SAXSdb — 5jg6

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

Anaphase-promoting complex subunit 11

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Polyubiquitin-B × 1 （P0CG47） ZINC ION × 3 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Polyubiquitin-B × 1 （P0CG47） ZINC ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	APC11_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–70； UniProt 17–84 Author chain D； PDBConstruct 3–70； UniProt 17–84

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 heterocomplex	Heteromer	Protein 2	Anaphase-promoting complex subunit 11 × 1 （Q9NYG5） ZINC ION × 3 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Anaphase-promoting complex subunit 11 × 1 （Q9NYG5） ZINC ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–84； UniProt 76–154 Author chain C； PDBConstruct 6–84； UniProt 76–154

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	5jg6
Deposition date deposition_date	2016-04-19
Structure title title	APC11-Ubv shows role of noncovalent RING-Ubiquitin interactions in processive multiubiquitination and Ubiquitin chain elongation by APC/C
Keywords keywords	RING Ubiquitin Cell Cycle Anaphase-promoting complex-Cyclosome, CELL CYCLE; CELL CYCLE
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.

5jg6__assembly_1__model_1

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

Download this curve (.dat)

5jg6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5jg6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.38 Å
Rg (electron density)	15.03 Å
Total Rg	16.12 Å
Atom count	1070
Residues	138
Excluded volume	19094 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5jg6__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5jg6__assembly_2__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	Anaphase-promoting complex subunit 11
Molecular weight formula_weight	8050.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	2279

GSVANDENCGICRMAFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCILKWLHAQQVQQHCPMCRQEWKFKE

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 2 Entity 2 polymer

Description description	Polyubiquitin-B
Molecular weight formula_weight	9255.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSGGSGMQILVKTPRGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQILFFAVKRLEDGRTLSDYNIQKKSSLLLAMRVPGKMK

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 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	nat
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	116

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5jg6b1
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.15.1.0 — automated matches

Domain ID domain_id	d5jg6b2
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	d5jg6c_
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.15.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5jg6A00
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	5jg6D00
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)

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Unit-cell length a length_a	131.066 Å
Unit-cell length b length_b	35.193 Å
Unit-cell length c length_c	72.768 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	120.42 °
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	2.001 Å
Low-resolution limit resolution_low	36.326 Å
R factor r_factor	0.1870
R_work r_work	0.1852
R_free r_free	0.2195

APC11-Ubv shows role of noncovalent RING-Ubiquitin interactions in processive multiubiquitination and Ubiquitin chain elongation by APC/C

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

Anaphase-promoting complex subunit 11

State in the Current Structure

Other States of the Same Protein in the Database

Polyubiquitin-B

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

5jg6__assembly_1__model_1

5jg6__assembly_1__model_1 | I(q)

5jg6__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

APC11-Ubv shows role of noncovalent RING-Ubiquitin interactions in processive multiubiquitination and Ubiquitin chain elongation by APC/C

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

Anaphase-promoting complex subunit 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5jg6__assembly_1__model_1

5jg6__assembly_1__model_1 | I(q)

5jg6__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)