5JNE: E2-SUMO-Siz1 E3-SUMO-PCNA complex

E2-SUMO-Siz1 E3-SUMO-PCNA complex. Determined by X-ray diffraction at 2.85 Å resolution. Released 10 Aug 2016.

Method: X-ray diffraction
Resolution: 2.85 Å
Organisms: Saccharomyces cerevisiae, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 8
Atoms: 13,744
Mol. weight: 199.28 kDa
Ligands: 6LN, ZN
Released: 10 Aug 2016

Explore 5JNE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5JNE contains 60 α-helices and 123 β-strands across 8 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, 28 β-strands

Element	Residues	Length	Sheet
β-strand	177	1	1
α-helix	178-179	2
β-strand	180	1	2
β-strand	183-196	14	2
β-strand	199-209	11	3
α-helix	213-220	8
β-strand	226-234	9	2
β-strand	244	1	1
α-helix	245-246	2
β-strand	252-256	5	3
β-strand	259-260	2	3
α-helix	275-277	3
β-strand	278-279	2	2
α-helix	281-283	3
α-helix	284-286	3
α-helix	290	1
β-strand	291-300	10	3
β-strand	304-313	10	2
α-helix	316-325	10
α-helix	327-328	2
β-strand	329	1	4
α-helix	331-347	17
β-strand	354-358	5	5
β-strand	360	1	6
β-strand	367	1	6
β-strand	371-374	4	7
β-strand	383-384	2	7
α-helix	385-394	10
β-strand	399	1	8
β-strand	406	1	8
α-helix	409-411	3
β-strand	412-414	3	7
β-strand	415	1	4
α-helix	416-423	8
β-strand	431-434	4	5
β-strand	440-442	3	5
β-strand	456-462	7	9
β-strand	467-473	7	9
α-helix	479-488	10
α-helix	493-495	3
β-strand	497-500	4	9
β-strand	503-504	2	9
β-strand	520-525	6	9

Chains B and F: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-18	16
β-strand	25-30	6	10
β-strand	36-46	11	10
α-helix	47-48	2
β-strand	57-63	7	10
β-strand	74-76	3	10
α-helix	77-78	2
β-strand	91	1	10
β-strand	94	1	11
α-helix	95-97	3
α-helix	109-120	12
α-helix	132-139	8
α-helix	141-154	14

Chain C: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	23-29	7	5
β-strand	34-40	7	5
α-helix	45-54	10
α-helix	60-62	3
β-strand	63-67	5	5
β-strand	70-71	2	5
β-strand	87-93	7	5
β-strand	97	1	11

Chain D: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	12
α-helix	9-17	9
β-strand	25-31	7	13
β-strand	34-40	7	13
β-strand	46-53	8	13
β-strand	59	1	12
β-strand	62	1	12
β-strand	66-71	6	13
α-helix	72-81	10
β-strand	86-92	7	12
β-strand	98-105	8	12
β-strand	111-117	7	12
β-strand	135-140	6	13
α-helix	141-152	12
β-strand	157-162	6	14
β-strand	167-172	6	14
β-strand	177-182	6	14
β-strand	185	1	15
α-helix	191-193	3
β-strand	195	1	15
β-strand	196-199	4	13
β-strand	204-208	5	14
α-helix	209-215	7
α-helix	216-220	5
β-strand	224-229	6	13
β-strand	235-240	6	13
β-strand	245-250	6	13
α-helix	251-253	3

Chain E: 14 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	177	1	16
α-helix	178-179	2
β-strand	180	1	17
β-strand	183-196	14	17
β-strand	199-209	11	18
α-helix	213-220	8
β-strand	226-235	10	17
β-strand	244	1	16
β-strand	252-256	5	18
β-strand	259-261	3	18
β-strand	268	1	19
β-strand	271	1	19
β-strand	278-279	2	17
α-helix	281-283	3
α-helix	284-286	3
α-helix	290	1
β-strand	291-300	10	18
β-strand	303-313	11	17
α-helix	316-325	10
α-helix	327-328	2
β-strand	329	1	20
α-helix	331-348	18
β-strand	351-358	8	21
β-strand	360	1	22
β-strand	367	1	22
β-strand	371-374	4	23
β-strand	383-384	2	23
α-helix	385-394	10
β-strand	399	1	24
β-strand	406	1	24
α-helix	409-411	3
β-strand	412-414	3	23
β-strand	415	1	20
α-helix	416-423	8
β-strand	431-434	4	21
β-strand	440-442	3	21
β-strand	456-462	7	25
β-strand	467-473	7	25
α-helix	479-488	10
α-helix	493-495	3
β-strand	496-500	5	25
β-strand	503-504	2	25
α-helix	505-506	2
β-strand	520-526	7	25

