SAXSdb — 4jhj

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

MIF4G domain-containing protein B

Danio rerio

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 19 (DBP5 homolog, yeast) × 2 （Q7ZU28） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 19 (DBP5 homolog, yeast) × 2 （Q7ZU28） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	M4GDB_DANRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–222； UniProt 1–222 Author chain B； PDBConstruct 1–222； UniProt 1–222

DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 19 (DBP5 homolog, yeast)

Danio rerio

UniProt Q7ZU28

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	MIF4G domain-containing protein B × 2 （Q5EAQ1） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	MIF4G domain-containing protein B × 2 （Q5EAQ1） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7ZU28_DANRE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–32； UniProt 1–32 Author chain D； PDBConstruct 1–32； UniProt 1–32

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	4jhj
Deposition date deposition_date	2013-03-05
Structure title title	Crystal structure of Danio rerio Slip1 in complex with Dbp5
Keywords keywords	;DEAD-BOX HELICASE, MRNA EXPORT, RECA-LIKE, RNA-DEPENDENT ATPASE, DDX19, DEAD-BOX PROTEIN 19B, MRNA TRANSPORT, ATP BINDING, HELICASE, HYDROLASE, NUCLEOTIDE BINDING, RNA BINDING, TRANSPORT HISTONE MRNA PROCESSING, TRANSLATION, 3'-UTR, 3'-PROCESSING, NUP214 ;; TRANSLATION
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.

4jhj__assembly_1__model_1

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

Download this curve (.dat)

4jhj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4jhj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.02 Å
Rg (electron density)	30.83 Å
Total Rg	31.30 Å
Atom count	3761
Residues	465
Excluded volume	67021 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4jhj__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4jhj__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	MIF4G domain-containing protein B
Molecular weight formula_weight	25794.5 kDa
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	3772

MENSSKEDYKIQSFDLETQKLLKTALKDPGSVDLEKVSSVIVDQSLKDQVFSREAGRICYTIVQAEAKQTNGSVFRRNLLNRLQQEFKAREETRKRSTQEWVCLVSFICNIFDYLKVNNMPMVALVHPVYDCLFRLAQSDALKNEEEVDCLVLQLHRIGDQLEKMNVQLMDELFNLLRDGFLLQEDLSSMGRLLLLEILEFRAGGWKLSDTAQKYYYSEVTD

Source Source

Source organism organism	Danio rerio
Common name common_name	leopard danio,zebra danio,zebra fish
NCBI taxonomy ID ncbi_taxonomy_id	7955
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 19 (DBP5 homolog, yeast)
Molecular weight formula_weight	3495.7 kDa
EC 编号 ec_number	3.6.1.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MATDSWAQAVDEQEAAAESISTLQISEKEEKP

Source Source

Source organism organism	Danio rerio
Common name common_name	leopard danio,zebra danio,zebra fish
NCBI taxonomy ID ncbi_taxonomy_id	7955
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	11

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4jhjA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	180 —

Domain ID domain_id	4jhjB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	180 —

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Unit-cell length a length_a	85.185 Å
Unit-cell length b length_b	85.185 Å
Unit-cell length c length_c	258.266 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	3.250 Å
Low-resolution limit resolution_low	73.770 Å
R factor r_factor	0.2450
R_work r_work	0.2440
R_free r_free	0.2770

Crystal structure of Danio rerio Slip1 in complex with Dbp5

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

MIF4G domain-containing protein B

State in the Current Structure

Other States of the Same Protein in the Database

DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 19 (DBP5 homolog, yeast)

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

4jhj__assembly_1__model_1

4jhj__assembly_1__model_1 | I(q)

4jhj__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Danio rerio Slip1 in complex with Dbp5

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

MIF4G domain-containing protein B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 19 (DBP5 homolog, yeast)

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

4jhj__assembly_1__model_1

4jhj__assembly_1__model_1 | I(q)

4jhj__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)