18
β-strand	104-113	10	18
β-strand	119-128	10	18
α-helix	132-134	3
α-helix	137-148	12
β-strand	154-160	7	17
α-helix	161-166	6
α-helix	169-174	6
β-strand	176-179	4	17
α-helix	188-194	7
α-helix	205-218	14
β-strand	219	1	19
β-strand	225-226	2	19
α-helix	235-245	11
β-strand	248-252	5	19
β-strand	264-268	5	19
α-helix	285-293	9
β-strand	296	1	20
β-strand	301	1	20
α-helix	306-309	4
α-helix	312-326	15
β-strand	327-330	4	21
β-strand	332	1	22
β-strand	334	1	22
β-strand	336-341	6	21
α-helix	344-357	14
β-strand	360-366	7	21
β-strand	380-386	7	21
α-helix	389-395	7
α-helix	406-408	3
β-strand	417-419	3	17
β-strand	421-425	5	13
β-strand	430-432	3	13
β-strand	435-436	2	16
β-strand	443-445	3	23
β-strand	446	1	14
β-strand	450	1	17
β-strand	451-453	3	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pi-scei	A, B	protein	454	Saccharomyces cerevisiae	P17255 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1VDE_1 PI-SCEI (chains A, B)
CFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSQHRAHK
SDSSREVPELLKFTCNATHELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQKKAPDGRIV
ELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDLSLLGSHVRKATYQTYA
PILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDRATFSVDSRDTSLMERVT
EYAEKLNLCAEYKDRKEPQVAKTVNLYSKVVRGNGIRNNLNTENPLWDAIVGLGFLKDGV
KNIPSFLSTDNIGTRETFLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLV
VSVNAEPAKVDMNGTKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFY
FELQELKEDDYYGITLSDDSDHQFLLANQVVVHN

Primary citation

Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity. Duan, X., Gimble, F.S., Quiocho, F.A. Cell (1997) 89:555-564. DOI 10.1016/S0092-8674(00)80237-8 · 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
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
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

Browse structure collections

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