2hyi

Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA

Method: X-RAY DIFFRACTION

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

Protein mago nashi homolog

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	5'-R(UPUPUPUPUPU)-3' × 1 RNA-binding protein 8A × 1 （Q9Y5S9） Probable ATP-dependent RNA helicase DDX48 × 1 （P38919） Protein CASC3 × 1 （O15234） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 5	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 4 RNA 1	5'-R(UPUPUPUPUPU)-3' × 1 RNA-binding protein 8A × 1 （Q9Y5S9） Probable ATP-dependent RNA helicase DDX48 × 1 （P38919） Protein CASC3 × 1 （O15234） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 5	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 A； PDBConstruct 1–146； UniProt 1–146 Author chain G； 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	5'-R(UPUPUPUPUPU)-3' × 1 Protein mago nashi homolog × 1 （P61326） Probable ATP-dependent RNA helicase DDX48 × 1 （P38919） Protein CASC3 × 1 （O15234） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 5	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 4 RNA 1	5'-R(UPUPUPUPUPU)-3' × 1 Protein mago nashi homolog × 1 （P61326） Probable ATP-dependent RNA helicase DDX48 × 1 （P38919） Protein CASC3 × 1 （O15234） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 5	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 B； PDBConstruct 1–91； UniProt 64–154 Author chain H； PDBConstruct 1–91； UniProt 64–154

Probable ATP-dependent RNA helicase DDX48

Homo sapiens

UniProt P38919

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	5'-R(UPUPUPUPUPU)-3' × 1 Protein mago nashi homolog × 1 （P61326） RNA-binding protein 8A × 1 （Q9Y5S9） Protein CASC3 × 1 （O15234） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 5	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 4 RNA 1	5'-R(UPUPUPUPUPU)-3' × 1 Protein mago nashi homolog × 1 （P61326） RNA-binding protein 8A × 1 （Q9Y5S9） Protein CASC3 × 1 （O15234） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 5	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	4
Chains and sequence ranges	Author chain C； PDBConstruct 1–411； UniProt 0–410 Author chain I； PDBConstruct 1–411； UniProt 0–410

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	5'-R(UPUPUPUPUPU)-3' × 1 Protein mago nashi homolog × 1 （P61326） RNA-binding protein 8A × 1 （Q9Y5S9） Probable ATP-dependent RNA helicase DDX48 × 1 （P38919） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 5	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 4 RNA 1	5'-R(UPUPUPUPUPU)-3' × 1 Protein mago nashi homolog × 1 （P61326） RNA-binding protein 8A × 1 （Q9Y5S9） Probable ATP-dependent RNA helicase DDX48 × 1 （P38919） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 5	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 D； PDBConstruct 1–77； UniProt 170–246 Author chain J； PDBConstruct 1–77； UniProt 170–246

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	2hyi
Deposition date deposition_date	2006-08-06
Structure title title	Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA
Keywords keywords	;exon junction, splicing, mRNA processing, translation, DEAD-box ATPase, nonsense mediated decay, hydrolase-RNA binding protein-RNA COMPLEX ;; hydrolase/RNA binding protein/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.

2hyi__assembly_1__model_1

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

Download this curve (.dat)

2hyi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2hyi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.88 Å
Rg (electron density)	26.88 Å
Total Rg	27.58 Å
Atom count	5709
Residues	689
Excluded volume	101110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2hyi__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2hyi__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	5'-R(UPUPUPUPUPU)-3'
Molecular weight formula_weight	1792.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	F,L
Atom count atom_count	12033

UUUUUU

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	A,G

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	10370.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,H

PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP

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	Probable ATP-dependent RNA helicase DDX48
Molecular weight formula_weight	47173.2 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,I

MATTATMATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLILE

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 5 Entity 5 polymer

Description description	Protein CASC3
Molecular weight formula_weight	9435.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

LDDDEDRKNPAYIPRKGLFFEHDLRGQTQEEEVRPKGRQRKLWKDEGRWEHDKFREDEQAPKSRQELIALYGYDIRS

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	660

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d2hyia_
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	d2hyib_
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	d2hyic1
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	d2hyic2
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	d2hyic3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2hyig_
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	d2hyih_
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	d2hyii1
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	d2hyii2
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	d2hyii3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	2hyiA00
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	2hyiB00
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	2hyiC01
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	2hyiC02
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	2hyiG00
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	2hyiH00
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	2hyiI01
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	2hyiI02
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

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Unit-cell length a length_a	185.830 Å
Unit-cell length b length_b	88.260 Å
Unit-cell length c length_c	145.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.77 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2130
R_work r_work	0.2120
R_free r_free	0.2310

Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA

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

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

Probable 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 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

2hyi__assembly_1__model_1

2hyi__assembly_1__model_1 | I(q)

2hyi__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

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 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) 18 domains

SCOP 2.08 (10 domains)

CATH v4.4 (8 domains)

7. Citations (1)