SAXSdb — 6vjz

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

Degradation in the endoplasmic reticulum protein 1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	ERAD-associated E3 ubiquitin-protein ligase HRD1 × 1 （Q08109） ERAD-associated E3 ubiquitin-protein ligase component HRD3 × 1 （Q05787） U1 SNP1-associating protein 1 × 1 （Q03714）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DER1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–211； UniProt 1–211

ERAD-associated E3 ubiquitin-protein ligase HRD1

Saccharomyces cerevisiae

UniProt Q08109

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Degradation in the endoplasmic reticulum protein 1 × 1 （P38307） ERAD-associated E3 ubiquitin-protein ligase component HRD3 × 1 （Q05787） U1 SNP1-associating protein 1 × 1 （Q03714）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HRD1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–480； UniProt 1–480

ERAD-associated E3 ubiquitin-protein ligase component HRD3

Saccharomyces cerevisiae

UniProt Q05787

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Degradation in the endoplasmic reticulum protein 1 × 1 （P38307） ERAD-associated E3 ubiquitin-protein ligase HRD1 × 1 （Q08109） U1 SNP1-associating protein 1 × 1 （Q03714）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HRD3_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–767； UniProt 1–767

U1 SNP1-associating protein 1

Saccharomyces cerevisiae

UniProt Q03714

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Degradation in the endoplasmic reticulum protein 1 × 1 （P38307） ERAD-associated E3 ubiquitin-protein ligase HRD1 × 1 （Q08109） ERAD-associated E3 ubiquitin-protein ligase component HRD3 × 1 （Q05787）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	USA1_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–339； UniProt 500–838

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	6vjz
Deposition date deposition_date	2020-01-18
Structure title title	CryoEM structure of Hrd1-Usa1/Der1/Hrd3 complex of the expected topology
Keywords keywords	retro-translocation, ERAD, protein degradation, ubiquitination, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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.

6vjz__assembly_1__model_1

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

Download this curve (.dat)

6vjz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6vjz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.41 Å
Rg (electron density)	42.18 Å
Total Rg	42.41 Å
Atom count	8996
Residues	1093
Excluded volume	162270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6vjz__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	Degradation in the endoplasmic reticulum protein 1
Molecular weight formula_weight	24411.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	8996

MDAVILNLLGDIPLVTRLWTIGCLVLSGLTSLRIVDPGKVVYSYDLVFKKGQYGRLLYSIFDYGAFNWISMINIFVSANHLSTLENSFNLRRKFCWIIFLLLVILVKMTSIEQPAASLGVLLHENLVYYELKKNGNQMNVRFFGAIDVSPSIFPIYMNAVMYFVYKRSWLEIAMNFMPGHVIYYMDDIIGKIYGIDLCKSPYDWFRNTETP

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	ERAD-associated E3 ubiquitin-protein ligase HRD1
Molecular weight formula_weight	55638.8 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	B

MVPENRRKQLAIFVVVTYLLTFYCVYSATKTSVSFLQVTLKLNEGFNLMVLSIFILLNSTLLWQLLTKLLFGELRLIEHEHIFERLPFTIINTLFMSSLFHERYFFTVAFFGLLLLYLKVFHWILKDRLEALLQSINDSTTMKTLIFSRFSFNLVLLAVVDYQIITRCISSIYTNQKSDIESTSLYLIQVMEFTMLLIDLLNLFLQTCLNFWEFYRSQQSLSNENNHIVHGDPTDENTVESDQSQPVLNDDDDDDDDDRQFTGLEGKFMYEKAIDVFTRFLKTALHLSMLIPFRMPMMLLKDVVWDILALYQSGTSLWKIWRNNKQLDDTLVTVTVEQLQNSANDDNICIICMDELIHSPNQQTWKNKNKKPKRLPCGHILHLSCLKNWMERSQTCPICRLPVFDEKGNVVQTTFTSNSDITTQTTVTDSTGIATDQQGFANEVDLLPTRTTSPDIRIVPTQNIDTLAMRTRSTSTPSPT

