4zux

SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome

Method: X-RAY DIFFRACTION

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

Histone H3.2

Xenopus laevis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (145-MER) × 1 DNA (145-MER) × 1 Ubiquitin carboxyl-terminal hydrolase 8 × 2 （P50102） Transcription and mRNA export factor SUS1 × 2 （Q6WNK7） SAGA-associated factor 11 × 2 （A6ZWK1） Polyubiquitin-B × 2 （P0CG47） SAGA-associated factor 73 × 2 （P53165） ZINC ION × 16	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (145-MER) × 1 DNA (145-MER) × 1 Ubiquitin carboxyl-terminal hydrolase 8 × 2 （P50102） Transcription and mRNA export factor SUS1 × 2 （Q6WNK7） SAGA-associated factor 11 × 2 （A6ZWK1） Polyubiquitin-B × 2 （P0CG47） SAGA-associated factor 73 × 2 （P53165） ZINC ION × 16	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H32_XENLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–136； UniProt 1–136 Author chain E； PDBConstruct 1–136； UniProt 1–136 Author chain K； PDBConstruct 1–136； UniProt 1–136 Author chain O； PDBConstruct 1–136； UniProt 1–136

Histone H4

Xenopus laevis

UniProt P62799

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H3.2 × 2 （P84233） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (145-MER) × 1 DNA (145-MER) × 1 Ubiquitin carboxyl-terminal hydrolase 8 × 2 （P50102） Transcription and mRNA export factor SUS1 × 2 （Q6WNK7） SAGA-associated factor 11 × 2 （A6ZWK1） Polyubiquitin-B × 2 （P0CG47） SAGA-associated factor 73 × 2 （P53165） ZINC ION × 16	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H3.2 × 2 （P84233） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (145-MER) × 1 DNA (145-MER) × 1 Ubiquitin carboxyl-terminal hydrolase 8 × 2 （P50102） Transcription and mRNA export factor SUS1 × 2 （Q6WNK7） SAGA-associated factor 11 × 2 （A6ZWK1） Polyubiquitin-B × 2 （P0CG47） SAGA-associated factor 73 × 2 （P53165） ZINC ION × 16	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_XENLA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–103； UniProt 1–103 Author chain F； PDBConstruct 1–103； UniProt 1–103 Author chain L； PDBConstruct 1–103； UniProt 1–103 Author chain P； PDBConstruct 1–103； UniProt 1–103

Histone H2A type 1

Xenopus laevis

UniProt P06897

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2B 1.1 × 2 （P02281） DNA (145-MER) × 1 DNA (145-MER) × 1 Ubiquitin carboxyl-terminal hydrolase 8 × 2 （P50102） Transcription and mRNA export factor SUS1 × 2 （Q6WNK7） SAGA-associated factor 11 × 2 （A6ZWK1） Polyubiquitin-B × 2 （P0CG47） SAGA-associated factor 73 × 2 （P53165） ZINC ION × 16	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2B 1.1 × 2 （P02281） DNA (145-MER) × 1 DNA (145-MER) × 1 Ubiquitin carboxyl-terminal hydrolase 8 × 2 （P50102） Transcription and mRNA export factor SUS1 × 2 （Q6WNK7） SAGA-associated factor 11 × 2 （A6ZWK1） Polyubiquitin-B × 2 （P0CG47） SAGA-associated factor 73 × 2 （P53165） ZINC ION × 16	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1_XENLA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–130； UniProt 1–130 Author chain G； PDBConstruct 1–130； UniProt 1–130 Author chain M； PDBConstruct 1–130； UniProt 1–130 Author chain Q； PDBConstruct 1–130； UniProt 1–130

Histone H2B 1.1

Xenopus laevis

UniProt P02281

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） DNA (145-MER) × 1 DNA (145-MER) × 1 Ubiquitin carboxyl-terminal hydrolase 8 × 2 （P50102） Transcription and mRNA export factor SUS1 × 2 （Q6WNK7） SAGA-associated factor 11 × 2 （A6ZWK1） Polyubiquitin-B × 2 （P0CG47） SAGA-associated factor 73 × 2 （P53165） ZINC ION × 16	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） DNA (145-MER) × 1 DNA (145-MER) × 1 Ubiquitin carboxyl-terminal hydrolase 8 × 2 （P50102） Transcription and mRNA export factor SUS1 × 2 （Q6WNK7） SAGA-associated factor 11 × 2 （A6ZWK1） Polyubiquitin-B × 2 （P0CG47） SAGA-associated factor 73 × 2 （P53165） ZINC ION × 16	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B11_XENLA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 2–123； UniProt 5–126 Author chain H； PDBConstruct 2–123； UniProt 5–126 Author chain N； PDBConstruct 2–123； UniProt 5–126 Author chain R； PDBConstruct 2–123； UniProt 5–126

