SAXSdb — 9qgr

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

BIR repeat containing ubiquitin-conjugating enzyme, isoform B

Drosophila melanogaster

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	E1 ubiquitin-activating enzyme × 1 （Q8T0L3） Polyubiquitin-C × 2 （P0CG48） ADENOSINE MONOPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0B4KG50_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–305； UniProt 4577–4879

E1 ubiquitin-activating enzyme

Drosophila melanogaster

UniProt Q8T0L3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	BIR repeat containing ubiquitin-conjugating enzyme, isoform B × 1 （A0A0B4KG50） Polyubiquitin-C × 2 （P0CG48） ADENOSINE MONOPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8T0L3_DROME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–1010； UniProt 184–1191

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 4	BIR repeat containing ubiquitin-conjugating enzyme, isoform B × 1 （A0A0B4KG50） E1 ubiquitin-activating enzyme × 1 （Q8T0L3） ADENOSINE MONOPHOSPHATE × 1	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	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–76； UniProt 1–76 Author chain E； 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	9qgr
Deposition date deposition_date	2025-03-14
Structure title title	Structure of dUBA1-UbDha-dBIRC6 trapped ternary complex (Cluster 4)
Keywords keywords	Ubiquitin, E1, E2, Ligase, SIGNALING PROTEIN; 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.

9qgr__assembly_1__model_1

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

Download this curve (.dat)

9qgr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9qgr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.19 Å
Rg (electron density)	35.35 Å
Total Rg	35.88 Å
Atom count	11311
Residues	1422
Excluded volume	201560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9qgr__assembly_1__model_1`	tetrameric （4）	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	BIR repeat containing ubiquitin-conjugating enzyme, isoform B
Molecular weight formula_weight	35565.3 kDa
EC 编号 ec_number	2.3.2.23
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	11311

GPEPQSKSIEQRYLELMKKRQFDTFDMIVESDNNSFRFVVSHHFEKMVRLAGDRYHPSRVKRLAQEAVTLSTSLPLSFSSSVFVRCDTDRLDIMKVLITGPADTPYANGCFEFDVFFPPDYPNQPMLINLETTGRHSVRFNPNLYNDGKVCLSVLNTWHGRPEEKWNAQTSSFLQVLVSIQSLILVPEPYFNEPGFERSRGSPSGTNSSREYNSNIYQACVRWAMLEQIRSPSQCFKDVIHKHFWLKREEICAQIEGWIEELGKPQYTERASRTISFNSMVLRRHYRHLREELSKLKPPRGLEDL

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	E1 ubiquitin-activating enzyme
Molecular weight formula_weight	112045.2 kDa
EC 编号 ec_number	6.2.1.45
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPMAGNSAAAGGDIDESLYSRQLYVLGHDAMRRMANSDILLSGLGGLGLEIAKNVILGGVKSITLHDTATCGLHDLSSQFYLTEADIGKNRAEASCAQLAELNNYVRTVSHTGPLTEEFLRKFRVVVLTNSDGEEQQRIAKFAHENGIALIIAETRGLFAKVFCDFGESFTIYDQDGTQPISTMIASITHDAQGVVTCLDETRHGFNDGDYVTFSEVQGMQELNGCQPLKITVLGPYTFSIGDTSKFGEYKSGGVATQVKMPKTISFKPLAQATEEPEFLISDFAKLDSPATLHVAFNALSCYRKAHNGALPRPWNEEDANSFLEVVRASSNAEVDEKLVLQFAKICSGNTCPLDAAVGGIVAQEVLKACSGKFTPIYQWLYFDALECLPTEGVEEADAQPVGSRYDSQIAIFGKKFQEKLADSKWFIVGAGAIGCELLKNFGMLGLGTGNGQIFVTDMDLIEKSNLNRQFLFRPHDVQKPKSMTAADAIKRMNPEVNVTAYELRVGAETEKVFSEDFFGKLDGVANALDNVDARIYMDRKCIFNRIPLVETGTLGTLGNVQVIVPFATESYSSSQDPPEKSIPICTLKNFPNAIEHTLQWARDAFEGVFKQSAENAAQYIADPQFTERIAKLPGIQPLEILDSIKKALIDDKPKSFAHCVEWARLYWEDQYVNQIKQLLFNFPPDQITSSGQPFWSGPKRCPDPLVFDVNDPMHLDFIYAAANLRAEVYGIEQVRNRETIAELVQKVKVPEFKPRSGVKIETNEAAAAASANNFDDGELDQDRVDKIISELLKNADKSSKITPLEFEKDDDSNLHMDFIVACSNLRAANYKIPPADRHKSKLIAGKIIPAIATTTSVLSGLAVLEVIKLIVGHRDLVKFKNGFANLALPFMAFSEPLPAAKNTYYGKEWTLWDRFEVTGELSLQEFLNYFEENEKLKITMLSQGVSMLYSFFMPKAKCSERLPLPMSEVVRRVSKRRLEPHERSLVFEICCNDVDGEDVEVPYVRYTLP

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	Polyubiquitin-C
Molecular weight formula_weight	8590.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGA

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	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	1

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Resolution resolution	3.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	20475

Structure of dUBA1-UbDha-dBIRC6 trapped ternary complex (Cluster 4)

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

BIR repeat containing ubiquitin-conjugating enzyme, isoform B

State in the Current Structure

Other States of the Same Protein in the Database

E1 ubiquitin-activating enzyme

State in the Current Structure

Other States of the Same Protein in the Database

Polyubiquitin-C

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

9qgr__assembly_1__model_1

9qgr__assembly_1__model_1 | I(q)

9qgr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

7. Citations (1)

Structure of dUBA1-UbDha-dBIRC6 trapped ternary complex (Cluster 4)

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

BIR repeat containing ubiquitin-conjugating enzyme, isoform 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

E1 ubiquitin-activating enzyme

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9qgr__assembly_1__model_1

9qgr__assembly_1__model_1 | I(q)

9qgr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

7. Citations (1)