SAXSdb — 5bw8

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

ATPase GET3

Saccharomyces cerevisiae (strain RM11-1a)

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GET3_YEAS1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–373； UniProt 2–354 Author chain B； PDBConstruct 21–373； UniProt 2–354

Golgi to ER traffic protein 4

Saccharomyces cerevisiae (strain ATCC 204508 / 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 5	ATPase GET3 × 2 （B3LGZ3） Ubiquitin-like protein MDY2 × 1 （Q12285） Unknown Protein × 1 ZINC ION × 1	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	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–290； UniProt 1–290

Ubiquitin-like protein MDY2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q12285

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	ATPase GET3 × 2 （B3LGZ3） Golgi to ER traffic protein 4 × 1 （Q12125） Unknown Protein × 1 ZINC ION × 1	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	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–54； UniProt 1–54

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	5bw8
Deposition date deposition_date	2015-06-06
Structure title title	2.8 A crystal structure of a Get3-Get4-Get5 intermediate complex from S.cerevisiae
Keywords keywords	Tail-anchored targeting, ATPase, electrostatic interaction, Hydrolase-Transport complex; Hydrolase/Transport
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.

5bw8__assembly_1__model_1

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

Download this curve (.dat)

5bw8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5bw8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.87 Å
Rg (electron density)	38.74 Å
Total Rg	38.89 Å
Atom count	7742
Residues	971
Excluded volume	138420 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5bw8__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	ATPase GET3
Molecular weight formula_weight	41576.8 kDa
EC 编号 ec_number	3.6.-.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7742

MGGSHHHHHHGENLYFQSVDDLTVEPNLHSLITSTTHKWIFVGGKGGVGKTTSSCSIAIQMALSQPNKQFLLISTDPAHNLSDAFGEKFGKDARKVTGMNNLSCMEIDPSAALKDMNDMAVSRANNNGSDGQGDDLGSLLQGGALADLTGSIPGIDEALSFMEVMKHIKRQEQGEGETFDTVIFDTAPTGHTLRFLQLPNTLSKLLEKFGEITNKLGPMLNSFMGAGNVDISGKLNELKANVETIRQQFTDPDLTTFVCVCISEFLSLYETERLIQELISYDMDVNSIIVNQLLFAENDQEHNCKRCQARWKMQKKYLDQIDELYEDFHVVKMPLCAGEIRGLNNLTKFSQFLNKEYNPITDGKVIYELEDKE

Source Source

Source organism organism	Saccharomyces cerevisiae (strain RM11-1a)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	285006
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Golgi to ER traffic protein 4
Molecular weight formula_weight	35803.2 kDa
Mutation mutation	K258A, K260A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MVPAESNAVQAKLAKTLQRFENKIKAGDYYEAHQTLRTIANRYVRSKSYEHAIELISQGALSFLKAKQGGSGTDLIFYLLEVYDLAEVKVDDISVARLVRLIAELDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEAERYFMLGTHDSMIKYVDLLWDWLCQVDDIEDSTVAEFFSRLVFNYLFISNISFAHESKDIFLERFIEKFHPKYEKIDKNGYEIVFFEDYSDLNFLQLLLITCQTADASYFLNLKNHYLDFSQAYKSELEFLGQEYFNENLYFQSLEHHHHHH

Source Source

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

Entity 3 Entity 3 polymer

Description description	Ubiquitin-like protein MDY2
Molecular weight formula_weight	6034.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MSTSASGPEHEFVSKFLTLATLTEPKLPKSYTKPLKDVTNLGVPLPTLKYKYKQ

Source Source

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

Entity 4 Entity 4 polymer

Description description	Unknown Protein
Molecular weight formula_weight	1124.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z

XXXXXXXXXXXXX

Source Source

Source organism organism	Saccharomyces cerevisiae
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

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

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	5bw8A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5bw8B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5bw8C00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

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Unit-cell length a length_a	111.960 Å
Unit-cell length b length_b	238.050 Å
Unit-cell length c length_c	52.190 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	29.800 Å
R factor r_factor	0.2259
R_work r_work	0.2240
R_free r_free	0.2616

2.8 A crystal structure of a Get3-Get4-Get5 intermediate complex from S.cerevisiae

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

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

Ubiquitin-like protein MDY2

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

5bw8__assembly_1__model_1

5bw8__assembly_1__model_1 | I(q)

5bw8__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 (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 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

2.8 A crystal structure of a Get3-Get4-Get5 intermediate complex from S.cerevisiae

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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5bw8__assembly_1__model_1

5bw8__assembly_1__model_1 | I(q)

5bw8__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 (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 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)