Ubiquitin carboxyl-terminal hydrolase 8

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P50102

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (145-MER) × 1 DNA (145-MER) × 1 Transcription and mRNA export factor SUS1 × 2 （Q6WNK7） SAGA-associated factor 11 × 2 （A6ZWK1） Polyubiquitin-B × 2 （P0CG47） SAGA-associated factor 73 × 2 （P53165） ZINC ION × 16	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (145-MER) × 1 DNA (145-MER) × 1 Transcription and mRNA export factor SUS1 × 2 （Q6WNK7） SAGA-associated factor 11 × 2 （A6ZWK1） Polyubiquitin-B × 2 （P0CG47） SAGA-associated factor 73 × 2 （P53165） ZINC ION × 16	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBP8_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain U； PDBConstruct 2–472； UniProt 1–471 Author chain Z； PDBConstruct 2–472； UniProt 1–471 Author chain e； PDBConstruct 2–472； UniProt 1–471 Author chain j； PDBConstruct 2–472； UniProt 1–471

Transcription and mRNA export factor SUS1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q6WNK7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (145-MER) × 1 DNA (145-MER) × 1 Ubiquitin carboxyl-terminal hydrolase 8 × 2 （P50102） SAGA-associated factor 11 × 2 （A6ZWK1） Polyubiquitin-B × 2 （P0CG47） SAGA-associated factor 73 × 2 （P53165） ZINC ION × 16	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (145-MER) × 1 DNA (145-MER) × 1 Ubiquitin carboxyl-terminal hydrolase 8 × 2 （P50102） SAGA-associated factor 11 × 2 （A6ZWK1） Polyubiquitin-B × 2 （P0CG47） SAGA-associated factor 73 × 2 （P53165） ZINC ION × 16	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SUS1_YEAST
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain V； PDBConstruct 1–96； UniProt 1–96 Author chain a； PDBConstruct 1–96； UniProt 1–96 Author chain f； PDBConstruct 1–96； UniProt 1–96 Author chain k； PDBConstruct 1–96； UniProt 1–96

SAGA-associated factor 11

Saccharomyces cerevisiae (strain YJM789)

UniProt A6ZWK1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (145-MER) × 1 DNA (145-MER) × 1 Ubiquitin carboxyl-terminal hydrolase 8 × 2 （P50102） Transcription and mRNA export factor SUS1 × 2 （Q6WNK7） Polyubiquitin-B × 2 （P0CG47） SAGA-associated factor 73 × 2 （P53165） ZINC ION × 16	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (145-MER) × 1 DNA (145-MER) × 1 Ubiquitin carboxyl-terminal hydrolase 8 × 2 （P50102） Transcription and mRNA export factor SUS1 × 2 （Q6WNK7） Polyubiquitin-B × 2 （P0CG47） SAGA-associated factor 73 × 2 （P53165） ZINC ION × 16	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SGF11_YEAS7
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain W； PDBConstruct 1–99； UniProt 1–99 Author chain b； PDBConstruct 1–99； UniProt 1–99 Author chain g； PDBConstruct 1–99； UniProt 1–99 Author chain l； PDBConstruct 1–99； UniProt 1–99

Polyubiquitin-B

Homo sapiens

UniProt P0CG47

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (145-MER) × 1 DNA (145-MER) × 1 Ubiquitin carboxyl-terminal hydrolase 8 × 2 （P50102） Transcription and mRNA export factor SUS1 × 2 （Q6WNK7） SAGA-associated factor 11 × 2 （A6ZWK1） SAGA-associated factor 73 × 2 （P53165） ZINC ION × 16	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (145-MER) × 1 DNA (145-MER) × 1 Ubiquitin carboxyl-terminal hydrolase 8 × 2 （P50102） Transcription and mRNA export factor SUS1 × 2 （Q6WNK7） SAGA-associated factor 11 × 2 （A6ZWK1） SAGA-associated factor 73 × 2 （P53165） ZINC ION × 16	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBB_HUMAN
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain X； PDBConstruct 1–76； UniProt 1–76 Author chain c； PDBConstruct 1–76； UniProt 1–76 Author chain h； PDBConstruct 1–76； UniProt 1–76 Author chain m； PDBConstruct 1–76； UniProt 1–76

