SAXSdb — 9ns5

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

Ubiquitin-like protein MDY2

Saccharomyces cerevisiae S288C

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	ATPase GET3 × 2 （Q12154） Golgi to ER traffic protein 4 × 2 （Q12125） ZINC ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MDY2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–212； UniProt 1–212 Author chain F； PDBConstruct 1–212； UniProt 1–212

ATPase GET3

Saccharomyces cerevisiae S288C

UniProt Q12154

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Ubiquitin-like protein MDY2 × 2 （Q12285） Golgi to ER traffic protein 4 × 2 （Q12125） ZINC ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GET3_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 23–376； UniProt 1–354 Author chain D； PDBConstruct 23–376； UniProt 1–354

Golgi to ER traffic protein 4

Saccharomyces cerevisiae S288C

UniProt Q12125

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Ubiquitin-like protein MDY2 × 2 （Q12285） ATPase GET3 × 2 （Q12154） ZINC ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GET4_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–312； UniProt 1–312 Author chain E； PDBConstruct 1–312； UniProt 1–312

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	9ns5
Deposition date deposition_date	2025-03-15
Structure title title	Get3(D57N)-Get4/5 Complex (ATP-bound)
Keywords keywords	membrane protein targeting, ATPase, chaperone, protein complex; CHAPERONE
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.

9ns5__assembly_1__model_1

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

Download this curve (.dat)

9ns5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ns5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.97 Å
Rg (electron density)	40.34 Å
Total Rg	40.26 Å
Atom count	10901
Residues	1344
Excluded volume	195130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ns5__assembly_1__model_1`	hexameric （6）	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 (6)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-like protein MDY2
Molecular weight formula_weight	23768.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F
Atom count atom_count	10901

MSTSASGPEHEFVSKFLTLATLTEPKLPKSYTKPLKDVTNLGVPLPTLKYKYKQNRAKKLKLHQDQQGQDNAAVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKPNPTISKEPEAEKSTNSPAPAPPQELTVPWDDIEALLKNNFENDQAAVRQVMERLQKGWSLAK

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	ATPase GET3
Molecular weight formula_weight	41936.3 kDa
EC 编号 ec_number	3.6.-.-
Mutation mutation	D57N
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D

MGSSHHHHHHSSGENLYFQGHMMDLTVEPNLHSLITSTTHKWIFVGGKGGVGKTTSSCSIAIQMALSQPNKQFLLISTNPAHNLSDAFGEKFGKDARKVTGMNNLSCMEIDPSAALKDMNDMAVSRANNNGSDGQGDDLGSLLQGGALADLTGSIPGIDEALSFMEVMKHIKRQEQGEGETFDTVIFDTAPTGHTLRFLQLPNTLSKLLEKFGEITNKLGPMLNSFMGAGNVDISGKLNELKANVETIRQQFTDPDLTTFVCVCISEFLSLYETERLIQELISYDMDVNSIIVNQLLFAENDQEHNCKRCQARWKMQKKYLDQIDELYEDFHVVKMPLCAGEIRGLNNLTKFSQFLNKEYNPITDGKVIYELEDKE

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Golgi to ER traffic protein 4
Molecular weight formula_weight	38604.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MVPAESNAVQAKLAKTLQRFENKIKAGDYYEAHQTLRTIANRYVRSKSYEHAIELISQGALSFLKAKQGGSGTDLIFYLLEVYDLAEVKVDDISVARLVRLIAELDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEAERYFMLGTHDSMIKYVDLLWDWLCQVDDIEDSTVAEFFSRLVFNYLFISNISFAHESKDIFLERFIEKFHPKYEKIDKNGYEIVFFEDYSDLNFLQLLLITCQTKDKSYFLNLKNHYLDFSQAYKSELEFLGQEYFNIVAPKQTNFLQDMMSGFLGGSKSGGGGGENLYFQGGSSHHHHHH

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

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Resolution resolution	3.190 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.19 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	149868

Get3(D57N)-Get4/5 Complex (ATP-bound)

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

Ubiquitin-like protein MDY2

State in the Current Structure

Other States of the Same Protein in the Database

ATPase GET3

State in the Current Structure

Other States of the Same Protein in the Database

Golgi to ER traffic protein 4

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

9ns5__assembly_1__model_1

9ns5__assembly_1__model_1 | I(q)

9ns5__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)

Get3(D57N)-Get4/5 Complex (ATP-bound)

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

Ubiquitin-like protein MDY2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATPase GET3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Golgi to ER traffic protein 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9ns5__assembly_1__model_1

9ns5__assembly_1__model_1 | I(q)

9ns5__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)