SAXSdb — 6y3z

▼

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

m7GpppN-mRNA hydrolase

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 4	mRNA-decapping enzyme subunit 1 × 1 （Q12517） Enhancer of mRNA-decapping protein 3 × 1 （P39998） Probable tubulin--tyrosine ligase PBY1 × 1 （P38254） MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCP2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–271； UniProt 1–271

mRNA-decapping enzyme subunit 1

Saccharomyces cerevisiae S288C

UniProt Q12517

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	m7GpppN-mRNA hydrolase × 1 （P53550） Enhancer of mRNA-decapping protein 3 × 1 （P39998） Probable tubulin--tyrosine ligase PBY1 × 1 （P38254） MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCP1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–236； UniProt 1–231

Enhancer of mRNA-decapping protein 3

Saccharomyces cerevisiae S288C

UniProt P39998

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	m7GpppN-mRNA hydrolase × 1 （P53550） mRNA-decapping enzyme subunit 1 × 1 （Q12517） Probable tubulin--tyrosine ligase PBY1 × 1 （P38254） MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EDC3_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 6–71； UniProt 1–66

Probable tubulin--tyrosine ligase PBY1

Saccharomyces cerevisiae S288C

UniProt P38254

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	m7GpppN-mRNA hydrolase × 1 （P53550） mRNA-decapping enzyme subunit 1 × 1 （Q12517） Enhancer of mRNA-decapping protein 3 × 1 （P39998） MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TTL_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain P； PDBConstruct 6–429； UniProt 330–753

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6y3z
Deposition date deposition_date	2020-02-19
Structure title title	Crystal structure of the Pby1 ATP-grasp enzyme bound to the S. cerevisiae mRNA decapping complex (Dcp1-Dcp2-Edc3)
Keywords keywords	RNA decay enzyme, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6y3z__assembly_1__model_1

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

Download this curve (.dat)

6y3z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6y3z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.09 Å
Rg (electron density)	31.58 Å
Total Rg	32.26 Å
Atom count	5570
Residues	672
Excluded volume	99830 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6y3z__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	m7GpppN-mRNA hydrolase
Molecular weight formula_weight	32946.9 kDa
EC 编号 ec_number	3.6.1.62
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	5570

MSLPLRHALENVTSVDRILEDLLVRFIINCPNEDLSSVERELFHFEEASWFYTDFIKLMNPTLPSLKIKSFAQLIIKLCPLVWKWDIRVDEALQQFSKYKKSIPVRGAAIFNENLSKILLVQGTESDSWSFPRGKISKDENDIDCCIREVKEEIGFDLTDYIDDNQFIERNIQGKNYKIFLISGVSEVFNFKPQVRNEIDKIEWFDFKKISKTMYKSNIKYYLINSMMRPLSMWLRHQRQIKNEDQLKSYAEEQLKLLLGITKEEQIDPGRHHHHHH

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	mRNA-decapping enzyme subunit 1
Molecular weight formula_weight	26705.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPLGSMTGAATAAENSATQLEFYRKALNFNVIGRYDPKIKQLLFHTPHASLYKWDFKKDEWNKLEYQGVLAIYLRDVSQNTNLLPVSPQEVDIFDSQNGSNNIQVNNGSDNSNRNSSGNGNSYKSNDSLTYNCGKTLSGKDIYNYGLIILNRINPDNFSMGIVPNSVVNKRKVFNAEEDTLNPLECMGVEVKDELVIIKNLKHEVYGIWIHTVSDRQNIYELIKYLLENEPKDSFA

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 Entity 3 polymer

Description description	Enhancer of mRNA-decapping protein 3
Molecular weight formula_weight	7448.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GPLGSMSQFVGFGVQVELKDGKLIQGKIAKATSKGLTLNDVQFGDGGKSQAFKVRASRLKDLKVLTVASQS

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 4 Entity 4 polymer

Description description	Probable tubulin--tyrosine ligase PBY1
Molecular weight formula_weight	49895.7 kDa
EC 编号 ec_number	6.3.2.25
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

GPLGSSKTNNLIVVSIDPMEYIYKPLTHALKKYLPQVEIVSNLPEFDNGGCEKEMKVFHYGDYEQLDMDKLMELPNNYFTNSYIYRKALIRKHFLSHTIQTYTAKNPESILKKAYLESFTIDLDYAEFLDDALDENWELRQELENESQDKWWIVKPSMSDKGQGIRVFKTIEDLQAIFDSFDDEDSEAEESGNDDDADDVNGEFMDNNKVNISQLRHFIIQEYLTNPLLLASMDNRKFHIRCYVVCRGDLQVFVYDRMLALFAAKPFVPLDPYAYSVTDLKDLECHLTNTCLQSKKKDKDSSVLEFDSIEEIPNERKSNIKEQIHSITNDVFLAAVNVNRLNFQPLPNAFETYGVDFLIDSNYEVKLLEINAFPDFKQTGKDLKNLIDELFDDTVKYCVTPIFNENRNKTDDETDPNFVKVIDYTSNGW

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6y3zA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1050 — Dcp2, box A domain

Domain ID domain_id	6y3zA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

▶

Unit-cell length a length_a	71.210 Å
Unit-cell length b length_b	90.600 Å
Unit-cell length c length_c	194.240 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.490 Å
Low-resolution limit resolution_low	48.500 Å
R factor r_factor	0.2500
R_work r_work	0.2460
R_free r_free	0.3210

Crystal structure of the Pby1 ATP-grasp enzyme bound to the S. cerevisiae mRNA decapping complex (Dcp1-Dcp2-Edc3)

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

m7GpppN-mRNA hydrolase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

mRNA-decapping enzyme subunit 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

Enhancer of mRNA-decapping protein 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Probable tubulin--tyrosine ligase PBY1

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

6y3z__assembly_1__model_1

6y3z__assembly_1__model_1 | I(q)

6y3z__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)