1DFA: Pi-scei in C2 space group

Crystal structure of pi-scei in C2 space group. Determined by X-ray diffraction at 2.0 Å resolution. Released 8 Dec 1999.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Saccharomyces cerevisiae
Chains: 1
Atoms: 3,369
Mol. weight: 51 kDa
Released: 8 Dec 1999

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

Secondary structure: helices and β-sheets

1DFA contains 14 α-helices and 32 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: 14 helices, 32 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	27	1	3
β-strand	28	1	4
β-strand	34	1	4
β-strand	37	1	5
β-strand	43-52	10	1
α-helix	67-69	3
β-strand	72-76	5	1
β-strand	80-86	7	6
β-strand	88-90	3	7
β-strand	105-113	9	7
β-strand	119-126	8	7
β-strand	154-160	7	6
α-helix	161-166	6
α-helix	169-174	6
β-strand	176	1	6
β-strand	177-179	3	8
α-helix	205-218	14
β-strand	220	1	9
β-strand	223	1	9
α-helix	233-245	13
α-helix	287-292	6
β-strand	296	1	10
β-strand	301	1	10
α-helix	305-308	4
α-helix	312-326	15
β-strand	329-330	2	11
β-strand	336-341	6	11
α-helix	344-356	13
β-strand	360-367	8	11
α-helix	371-373	3
β-strand	379-386	8	11
α-helix	389-395	7
α-helix	406-408	3
α-helix	415-416	2
β-strand	417-419	3	8
β-strand	421-431	11	1
β-strand	436	1	5
β-strand	443-445	3	12
β-strand	446	1	2
β-strand	450	1	8
β-strand	451-453	3	12

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>1DFA_1 PI-SCEI ENDONUCLEASE (chains A)
CFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSQHRAHK
SDSSREVPELLKFTCNATHELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQKKAPDGRIV
ELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDLSLLGSHVRKATYQTYA
PILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDRATFSVDSRDTSLMERVT
EYAEKLNLCAEYKDRKEPQVAKTVNLYSKVVRGNGIRNNLNTENPLWDAIVGLGFLKDGV
KNIPSFLSTDNIGTRETFLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLV
VSVNAEPAKVDMNGTKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFY
FELQELKEDDYYGITLSDDSDHQFLLANQVVVHN

Primary citation

Probing the structure of the PI-SceI-DNA complex by affinity cleavage and affinity photocross-linking. Hu, D., Crist, M., Duan, X. et al. J Biol Chem (2000) 275:2705-2712. DOI 10.1074/jbc.275.4.2705 · 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
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
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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