SAXSdb — 4jhk

▼

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	Sb:cb157 protein × 2 （Q7SXI8） SULFATE ION × 4 water × 4	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

Sb:cb157 protein

Danio rerio

UniProt Q7SXI8

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） SULFATE ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7SXI8_DANRE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 6–22； UniProt 89–105

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	4jhk
Deposition date deposition_date	2013-03-05
Structure title title	Crystal structure of Danio rerio SLIP1 in complex with SLBP
Keywords keywords	;MRNA EXPORT, MRNA TRANSPORT, RNA BINDING, HISTONE MRNA PROCESSING, TRANSLATION, 3'-UTR, 3'-PROCESSING, SLBP, U7 snRNP, stem loop RNA ;; TRANSLATION
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.

4jhk__assembly_1__model_1

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

Download this curve (.dat)

4jhk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4jhk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.10 Å
Rg (electron density)	30.86 Å
Total Rg	31.43 Å
Atom count	3836
Residues	468
Excluded volume	68343 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4jhk__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 (4)

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1992

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	Sb:cb157 protein
Molecular weight formula_weight	2595.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

PLGSMSRIKNWGDEVEEQEMRT

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 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 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	61

▼

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4jhkA00
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 —

▶

Unit-cell length a length_a	70.650 Å
Unit-cell length b length_b	70.650 Å
Unit-cell length c length_c	242.550 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 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.507 Å
Low-resolution limit resolution_low	43.069 Å
R factor r_factor	0.1948
R_work r_work	0.1924
R_free r_free	0.2432

Crystal structure of Danio rerio SLIP1 in complex with SLBP

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

Sb:cb157 protein

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

4jhk__assembly_1__model_1

4jhk__assembly_1__model_1 | I(q)

4jhk__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of Danio rerio SLIP1 in complex with SLBP

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

Sb:cb157 protein

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

4jhk__assembly_1__model_1

4jhk__assembly_1__model_1 | I(q)

4jhk__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)