SAXSdb — 9q8y

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

Ubiquitin-conjugating enzyme E2 D2

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	Isoform 2 of E3 ubiquitin-protein ligase RNF38 × 1 （Q9H0F5） Ubiquitin-40S ribosomal protein S27a × 1 （J3QTR3） ZINC ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Isoform 2 of E3 ubiquitin-protein ligase RNF38 × 1 （Q9H0F5） Ubiquitin-40S ribosomal protein S27a × 1 （J3QTR3） ZINC ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UB2D2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–146； UniProt 2–147 Author chain B； PDBConstruct 1–146； UniProt 2–147

Isoform 2 of E3 ubiquitin-protein ligase RNF38

Homo sapiens

UniProt Q9H0F5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-conjugating enzyme E2 D2 × 1 （P62837） Ubiquitin-40S ribosomal protein S27a × 1 （J3QTR3） ZINC ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-conjugating enzyme E2 D2 × 1 （P62837） Ubiquitin-40S ribosomal protein S27a × 1 （J3QTR3） ZINC ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNF38_HUMAN
Isoform	Q9H0F5-2
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–69； UniProt 390–458 Author chain D； PDBConstruct 1–69； UniProt 390–458

Ubiquitin-40S ribosomal protein S27a

Homo sapiens

UniProt J3QTR3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-conjugating enzyme E2 D2 × 1 （P62837） Isoform 2 of E3 ubiquitin-protein ligase RNF38 × 1 （Q9H0F5） ZINC ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-conjugating enzyme E2 D2 × 1 （P62837） Isoform 2 of E3 ubiquitin-protein ligase RNF38 × 1 （Q9H0F5） ZINC ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	J3QTR3_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain F； PDBConstruct 2–77； UniProt 1–76 Author chain G； PDBConstruct 2–77； 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	9q8y
Deposition date deposition_date	2025-02-25
Structure title title	Structure of RNF38 RING with linchpin mutant R454Y in complex with Ubch5B-Ub
Keywords keywords	Ubiquitination, linchpin, RING ligase, LIGASE; LIGASE
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.

9q8y__assembly_1__model_1

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

Download this curve (.dat)

9q8y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9q8y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.39 Å
Rg (electron density)	25.00 Å
Total Rg	25.51 Å
Atom count	4298
Residues	292
Excluded volume	39333 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9q8y__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9q8y__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 (5)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-conjugating enzyme E2 D2
Molecular weight formula_weight	16720.2 kDa
EC 编号 ec_number	2.3.2.23,2.3.2.24
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7819

ALKRIHKELNDLARDPPAQCRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Isoform 2 of E3 ubiquitin-protein ligase RNF38
Molecular weight formula_weight	8041.2 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	C,D

KADIEQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICYADAS

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 BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Ubiquitin-40S ribosomal protein S27a
Molecular weight formula_weight	8663.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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 BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	nat
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

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Unit-cell length a length_a	116.079 Å
Unit-cell length b length_b	116.079 Å
Unit-cell length c length_c	90.315 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 62
Space-group number int_tables_number	171
Crystal system crystal_system	hexagonal

Resolution resolution	2.630 Å
Low-resolution limit resolution_low	43.920 Å
R factor r_factor	0.2338
R_work r_work	0.2317
R_free r_free	0.2746

Structure of RNF38 RING with linchpin mutant R454Y in complex with Ubch5B-Ub

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

Ubiquitin-conjugating enzyme E2 D2

State in the Current Structure

Other States of the Same Protein in the Database

Isoform 2 of E3 ubiquitin-protein ligase RNF38

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

9q8y__assembly_1__model_1

9q8y__assembly_1__model_1 | I(q)

9q8y__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 (5)

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 water

7. Citations (1)

Structure of RNF38 RING with linchpin mutant R454Y in complex with Ubch5B-Ub

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

Ubiquitin-conjugating enzyme E2 D2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Isoform 2 of E3 ubiquitin-protein ligase RNF38

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

9q8y__assembly_1__model_1

9q8y__assembly_1__model_1 | I(q)

9q8y__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 (5)

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 water

7. Citations (1)