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Saccharomyces cerevisiae

Entity 3 Entity 3 polymer

Description description	ERAD-associated E3 ubiquitin-protein ligase component HRD3
Molecular weight formula_weight	88239.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MITLLLYLCVICNAIVLIRADSIADPWPEARHLLNTIAKSRDPMKEAAMEPNADEFVGFYVPMDYSPRNEEKNYQSIWQNEITDSQRHIYELLVQSSEQFNNSEATYTLSQIHLWSQYNFPHNMTLAHKYLEKFNDLTHFTNHSAIFDLAVMYATGGCASGNDQTVIPQDSAKALLYYQRAAQLGNLKAKQVLAYKYYSGFNVPRNFHKSLVLYRDIAEQLRKSYSRDEWDIVFPYWESYNVRISDFESGLLGKGLNSVPSSTVRKRTTRPDIGSPFIAQVNGVQMTLQIEPMGRFAFNGNDGNINGDEDDEDASERRIIRIYYAALNDYKGTYSQSRNCERAKNLLELTYKEFQPHVDNLDPLQVFYYVRCLQLLGHMYFTGEGSSKPNIHMAEEILTTSLEISRRAQGPIGRACIDLGLINQYITNNISQAISYYMKAMKTQANNGIVEFQLSKLATSFPEEKIGDPFNLMETAYLNGFIPAIYEFAVMIESGMNSKSSVENTAYLFKTFVDKNEAIMAPKLRTAFAALINDRSEVALWAYSQLAEQGYETAQVSAAYLMYQLPYEFEDPPRTTDQRKTLAISYYTRAFKQGNIDAGVVAGDIYFQMQNYSKAMALYQGAALKYSIQAIWNLGYMHEHGLGVNRDFHLAKRYYDQVSEHDHRFYLASKLSVLKLHLKSWLTWITREKVNYWKPSSPLNPNEDTQHSKTSWYKQLTKILQRMRHKEDSDKAAEDSHKHRTVVQNGANHRGDDQEEASEILGFQMED

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Saccharomyces cerevisiae

Entity 4 Entity 4 polymer

Description description	U1 SNP1-associating protein 1
Molecular weight formula_weight	39944.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

VRAADNTSSANDNNTVENDESAWNRRVVRPLRNSFPLLLVLIRTFYLIGYNSLVPFFIILEFGSFLPWKYIILLSLLFIFRTVWNTQEVWNLWRDYLHLNEIDEVKFSQIKEFINSNSLTLNFYKKCKDTQSAIDLLMIPNLHEQRLSVYSKYDIEYDTNTPDVGQLNLLFIKVLSGEIPKDALDELFKEFFELYETTRNMNTLYPQDSLNELLLMIWKESQKKDINTLPKYRRWFQTLCSQIAEHNVLDVVLRYIIPDPVNDRVITAVIKNFVLFWVTLLPYVKEKLDDIVAQRARDREQPAPSAQQQENEDEALIIPDEEEPTATGAQPHLYIPDED

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Saccharomyces cerevisiae

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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	4.30 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	172291

CryoEM structure of Hrd1-Usa1/Der1/Hrd3 complex of the expected topology

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

Degradation in the endoplasmic reticulum protein 1

State in the Current Structure

Other States of the Same Protein in the Database

ERAD-associated E3 ubiquitin-protein ligase HRD1

State in the Current Structure

Other States of the Same Protein in the Database

ERAD-associated E3 ubiquitin-protein ligase component HRD3

State in the Current Structure

Other States of the Same Protein in the Database

U1 SNP1-associating protein 1

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

6vjz__assembly_1__model_1

6vjz__assembly_1__model_1 | I(q)

6vjz__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

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 polymer

Polymer Polymer

Source Source

7. Citations (1)

CryoEM structure of Hrd1-Usa1/Der1/Hrd3 complex of the expected topology

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

Degradation in the endoplasmic reticulum protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ERAD-associated E3 ubiquitin-protein ligase HRD1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ERAD-associated E3 ubiquitin-protein ligase component HRD3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

U1 SNP1-associating protein 1

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

6vjz__assembly_1__model_1

6vjz__assembly_1__model_1 | I(q)

6vjz__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

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 polymer

Polymer Polymer

Source Source

7. Citations (1)