SAXSdb — 6rr0

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

Regulatory protein SIR4

Saccharomyces cerevisiae

UniProt P11978

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin carboxyl-terminal hydrolase 10 × 1 （P53874） CHLORIDE ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin carboxyl-terminal hydrolase 10 × 1 （P53874） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin carboxyl-terminal hydrolase 10 × 1 （P53874） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin carboxyl-terminal hydrolase 10 × 1 （P53874） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin carboxyl-terminal hydrolase 10 × 1 （P53874） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin carboxyl-terminal hydrolase 10 × 1 （P53874） water × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin carboxyl-terminal hydrolase 10 × 1 （P53874） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SIR4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–127； UniProt 961–1085 Author chain B； PDBConstruct 3–127； UniProt 961–1085 Author chain C； PDBConstruct 3–127； UniProt 961–1085 Author chain D； PDBConstruct 3–127； UniProt 961–1085 Author chain E； PDBConstruct 3–127； UniProt 961–1085 Author chain F； PDBConstruct 3–127； UniProt 961–1085 Author chain G； PDBConstruct 3–127； UniProt 961–1085

Ubiquitin carboxyl-terminal hydrolase 10

OrganismNot specified

UniProt P53874

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Regulatory protein SIR4 × 1 （P11978） CHLORIDE ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Regulatory protein SIR4 × 1 （P11978） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Regulatory protein SIR4 × 1 （P11978） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Regulatory protein SIR4 × 1 （P11978） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Regulatory protein SIR4 × 1 （P11978） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Regulatory protein SIR4 × 1 （P11978） water × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Regulatory protein SIR4 × 1 （P11978） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBP10_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 1–12； UniProt 117–128 Author chain I； PDBConstruct 1–12； UniProt 117–128 Author chain J； PDBConstruct 1–12； UniProt 117–128 Author chain K； PDBConstruct 1–12； UniProt 117–128 Author chain L； PDBConstruct 1–12； UniProt 117–128 Author chain M； PDBConstruct 1–12； UniProt 117–128 Author chain N； PDBConstruct 1–12； UniProt 117–128

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	6rr0
Deposition date deposition_date	2019-05-16
Structure title title	Crystal structure of the Sir4 H-BRCT domain in complex with Ubp10 pT123 peptide
Keywords keywords	heterochromatin, NUCLEAR PROTEIN; NUCLEAR 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.

6rr0__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6rr0__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6rr0__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	15.88 Å
Rg (electron density)	14.41 Å
Total Rg	15.64 Å
Atom count	1011
Residues	121
Excluded volume	18029 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6rr0__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6rr0__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6rr0__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6rr0__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6rr0__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`6rr0__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`6rr0__assembly_7__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	Regulatory protein SIR4
Molecular weight formula_weight	14871.9 kDa
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	7527

GPKPKNTKENLSKSSWRQEWLANLKLISVSLVDEFPSELSDSDRQIINEKMQLLKDIFANNLKSAISNNFRESDIIILKGEIEDYPMSSEIKIYYNELQNKPDAKKARFWSFMKTQRFVSNMGFDIQ

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase 10
Molecular weight formula_weight	1327.3 kDa
EC 编号 ec_number	3.4.19.12
Source method src_method	syn
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,I,J,K,L,M,N

LSTELSTEPPSS

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	317

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Unit-cell length a length_a	70.040 Å
Unit-cell length b length_b	75.280 Å
Unit-cell length c length_c	95.910 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.24 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	14

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.180 Å
Low-resolution limit resolution_low	47.570 Å
R factor r_factor	0.1975
R_work r_work	0.1963
R_free r_free	0.2180

Crystal structure of the Sir4 H-BRCT domain in complex with Ubp10 pT123 peptide

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

Regulatory protein SIR4

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin carboxyl-terminal hydrolase 10

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6rr0__assembly_5__model_1

6rr0__assembly_5__model_1 | I(q)

6rr0__assembly_5__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal structure of the Sir4 H-BRCT domain in complex with Ubp10 pT123 peptide

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

Regulatory protein SIR4

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 10

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

6rr0__assembly_5__model_1

6rr0__assembly_5__model_1 | I(q)

6rr0__assembly_5__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)