SAXSdb — 2xgj

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

ATP-DEPENDENT RNA HELICASE DOB1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 1	;RNA (5'-(APAPAPAP*A)-3') ; × 1 ADENOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 1	;RNA (5'-(APAPAPAP*A)-3') ; × 1 ADENOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTR4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 18–1010； UniProt 81–1073 Author chain B； PDBConstruct 18–1010； UniProt 81–1073

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	2xgj
Deposition date deposition_date	2010-06-04
Structure title title	Structure of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance
Keywords keywords	HYDROLASE-RNA COMPLEX, HYDROLASE, TRAMP, EXOSOME, DEAD, NUCLEOTIDE-BINDING; HYDROLASE/RNA
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.

2xgj__assembly_1__model_1

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

Download this curve (.dat)

2xgj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2xgj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.99 Å
Rg (electron density)	32.24 Å
Total Rg	32.87 Å
Atom count	7647
Residues	969
Excluded volume	136400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2xgj__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2xgj__assembly_2__model_1`	dimeric （2）	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	ATP-DEPENDENT RNA HELICASE DOB1
Molecular weight formula_weight	115203.6 kDa
EC 编号 ec_number	3.6.4.13, 3.6.1.-
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	13889

HHHHHHENLYFQGAASMLADSFEQEASREVDASKGLTNSETLQVEQDGKVRLSHQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLGYNMILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRINKRNPSAVYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKKIDVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISESQAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIVSAGSLYL

Entity 2 Entity 2 polymer

Description description	;RNA (5'-(APAPAPAP*A)-3') ;
Molecular weight formula_weight	1601.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C,D

AAAAA

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	81

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6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id	2xgjA01
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	2xgjA02
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	2xgjA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3380 — Sec63 N-terminal domain-like fold
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	2xgjA04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1500 — YheA-like fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2xgjA05
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	2xgjB01
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	2xgjB02
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	2xgjB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3380 — Sec63 N-terminal domain-like fold
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	2xgjB04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1500 — YheA-like fold
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	100.110 Å
Unit-cell length b length_b	126.019 Å
Unit-cell length c length_c	102.272 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.21 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	53.453 Å
R factor r_factor	0.2030
R_work r_work	0.2005
R_free r_free	0.2474

Structure of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance

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

ATP-DEPENDENT RNA HELICASE DOB1

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

2xgj__assembly_1__model_1

2xgj__assembly_1__model_1 | I(q)

2xgj__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)

Structure of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance

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

ATP-DEPENDENT RNA HELICASE DOB1

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

2xgj__assembly_1__model_1

2xgj__assembly_1__model_1 | I(q)

2xgj__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)