3mhs

Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde

Method: X-RAY DIFFRACTION

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

Ubiquitin carboxyl-terminal hydrolase 8

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Protein SUS1 × 1 （Q6WNK7） SAGA-associated factor 11 × 1 （Q03067） Ubiquitin × 1 （P62988） SAGA-associated factor 73 × 1 （P53165） 1,2-ETHANEDIOL × 1 GLYCEROL × 1 ZINC ION × 8 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBP8_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–476； UniProt 1–471

Protein SUS1

Saccharomyces cerevisiae

UniProt Q6WNK7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Ubiquitin carboxyl-terminal hydrolase 8 × 1 （P50102） SAGA-associated factor 11 × 1 （Q03067） Ubiquitin × 1 （P62988） SAGA-associated factor 73 × 1 （P53165） 1,2-ETHANEDIOL × 1 GLYCEROL × 1 ZINC ION × 8 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SUS1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–96； UniProt 1–96

SAGA-associated factor 11

Saccharomyces cerevisiae

UniProt Q03067

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Ubiquitin carboxyl-terminal hydrolase 8 × 1 （P50102） Protein SUS1 × 1 （Q6WNK7） Ubiquitin × 1 （P62988） SAGA-associated factor 73 × 1 （P53165） 1,2-ETHANEDIOL × 1 GLYCEROL × 1 ZINC ION × 8 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SGF11_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–99； UniProt 1–99

Ubiquitin

Homo sapiens

UniProt P62988

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Ubiquitin carboxyl-terminal hydrolase 8 × 1 （P50102） Protein SUS1 × 1 （Q6WNK7） SAGA-associated factor 11 × 1 （Q03067） SAGA-associated factor 73 × 1 （P53165） 1,2-ETHANEDIOL × 1 GLYCEROL × 1 ZINC ION × 8 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBIQ_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–76； UniProt 1–76

SAGA-associated factor 73

Saccharomyces cerevisiae

UniProt P53165

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Ubiquitin carboxyl-terminal hydrolase 8 × 1 （P50102） Protein SUS1 × 1 （Q6WNK7） SAGA-associated factor 11 × 1 （Q03067） Ubiquitin × 1 （P62988） 1,2-ETHANEDIOL × 1 GLYCEROL × 1 ZINC ION × 8 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SGF73_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–96； UniProt 1–96

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	3mhs
Deposition date deposition_date	2010-04-08
Structure title title	Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde
Keywords keywords	;Multi-protein complex, Hydrolase-transcription regulator-protein binding complex, Acetylation, Cytoplasm, Isopeptide bond, Nucleus, Phosphoprotein, Ubl conjugation ;; Hydrolase/transcription regulator/protein binding
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.

3mhs__assembly_1__model_1

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

Download this curve (.dat)

3mhs__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3mhs__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.90 Å
Rg (electron density)	28.63 Å
Total Rg	29.53 Å
Atom count	6409
Residues	800
Excluded volume	114170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3mhs__assembly_1__model_1`	pentameric （5）	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 (9)

Entity 1 Entity 1 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase 8
Molecular weight formula_weight	54033.6 kDa
EC 编号 ec_number	3.1.2.15
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7460

GAAAAMSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILAKYWDDVCTKTMVPSMERRDGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Protein SUS1
Molecular weight formula_weight	11094.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MTMDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	SAGA-associated factor 11
Molecular weight formula_weight	11297.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MTEETITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDLRSYYFDPNGSLDINGLQKQQESSQYIHCENCGRDVSANRLAAHLQRCLSRGARR

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8560.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	SAGA-associated factor 73
Molecular weight formula_weight	10824.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MRSGDAEIKGIKPKVIEEYSLSQGSGPSNDSWKSLMSSAKDTPLQYDHMNRESLKKYFNPNAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLEN

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	845

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3mhsb_
Class class	a — All alpha proteins
Fold Fold fold	a.301 — Sus1-like
Superfamily Superfamily superfamily	a.301.1 — Sus1-like
Family Family family	a.301.1.1 — Sus1-like

Domain ID domain_id	d3mhsd_
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

CATH v4.4 (6 domains)

Domain ID domain_id	3mhsA01
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	3mhsA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	3mhsB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	140 — ENY2/SUS1

Domain ID domain_id	3mhsC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	3mhsC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	3mhsD00
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

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Unit-cell length a length_a	78.600 Å
Unit-cell length b length_b	102.084 Å
Unit-cell length c length_c	120.903 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.890 Å
Low-resolution limit resolution_low	35.100 Å
R factor r_factor	0.1615
R_work r_work	0.1590
R_free r_free	0.2076

Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde

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

Ubiquitin carboxyl-terminal hydrolase 8

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein SUS1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SAGA-associated factor 11

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SAGA-associated factor 73

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

3mhs__assembly_1__model_1

3mhs__assembly_1__model_1 | I(q)

3mhs__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 (9)

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 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)