2j0q

The crystal structure of the Exon Junction Complex at 3.2 A resolution

Method: X-RAY DIFFRACTION

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

ATP-DEPENDENT RNA HELICASE DDX48

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 1	PROTEIN MAGO NASHI HOMOLOG × 1 （P61326） RNA-BINDING PROTEIN 8A × 1 （Q9Y5S9） 5'-R(UPUPUPUPUPUPUPUPUPUPUPUPUPUP*U)-3' × 1 PROTEIN CASC3 × 1 （O15234） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 1	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 4 RNA 1	PROTEIN MAGO NASHI HOMOLOG × 1 （P61326） RNA-BINDING PROTEIN 8A × 1 （Q9Y5S9） 5'-R(UPUPUPUPUPUPUPUPUPUPUPUPUPUP*U)-3' × 1 PROTEIN CASC3 × 1 （O15234） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DDX48_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–410； UniProt 1–410 Author chain B； PDBConstruct 1–410； UniProt 1–410

PROTEIN MAGO NASHI HOMOLOG

HOMO SAPIENS

UniProt P61326

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 1	ATP-DEPENDENT RNA HELICASE DDX48 × 1 （P38919） RNA-BINDING PROTEIN 8A × 1 （Q9Y5S9） 5'-R(UPUPUPUPUPUPUPUPUPUPUPUPUPUP*U)-3' × 1 PROTEIN CASC3 × 1 （O15234） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 1	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 4 RNA 1	ATP-DEPENDENT RNA HELICASE DDX48 × 1 （P38919） RNA-BINDING PROTEIN 8A × 1 （Q9Y5S9） 5'-R(UPUPUPUPUPUPUPUPUPUPUPUPUPUP*U)-3' × 1 PROTEIN CASC3 × 1 （O15234） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MGN_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–146； UniProt 1–146 Author chain F； PDBConstruct 1–146； UniProt 1–146

RNA-BINDING PROTEIN 8A

HOMO SAPIENS

UniProt Q9Y5S9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 1	ATP-DEPENDENT RNA HELICASE DDX48 × 1 （P38919） PROTEIN MAGO NASHI HOMOLOG × 1 （P61326） 5'-R(UPUPUPUPUPUPUPUPUPUPUPUPUPUP*U)-3' × 1 PROTEIN CASC3 × 1 （O15234） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 1	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 4 RNA 1	ATP-DEPENDENT RNA HELICASE DDX48 × 1 （P38919） PROTEIN MAGO NASHI HOMOLOG × 1 （P61326） 5'-R(UPUPUPUPUPUPUPUPUPUPUPUPUPUP*U)-3' × 1 PROTEIN CASC3 × 1 （O15234） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBM8A_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–109； UniProt 66–174 Author chain G； PDBConstruct 1–109； UniProt 66–174

PROTEIN CASC3

HOMO SAPIENS

UniProt O15234

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 1	ATP-DEPENDENT RNA HELICASE DDX48 × 1 （P38919） PROTEIN MAGO NASHI HOMOLOG × 1 （P61326） RNA-BINDING PROTEIN 8A × 1 （Q9Y5S9） 5'-R(UPUPUPUPUPUPUPUPUPUPUPUPUPUP*U)-3' × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 1	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 4 RNA 1	ATP-DEPENDENT RNA HELICASE DDX48 × 1 （P38919） PROTEIN MAGO NASHI HOMOLOG × 1 （P61326） RNA-BINDING PROTEIN 8A × 1 （Q9Y5S9） 5'-R(UPUPUPUPUPUPUPUPUPUPUPUPUPUP*U)-3' × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CASC3_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain I； PDBConstruct 1–150； UniProt 137–286 Author chain T； PDBConstruct 1–150； UniProt 137–286

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	2j0q
Deposition date deposition_date	2006-08-04
Structure title title	The crystal structure of the Exon Junction Complex at 3.2 A resolution
Keywords keywords	HYDROLASE, MRNA PROCESSING, MRNA SPLICING, MRNA TRANSPORT, NUCLEAR PROTEIN, DEAD-BOX HELICASE, RNA-BINDING; HYDROLASE
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.

2j0q__assembly_1__model_1

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

Download this curve (.dat)

2j0q__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2j0q__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.96 Å
Rg (electron density)	26.96 Å
Total Rg	27.62 Å
Atom count	5630
Residues	693
Excluded volume	99480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2j0q__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2j0q__assembly_2__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 (8)

Entity 1 Entity 1 polymer

Description description	ATP-DEPENDENT RNA HELICASE DDX48
Molecular weight formula_weight	46799.8 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	11226

ATTATMATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	PROTEIN MAGO NASHI HOMOLOG
Molecular weight formula_weight	17189.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MESDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIGLHFKIKPI

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 polymer

Description description	RNA-BINDING PROTEIN 8A
Molecular weight formula_weight	12701.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSPDRRRR

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 4 Entity 4 polymer

Description description	5'-R(UPUPUPUPUPUPUPUPUPUPUPUPUPUP*U)-3'
Molecular weight formula_weight	4547.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E,H

UUUUUUUUUUUUUUU

Entity 5 Entity 5 polymer

Description description	PROTEIN CASC3
Molecular weight formula_weight	17713.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,T

DTKSTVTGERQSGDGQESTEPVENKVGKKGPKHLDDDEDRKNPAYIPRKGLFFEHDLRGQTQEEEVRPKGRQRKLWKDEGRWEHDKFREDEQAPKSRQELIALYGYDIRSAHNPDDIKPRRIRKPRYGSPPQRDPNWNGERLNKSHRHQG

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2j0qa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

Domain ID domain_id	d2j0qa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

Domain ID domain_id	d2j0qb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

Domain ID domain_id	d2j0qb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

Domain ID domain_id	d2j0qc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.232 — Mago nashi protein
Superfamily Superfamily superfamily	d.232.1 — Mago nashi protein
Family Family family	d.232.1.1 — Mago nashi protein

Domain ID domain_id	d2j0qd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.1 — Canonical RBD

Domain ID domain_id	d2j0qf1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.232 — Mago nashi protein
Superfamily Superfamily superfamily	d.232.1 — Mago nashi protein
Family Family family	d.232.1.1 — Mago nashi protein

Domain ID domain_id	d2j0qg1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.1 — Canonical RBD

CATH v4.4 (8 domains)

Domain ID domain_id	2j0qA01
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	2j0qA02
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	2j0qB01
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	2j0qB02
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	2j0qC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1560 — Mago nashi protein
Homologous superfamily homologous superfamily	10 — Mago nashi

Domain ID domain_id	2j0qD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	2j0qF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1560 — Mago nashi protein
Homologous superfamily homologous superfamily	10 — Mago nashi

Domain ID domain_id	2j0qG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

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Unit-cell length a length_a	69.150 Å
Unit-cell length b length_b	161.240 Å
Unit-cell length c length_c	193.240 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	8

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

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	46.980 Å
R factor r_factor	0.2350
R_work r_work	0.2320
R_free r_free	0.2770

The crystal structure of the Exon Junction Complex at 3.2 A resolution

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

ATP-DEPENDENT RNA HELICASE DDX48

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PROTEIN MAGO NASHI HOMOLOG

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RNA-BINDING PROTEIN 8A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PROTEIN CASC3

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

2j0q__assembly_1__model_1

2j0q__assembly_1__model_1 | I(q)

2j0q__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 (8)

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

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)