1JVA: VMA1-derived homing endonuclease X10SSS

Crystal structure of the VMA1-derived endonuclease bearing the N and C extein propeptides. Determined by X-ray diffraction at 2.1 Å resolution. Released 29 Aug 2002.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 6,960
Mol. weight: 106.3 kDa
Released: 29 Aug 2002

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

Secondary structure: helices and β-sheets

1JVA contains 31 α-helices and 67 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: 15 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	285-286	2	1
β-strand	290-292	3	2
β-strand	293	1	3
β-strand	298-300	3	2
α-helix	301-303	3
β-strand	309-311	3	3
α-helix	312	1
β-strand	317-319	3	3
β-strand	322	1	4
β-strand	325-335	11	1
β-strand	355-359	5	1
β-strand	363-369	7	5
β-strand	372-379	8	6
β-strand	382-396	15	6
β-strand	402-414	13	6
α-helix	415-417	3
α-helix	420-430	11
β-strand	437-443	7	5
α-helix	444-449	6
α-helix	452-457	6
β-strand	459	1	5
β-strand	460-462	3	7
α-helix	471-478	8
α-helix	487-501	15
β-strand	502	1	8
β-strand	508-512	5	8
α-helix	516-528	13
β-strand	532-534	3	8
β-strand	544-550	7	8
α-helix	568-572	5
α-helix	573-577	5
β-strand	579-580	2	9
β-strand	583-584	2	9
α-helix	588-592	5
α-helix	595-609	15
β-strand	610-613	4	10
β-strand	615	1	11
β-strand	617	1	11
β-strand	619-624	6	10
α-helix	627-640	14
β-strand	643-649	7	10
β-strand	663-669	7	10
α-helix	672-678	7
β-strand	700-702	3	7
β-strand	704-715	12	1
β-strand	718	1	4
β-strand	726-728	3	12
β-strand	729	1	2
β-strand	733	1	7
β-strand	734-736	3	12

Chain B: 16 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	282	1	13
β-strand	285-286	2	14
β-strand	290-292	3	15
β-strand	293	1	16
β-strand	298-300	3	15
α-helix	301-303	3
β-strand	309-311	3	16
α-helix	312	1
β-strand	317-319	3	16
β-strand	320-322	3	17
β-strand	325-335	11	14
β-strand	355-359	5	14
α-helix	362	1
β-strand	363-369	7	18
β-strand	371-378	8	19
β-strand	383-396	14	19
β-strand	402-414	13	19
α-helix	415-417	3
α-helix	420-430	11
β-strand	437-443	7	18
α-helix	444-449	6
α-helix	452-457	6
β-strand	459-462	4	18
α-helix	471-477	7
α-helix	487-501	15
β-strand	508-512	5	20
α-helix	516-528	13
β-strand	532-535	4	20
β-strand	544-550	7	20
α-helix	568-575	8
β-strand	579-580	2	21
β-strand	583-584	2	21
α-helix	589-592	4
α-helix	595-609	15
β-strand	610-613	4	22
β-strand	619-624	6	22
α-helix	627-639	13
β-strand	643-649	7	22
β-strand	663-669	7	22
α-helix	672-678	7
β-strand	700-702	3	18
β-strand	704-715	12	14
β-strand	718-719	2	17
α-helix	720	1
β-strand	726-728	3	18
β-strand	729	1	15
β-strand	733-736	4	18
β-strand	740	1	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
VMA1-derived homing endonuclease X10SSS	A, B	protein	475	Saccharomyces cerevisiae	P17255 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1JVA_1 VMA1-DERIVED HOMING ENDONUCLEASE X10SSS (chains A, B)
MSNSDAIIYVGSFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYS
VVQKSQHRAHKSDSSREVPELLKFTCNATNELVVRTPRSVRRLSRTIKGVEYFEVITFEM
GQKKAPDGRIVELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDLSLLGS
HVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDRATFSVD
SRDTSLMERVTEYAEKLNLCAEYKDRKEPQVAKTVNLYSKVVRGNGIRNNLNTENPLWDA
IVGLGFLKDGVKNIPSFLSTDNIGTRETFLAGLIDSDGYVTDEHGIKATIKTIHTSVRDG
LVSLARSLGLVVSVNAEPAKVDMNGTKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPA
AAFARECRGFYFELQELKEDDYYGITLSDDSDHQFLLANQVVVHSSGERGNEMAE

Primary citation

Protein-splicing reaction via a thiazolidine intermediate: crystal structure of the VMA1-derived endonuclease bearing the N and C-terminal propeptides. Mizutani, R., Nogami, S., Kawasaki, M. et al. J Mol Biol (2002) 316:919-929. DOI 10.1006/jmbi.2001.5357 · 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
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

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