5jne

E2-SUMO-Siz1 E3-SUMO-PCNA complex

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	SUMO-conjugating enzyme UBC9 × 1 （P50623） Ubiquitin-like protein SMT3 × 1 （Q12306） Proliferating cell nuclear antigen × 1 （P15873） ZINC ION × 1 GLYCEROL × 6 ethane-1,2-dithiol × 1 water × 4	Consistent with protein count
2	Insufficient information	Heteromer	Protein 4	SUMO-conjugating enzyme UBC9 × 1 （P50623） Ubiquitin-like protein SMT3 × 1 （Q12306） Proliferating cell nuclear antigen × 1 （P15873） ZINC ION × 1 GLYCEROL × 4 ethane-1,2-dithiol × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SIZ1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–281； UniProt 167–445 Author chain E； PDBConstruct 3–281； UniProt 167–445

E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3

Saccharomyces cerevisiae

UniProt Q12306

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	SUMO-conjugating enzyme UBC9 × 1 （P50623） Proliferating cell nuclear antigen × 1 （P15873） ZINC ION × 1 GLYCEROL × 6 ethane-1,2-dithiol × 1 water × 4	Consistent with protein count
2	Insufficient information	Heteromer	Protein 4	SUMO-conjugating enzyme UBC9 × 1 （P50623） Proliferating cell nuclear antigen × 1 （P15873） ZINC ION × 1 GLYCEROL × 4 ethane-1,2-dithiol × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMT3_YEAST
Isoform	—
PDB entities	1, 3
Chains and sequence ranges	Author chain A； PDBConstruct 289–367； UniProt 20–98 Author chain E； PDBConstruct 289–367； UniProt 20–98 Author chain C； PDBConstruct 5–84； UniProt 19–98 Author chain G； PDBConstruct 5–84； UniProt 19–98

SUMO-conjugating enzyme UBC9

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P50623

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3 × 1 （Q04195,Q12306） Ubiquitin-like protein SMT3 × 1 （Q12306） Proliferating cell nuclear antigen × 1 （P15873） ZINC ION × 1 GLYCEROL × 6 ethane-1,2-dithiol × 1 water × 4	Consistent with protein count
2	Insufficient information	Heteromer	Protein 4	E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3 × 1 （Q04195,Q12306） Ubiquitin-like protein SMT3 × 1 （Q12306） Proliferating cell nuclear antigen × 1 （P15873） ZINC ION × 1 GLYCEROL × 4 ethane-1,2-dithiol × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC9_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–160； UniProt 1–157 Author chain F； PDBConstruct 4–160； UniProt 1–157

Proliferating cell nuclear antigen

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P15873

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3 × 1 （Q04195,Q12306） SUMO-conjugating enzyme UBC9 × 1 （P50623） Ubiquitin-like protein SMT3 × 1 （Q12306） ZINC ION × 1 GLYCEROL × 6 ethane-1,2-dithiol × 1 water × 4	Consistent with protein count
2	Insufficient information	Heteromer	Protein 4	E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3 × 1 （Q04195,Q12306） SUMO-conjugating enzyme UBC9 × 1 （P50623） Ubiquitin-like protein SMT3 × 1 （Q12306） ZINC ION × 1 GLYCEROL × 4 ethane-1,2-dithiol × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCNA_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–258； UniProt 1–258 Author chain H； PDBConstruct 1–258； UniProt 1–258

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5jne
Deposition date deposition_date	2016-04-29
Structure title title	E2-SUMO-Siz1 E3-SUMO-PCNA complex
Keywords keywords	ubiquitin, ubiquitin-like, SUMO, E3 ligase, substrate complex, E2 conjugating enzyme, ligase-signaling protein complex, SIZ, PIAS; ligase/signaling protein
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5jne__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5jne__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5jne__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	34.30 Å
Rg (electron density)	33.78 Å
Total Rg	34.35 Å
Atom count	6748
Residues	840
Excluded volume	120890 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5jne__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5jne__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3
Molecular weight formula_weight	42195.4 kDa
EC 编号 ec_number	6.3.2.-
Mutation mutation	Siz1 C361D, Smt3 Delta N-terminus 1-18
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	13744

SLSSSFAVPTIHFKESPFYKIQRLIPELVMNVEVTGGRGMCSAKFKLSKADYNLLSNPNSKHRLYLFSGMINPLGSRGNEPIQFPFPNELRCNNVQIKDNIRGFKSKPGTAKPADLTPHLKPYTQQNNVELIYAFTTKEYKLFGYIVEMITPEQLLEKVLQHPKIIKQATLLYLKKTLREDEEMGLTTTSTIMSLQDPISYTRMKYPSKSINCKHLQCFDALWFLHSQLQIPTWQCPVCQIDIALENLAISEFVDDILQNCQKNVEQVELTSDGKWTAILEDDDDKLRPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	SUMO-conjugating enzyme UBC9
Molecular weight formula_weight	18288.8 kDa
EC 编号 ec_number	6.3.2.-
Mutation mutation	C5S, A129K, K153R
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F

GSHMSSLSLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPKQEPAWRSFSRNKAEYDKKVLLQARQYSK

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Ubiquitin-like protein SMT3
Molecular weight formula_weight	9720.0 kDa
Mutation mutation	N-terminal 1-18 delete, K19R
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G

GSHMRPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Proliferating cell nuclear antigen
Molecular weight formula_weight	28815.7 kDa
Mutation mutation	K77D, C81E, R110D, K127G, K164C
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H

MLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSDILREGNNTDTLTLIADNTPDSIILLFEDTKKDDIAEYSLKLMDIDADFLGIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITCETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKSGFLQFFLAPKFNDEE

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 7 Entity 7 non-polymer

Description description	ethane-1,2-dithiol
Molecular weight formula_weight	94.2 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	271

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6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d5jneb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.1 — UBC-related

Domain ID domain_id	d5jneb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5jnec_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d5jned1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d5jned2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d5jnef_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.1 — UBC-related

Domain ID domain_id	d5jneg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d5jneh1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d5jneh2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

CATH v4.4 (10 domains)

Domain ID domain_id	5jneA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	780 — PINIT domain

Domain ID domain_id	5jneA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	5jneA03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	5jneB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	5jneD00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	5jneE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	780 — PINIT domain

Domain ID domain_id	5jneE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	5jneE03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	5jneF00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	5jneH00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	93.421 Å
Unit-cell length b length_b	205.882 Å
Unit-cell length c length_c	142.501 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	48.385 Å
R factor r_factor	0.2135
R_work r_work	0.2115
R_free r_free	0.2499

E2-SUMO-Siz1 E3-SUMO-PCNA complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SUMO-conjugating enzyme UBC9

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Proliferating cell nuclear antigen

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5jne__assembly_1__model_1

5jne__assembly_1__model_1 | I(q)

5jne__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (9 domains)

CATH v4.4 (10 domains)

7. Citations (1)