SAXSdb — 3fn1

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

NEDD8-activating enzyme E1 catalytic subunit

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	NEDD8-conjugating enzyme UBE2F × 1 （Q969M7） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBA3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–98； UniProt 368–463

NEDD8-conjugating enzyme UBE2F

Homo sapiens

UniProt Q969M7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	NEDD8-activating enzyme E1 catalytic subunit × 1 （Q8TBC4） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBE2F_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 9–167； UniProt 21–185

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	3fn1
Deposition date deposition_date	2008-12-22
Structure title title	E2-RING expansion of the NEDD8 cascade confers specificity to cullin modification.
Keywords keywords	Ligase, ATP-binding, Cell cycle, Nucleotide-binding, Ubl conjugation pathway; 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.

3fn1__assembly_1__model_1

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

Download this curve (.dat)

3fn1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fn1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.28 Å
Rg (electron density)	21.52 Å
Total Rg	22.12 Å
Atom count	1992
Residues	250
Excluded volume	35553 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fn1__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	NEDD8-activating enzyme E1 catalytic subunit
Molecular weight formula_weight	10857.0 kDa
EC 编号 ec_number	6.3.2.-
Mutation mutation	L394M
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2127

GSSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYMQSVTSIEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHFTS

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	NEDD8-conjugating enzyme UBE2F
Molecular weight formula_weight	19104.6 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSATASDSTRRVSVRDKLLVKEVAELEANLPCTCKVHFPDPNKLHCFQLTVTPDEGYYQGGKFQFETEVPDAYNMVPPKVKCLTKIWHPNITETGEICLSLLREHSIDGTGWAPTRTLKDVVWGLNSLFTDLLNFDDPLNIEAAEHHLRDKEDFRNKVDDYIKRYAR

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	135

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3fn1a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.111 — Activating enzymes of the ubiquitin-like proteins
Superfamily Superfamily superfamily	c.111.1 — Activating enzymes of the ubiquitin-like proteins
Family Family family	c.111.1.2 — Ubiquitin activating enzymes (UBA)

Domain ID domain_id	d3fn1b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3fn1A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily	20 — Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3

Domain ID domain_id	3fn1B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

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Unit-cell length a length_a	81.171 Å
Unit-cell length b length_b	81.171 Å
Unit-cell length c length_c	212.755 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 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	24.880 Å
R factor r_factor	0.2260
R_work r_work	0.2238
R_free r_free	0.2650

E2-RING expansion of the NEDD8 cascade confers specificity to cullin modification.

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

NEDD8-activating enzyme E1 catalytic subunit

State in the Current Structure

Other States of the Same Protein in the Database

NEDD8-conjugating enzyme UBE2F

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

3fn1__assembly_1__model_1

3fn1__assembly_1__model_1 | I(q)

3fn1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

E2-RING expansion of the NEDD8 cascade confers specificity to cullin modification.

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

NEDD8-activating enzyme E1 catalytic subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NEDD8-conjugating enzyme UBE2F

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

3fn1__assembly_1__model_1

3fn1__assembly_1__model_1 | I(q)

3fn1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)