Chain G: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	23-29	7	21
β-strand	34-40	7	21
α-helix	46-55	10
α-helix	60-62	3
β-strand	63-67	5	21
β-strand	70-71	2	21
β-strand	87-93	7	21
β-strand	97	1	27

Chain H: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	28
α-helix	9-17	9
β-strand	25-30	6	29
β-strand	34-40	7	29
β-strand	46-53	8	29
β-strand	59-62	4	28
β-strand	66-71	6	29
α-helix	72-81	10
β-strand	86-92	7	28
β-strand	98-105	8	28
β-strand	111-117	7	28
β-strand	135-140	6	29
α-helix	141-152	12
β-strand	157-163	7	30
β-strand	166-172	7	30
β-strand	177-182	6	30
β-strand	185	1	31
α-helix	191-193	3
β-strand	195	1	31
β-strand	196-199	4	29
β-strand	203-208	6	30
α-helix	209-215	7
α-helix	216-218	3
β-strand	224-229	6	29
β-strand	235-241	7	29
β-strand	244-250	7	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3	A, E	protein	367	Saccharomyces cerevisiae	Q04195 (AlphaFold model), Q12306 (AlphaFold model)
SUMO-conjugating enzyme UBC9	B, F	protein	160	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P50623 (AlphaFold model)
Ubiquitin-like protein SMT3	C, G	protein	84	Saccharomyces cerevisiae	Q12306 (AlphaFold model)
Proliferating cell nuclear antigen	D, H	protein	258	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P15873 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>5JNE_1 E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3 (chains A, E)
SLSSSFAVPTIHFKESPFYKIQRLIPELVMNVEVTGGRGMCSAKFKLSKADYNLLSNPNS
KHRLYLFSGMINPLGSRGNEPIQFPFPNELRCNNVQIKDNIRGFKSKPGTAKPADLTPHL
KPYTQQNNVELIYAFTTKEYKLFGYIVEMITPEQLLEKVLQHPKIIKQATLLYLKKTLRE
DEEMGLTTTSTIMSLQDPISYTRMKYPSKSINCKHLQCFDALWFLHSQLQIPTWQCPVCQ
IDIALENLAISEFVDDILQNCQKNVEQVELTSDGKWTAILEDDDDKLRPETHINLKVSDG
SSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEA
HREQIGG

Sequence of entity 2 (B, F), FASTA

>5JNE_2 SUMO-conjugating enzyme UBC9 (chains B, F)
GSHMSSLSLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGV
YPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQ
DLLDSPNPNSPKQEPAWRSFSRNKAEYDKKVLLQARQYSK

Sequence of entity 3 (C, G), FASTA

>5JNE_3 Ubiquitin-like protein SMT3 (chains C, G)
GSHMRPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQA
DQTPEDLDMEDNDIIEAHREQIGG

Sequence of entity 4 (D, H), FASTA

>5JNE_4 Proliferating cell nuclear antigen (chains D, H)
MLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEY
RCDHPVTLGMDLTSLSDILREGNNTDTLTLIADNTPDSIILLFEDTKKDDIAEYSLKLMD
IDADFLGIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITCETIKFVADGDIGSGSV
IIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFD
LKSGFLQFFLAPKFNDEE

Ligands and cofactors

ID	Name	Formula	Copies
6LN	ethane-1,2-dithiol	C2 H6 S2	2
ZN	Zinc ion	Zn	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Capturing a substrate in an activated RING E3/E2-SUMO complex. Streich, F.C., Lima, C.D. Nature (2016) 536:304-308. DOI 10.1038/nature19071 · PubMed

Other PDB entries of the same protein (UniProt Q04195 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3I2D 2.6 Å, Crystal Structure of S. Cerevisiae SUMO E3 Ligase SIZ1
2RNN Solution Structure of the N-terminal SAP Domain of SUMO E3 Ligases from Saccharomyces…

Browse structure collections

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