SAXSdb — 6cga

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

Ubiquitin carboxyl-terminal hydrolase calypso

Drosophila melanogaster

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Polycomb protein Asx × 2 （Q9V727）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CALYP_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–365； UniProt 43–404 Author chain C； PDBConstruct 4–365； UniProt 43–404

Polycomb protein Asx

Drosophila melanogaster

UniProt Q9V727

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Ubiquitin carboxyl-terminal hydrolase calypso × 2 （Q7K5N4）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ASX_DROME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–134； UniProt 207–340 Author chain D； PDBConstruct 1–134； UniProt 207–340

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	6cga
Deposition date deposition_date	2018-02-19
Structure title title	Structure of the PR-DUB complex
Keywords keywords	DUB complex, nucleosome binding protein, hetero-tetramer, HYDROLASE; HYDROLASE
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.

6cga__assembly_1__model_1

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

Download this curve (.dat)

6cga__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6cga__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.18 Å
Rg (electron density)	35.91 Å
Total Rg	36.45 Å
Atom count	5875
Residues	728
Excluded volume	104480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6cga__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase calypso
Molecular weight formula_weight	41081.4 kDa
EC 编号 ec_number	3.4.19.12
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	5885

GPGADGWLELESDPGLFTLLLKDFGCHDVQVEEVYDLQKPIESPYGFIFLFRWIEERRARRKIVETTAEIFVKDEEAISSIFFAQQVVPNSCATHALLSVLLNCNENNLQLGDTLSRLKTHTKGMSPENKGLAIGNTPELACAHNSHAMPQARRRLERTGAGVSSCRFTGEAFHFVSFVPINGQLFELDGLKPYPMNHGGWEDSEDWTDKFRRVMAERLGIATGEQDIRFNLMAVVPDRRIAITHKLKMLRTNQAIVSGTLQKLLKADEQGESGNGDSQRPDTPTTLLEPSAFTARDLQSLLKNLDTEIAINEQHLADENDRRHMFKVDASRRTHNYDKFICTFLSMLAHQGVLGELVSQHLLPS

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	Fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Polycomb protein Asx
Molecular weight formula_weight	15228.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

DGKIDLETPDSILASTNLRALLNKQTFSLLPPLYQYNLIQLLPSVDREASELEQPSSSASGGSPSEAIRLSASCLNNEFFARACLEWRERLSEGEFTPENQLKLKTEAEREKNKLDPWKLKHFEPFWGEKNSRG

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	Fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	6cgaA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	532 — Ubiquitin C-terminal Hydrolase UCH-l3
Homologous superfamily homologous superfamily	10 — Peptidase C12, ubiquitin carboxyl-terminal hydrolase

Domain ID domain_id	6cgaC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	532 — Ubiquitin C-terminal Hydrolase UCH-l3
Homologous superfamily homologous superfamily	10 — Peptidase C12, ubiquitin carboxyl-terminal hydrolase

Domain ID domain_id	6cgaC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	860 —

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Unit-cell length a length_a	150.170 Å
Unit-cell length b length_b	65.630 Å
Unit-cell length c length_c	162.760 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.35 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	43.672 Å
R factor r_factor	0.2465
R_work r_work	0.2442
R_free r_free	0.2940

Structure of the PR-DUB complex

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

Ubiquitin carboxyl-terminal hydrolase calypso

State in the Current Structure

Other States of the Same Protein in the Database

Polycomb protein Asx

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

6cga__assembly_1__model_1

6cga__assembly_1__model_1 | I(q)

6cga__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Structure of the PR-DUB complex

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

Ubiquitin carboxyl-terminal hydrolase calypso

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Polycomb protein Asx

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

6cga__assembly_1__model_1

6cga__assembly_1__model_1 | I(q)

6cga__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)