SAXSdb — 5xis

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

E3 ubiquitin-protein ligase RNF168

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-40S ribosomal protein S27a × 1 （P62983） Ubiquitin-40S ribosomal protein S27a × 1 （P62983） beta-D-xylofuranose × 1 MAGNESIUM ION × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-40S ribosomal protein S27a × 1 （P62983） Ubiquitin-40S ribosomal protein S27a × 1 （P62983） beta-D-xylofuranose × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RN168_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–84； UniProt 110–188 Author chain D； PDBConstruct 6–84； UniProt 110–188

Ubiquitin-40S ribosomal protein S27a

Mus musculus

UniProt P62983

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	E3 ubiquitin-protein ligase RNF168 × 1 （Q8IYW5） beta-D-xylofuranose × 1 MAGNESIUM ION × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	E3 ubiquitin-protein ligase RNF168 × 1 （Q8IYW5） beta-D-xylofuranose × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS27A_MOUSE
Isoform	—
PDB entities	2, 3
Chains and sequence ranges	Author chain B； PDBConstruct 1–76； UniProt 1–76 Author chain E； PDBConstruct 1–76； UniProt 1–76 Author chain C； PDBConstruct 1–76； UniProt 1–76 Author chain F； PDBConstruct 1–76； UniProt 1–76

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	5xis
Deposition date deposition_date	2017-04-27
Structure title title	Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I
Keywords keywords	ubiquitin, TRANSFERASE-RIBOSOMAL PROTEIN complex; TRANSFERASE/RIBOSOMAL 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.

5xis__assembly_1__model_1

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

Download this curve (.dat)

5xis__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5xis__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.42 Å
Rg (electron density)	32.74 Å
Total Rg	32.49 Å
Atom count	1850
Residues	227
Excluded volume	32814 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5xis__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5xis__assembly_2__model_1`	trimeric （3）	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 (6)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase RNF168
Molecular weight formula_weight	9947.9 kDa
EC 编号 ec_number	2.3.2.27
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	4048

GPGHMLSKPGELRREYEEEISKVAAERRASEEEENKASEEYIQRLLAEEEEEEKRQAEKRRRAMEEQLKSDEELARKLSIDINN

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	Ubiquitin-40S ribosomal protein S27a
Molecular weight formula_weight	8691.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGD

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Ubiquitin-40S ribosomal protein S27a
Molecular weight formula_weight	8604.8 kDa
Mutation mutation	K63R
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	beta-D-xylofuranose
Molecular weight formula_weight	150.1 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	312

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5xisb_
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

Domain ID domain_id	d5xisc_
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

Domain ID domain_id	d5xise_
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

Domain ID domain_id	d5xisf_
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

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Unit-cell length a length_a	35.273 Å
Unit-cell length b length_b	66.291 Å
Unit-cell length c length_c	74.173 Å
Unit-cell angle α angle_alpha	76.47 °
Unit-cell angle β angle_beta	79.29 °
Unit-cell angle γ angle_gamma	80.49 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.780 Å
Low-resolution limit resolution_low	43.286 Å
R factor r_factor	0.2198
R_work r_work	0.2185
R_free r_free	0.2451

Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I

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

E3 ubiquitin-protein ligase RNF168

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-40S ribosomal protein S27a

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

5xis__assembly_1__model_1

5xis__assembly_1__model_1 | I(q)

5xis__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)

Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I

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

E3 ubiquitin-protein ligase RNF168

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-40S ribosomal protein S27a

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

5xis__assembly_1__model_1

5xis__assembly_1__model_1 | I(q)

5xis__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)