SAXSdb — 9m7o

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

Ubiquitin-conjugating enzyme E2 4

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Polyubiquitin-C × 1 （P0CG48） Polyubiquitin-C × 1 （P0CG48） Ubiquitin × 1 （P62979） E4 ubiquitin-protein ligase UFD2 × 1 （P54860）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–148； UniProt 1–148

Polyubiquitin-C

Homo sapiens

UniProt P0CG48

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Ubiquitin-conjugating enzyme E2 4 × 1 （P15731） Ubiquitin × 1 （P62979） E4 ubiquitin-protein ligase UFD2 × 1 （P54860）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC_HUMAN
Isoform	—
PDB entities	2, 3
Chains and sequence ranges	Author chain D； PDBConstruct 1–76； UniProt 1–76 Author chain E； PDBConstruct 1–76； UniProt 1–76

Ubiquitin

Homo sapiens

UniProt P62979

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Ubiquitin-conjugating enzyme E2 4 × 1 （P15731） Polyubiquitin-C × 1 （P0CG48） Polyubiquitin-C × 1 （P0CG48） E4 ubiquitin-protein ligase UFD2 × 1 （P54860）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS27A_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain C； PDBConstruct 1–76； UniProt 1–76

E4 ubiquitin-protein ligase UFD2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P54860

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Ubiquitin-conjugating enzyme E2 4 × 1 （P15731） Polyubiquitin-C × 1 （P0CG48） Polyubiquitin-C × 1 （P0CG48） Ubiquitin × 1 （P62979）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UFD2_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain A； PDBConstruct 1–961； UniProt 1–961

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	9m7o
Deposition date deposition_date	2025-03-10
Structure title title	Cryo-EM structure of Ufd2/Ubc4-ub complex with K29triUb(monomeric conformation)
Keywords keywords	E4 enzyme, Ufd2, branch Ub chains, LIGASE; LIGASE
Experimental Method method	ELECTRON MICROSCOPY

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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.

9m7o__assembly_1__model_1

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

Download this curve (.dat)

9m7o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9m7o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.73 Å
Rg (electron density)	36.10 Å
Total Rg	36.60 Å
Atom count	9310
Residues	1179
Excluded volume	166770 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9m7o__assembly_1__model_1`	pentameric （5）	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 4
Molecular weight formula_weight	16442.6 kDa
EC 编号 ec_number	2.3.2.23
Mutation mutation	C22S/C102S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	9327

MSSSKRIAKELSDLERDPPTSSSAGPVGDDLYHWQASIMGPADSPYAGGVFFLSIHFPTDYPFKPPKISFTTKIYHPNINANGNICLDILKDQWSPALTLSKVLLSISSLLTDANPDDPLVPEIAHIYKTDRPKYEATAREWTKKYAV

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Polyubiquitin-C
Molecular weight formula_weight	8665.9 kDa
Mutation mutation	K48C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGCQLEDGRTLSDYNIQKESTLHLVLRLRGGD

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 polymer

Description description	Polyubiquitin-C
Molecular weight formula_weight	8604.8 kDa
Mutation mutation	K29R
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MQIFVKTLTGKTITLEVEPSDTIENVKARIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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 4 Entity 4 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8576.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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 5 Entity 5 polymer

Description description	E4 ubiquitin-protein ligase UFD2
Molecular weight formula_weight	110044.5 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MTAIEDILQITTDPSDTRGYSLLKSEEVPQGSTLGVDFIDTLLLYQLTENEKLDKPFEYLNDCFRRNQQQKRITKNKPNAESLHSTFQEIDRLVIGYGVVALQIENFCMNGAFINYITGIVSNVNSYTDFLSQIIQRAILEGTALDLLNAVFPTLLEYCNKHVSHFDLNESVIYNNVLTIFELFVTFKPIAEIFTKIDGFFADYSCKPQDFERKTILGPILSLSPIEAAVAIRNYGDNLLRSKQQTAMIHESLQAEHKVVIDRLFFIVDKLVRGSLNSRTDMISYFAHIANKNHLRRADHPPFKELSSNGFMSNITLLLVRFSQPFLDISYKKIDKIDANYFNNPSLFIDLSGETRLNSDFKEADAFYDKNRKTADSKPNFISDCFFLTLTYLHYGLGGTLSFEEKMGSEIKALKEEIEKVKKIAANHDVFARFITAQLSKMEKALKTTESLRFALQGFFAHRSLQLEVFDFICGASTFLIRVVDPEHEFPFKQIKLPLIPDQIGVENVDNADFLRAHAPVPFKYYPEFVVEGPVNYSLYISKYQTSPIFRNPRLGSFVEFTTMVLRCPELVSNPHLKGKLVQLLSVGAMPLTDNSPGFMMDIFEHDELVNKNLLYALLDFYVIVEKTGSSSQFYDKFNSRYSISIILEELYYKIPSYKNQLIWQSQNNADFFVRFVARMLNDLTFLLDEGLSNLAEVHNIQNELDNRARGAPPTREEEDKELQTRLASASRQAKSSCGLADKSMKLFEIYSKDIPAAFVTPEIVYRLASMLNYNLESLVGPKCGELKVKDPQSYSFNPKDLLKALTTVYINLSEQSEFISAVAKDERSFNRNLFVRAVDILGRKTGLASPEFIEKLLNFANKAEEQRKADEEEDLEYGDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTPNEELRQKILCFKKQKKEEAKHKASE

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Resolution resolution	4.140 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	4.14 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	347924

Cryo-EM structure of Ufd2/Ubc4-ub complex with K29triUb(monomeric conformation)

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

Ubiquitin-conjugating enzyme E2 4

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-C

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

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

E4 ubiquitin-protein ligase UFD2

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

9m7o__assembly_1__model_1

9m7o__assembly_1__model_1 | I(q)

9m7o__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

7. Citations (1)