SAGA-associated factor 73

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P53165

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (145-MER) × 1 DNA (145-MER) × 1 Ubiquitin carboxyl-terminal hydrolase 8 × 2 （P50102） Transcription and mRNA export factor SUS1 × 2 （Q6WNK7） SAGA-associated factor 11 × 2 （A6ZWK1） Polyubiquitin-B × 2 （P0CG47） ZINC ION × 16	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 18 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (145-MER) × 1 DNA (145-MER) × 1 Ubiquitin carboxyl-terminal hydrolase 8 × 2 （P50102） Transcription and mRNA export factor SUS1 × 2 （Q6WNK7） SAGA-associated factor 11 × 2 （A6ZWK1） Polyubiquitin-B × 2 （P0CG47） ZINC ION × 16	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SGF73_YEAST
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain Y； PDBConstruct 1–104； UniProt 1–104 Author chain d； PDBConstruct 1–104； UniProt 1–104 Author chain i； PDBConstruct 1–104； UniProt 1–104 Author chain n； PDBConstruct 1–104； UniProt 1–104

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	4zux
Deposition date deposition_date	2015-05-17
Structure title title	SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome
Keywords keywords	DUB, deubiquitinase, USP, chromatin, eraser, nucleosome, modified histone, macromolecular complex, Hydrolase-DNA complex; Hydrolase/DNA
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.

4zux__assembly_1__model_1

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

Download this curve (.dat)

4zux__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4zux__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	54.77 Å
Rg (electron density)	56.22 Å
Total Rg	56.21 Å
Atom count	24535
Residues	2620
Excluded volume	418510 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4zux__assembly_1__model_1`	eicosameric （20）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4zux__assembly_2__model_1`	eicosameric （20）	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 (12)

Entity 1 Entity 1 polymer

Description description	Histone H3.2
Molecular weight formula_weight	15435.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,K,O
Atom count atom_count	49079

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Histone H4
Molecular weight formula_weight	11394.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Histone H2A type 1
Molecular weight formula_weight	14109.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Histone H2B 1.1
Molecular weight formula_weight	13655.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	DNA (145-MER)
Molecular weight formula_weight	44520.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I,S

ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCGAT

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	DNA (145-MER)
Molecular weight formula_weight	44991.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J,T

ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTGAT

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase 8
Molecular weight formula_weight	53731.3 kDa
EC 编号 ec_number	3.4.19.12
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,Z,e,j

AMSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILAKYWDDVCTKTMVPSMERRDGLSGLINMGSTAFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN

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 8 Entity 8 polymer

Description description	Transcription and mRNA export factor SUS1
Molecular weight formula_weight	11094.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V,a,f,k

MTMDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ

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 9 Entity 9 polymer

Description description	SAGA-associated factor 11
Molecular weight formula_weight	11297.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W,b,g,l

MTEETITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDLRSYYFDPNGSLDINGLQKQQESSQYIHCENCGRDVSANRLAAHLQRCLSRGARR

Source Source

Source organism organism	Saccharomyces cerevisiae (strain YJM789)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	307796
Host organism host_organism	Escherichia coli

Entity 10 Entity 10 polymer

Description description	Polyubiquitin-B
Molecular weight formula_weight	8576.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,c,h,m

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 11 Entity 11 polymer

Description description	SAGA-associated factor 73
Molecular weight formula_weight	11538.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y,d,i,n

MRSGDAEIKGIKPKVIEEYSLSQGSGPSNDSWKSLMSSAKDTPLQYDHMNRESLKKYFNPNAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLENHCAGASGK

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 12 Entity 12 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	32

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6. Fold Classification (SCOP + CATH) 28 domains

CATH v4.4 (28 domains)

Domain ID domain_id	4zuxA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4zuxB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4zuxC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4zuxD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4zuxE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4zuxF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4zuxG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4zuxH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4zuxK00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4zuxL00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4zuxM00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4zuxN00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4zuxO00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4zuxP00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4zuxQ00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4zuxR00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4zuxU01
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	4zuxU02
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	4zuxV00
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	4zuxZ01
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	4zuxZ02
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	4zuxa00
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	4zuxe01
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	4zuxe02
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	4zuxf00
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	4zuxj01
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	4zuxj02
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	4zuxk00
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

▶

Unit-cell length a length_a	178.804 Å
Unit-cell length b length_b	179.174 Å
Unit-cell length c length_c	353.819 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	16

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

Resolution resolution	3.820 Å
Low-resolution limit resolution_low	49.498 Å
R factor r_factor	0.2369
R_work r_work	0.2338
R_free r_free	0.2559

SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome

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

Histone H3.2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H2A type 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H2B 1.1

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 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

Transcription and mRNA export factor 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

Polyubiquitin-B

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

4zux__assembly_1__model_1

4zux__assembly_1__model_1 | I(q)

4zux__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment