2xb2

Crystal structure of the core Mago-Y14-eIF4AIII-Barentsz-UPF3b assembly shows how the EJC is bridged to the NMD machinery

Method: X-RAY DIFFRACTION

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

EUKARYOTIC INITIATION FACTOR 4A-III

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 5 RNA 1	PROTEIN MAGO NASHI HOMOLOG × 1 （P61326） RNA-BINDING PROTEIN 8A × 1 （Q9Y5S9） RNA POLY-U-RIBONUCLEOTIDE × 1 REGULATOR OF NONSENSE TRANSCRIPTS 3B × 1 （Q9BZI7） PROTEIN CASC3 × 1 （O15234） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 5 RNA 1	PROTEIN MAGO NASHI HOMOLOG × 1 （P61326） RNA-BINDING PROTEIN 8A × 1 （Q9Y5S9） RNA POLY-U-RIBONUCLEOTIDE × 1 REGULATOR OF NONSENSE TRANSCRIPTS 3B × 1 （Q9BZI7） 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	IF4A3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–411； UniProt 1–411 Author chain X； PDBConstruct 1–411； UniProt 1–411

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 5 RNA 1	EUKARYOTIC INITIATION FACTOR 4A-III × 1 （P38919） RNA-BINDING PROTEIN 8A × 1 （Q9Y5S9） RNA POLY-U-RIBONUCLEOTIDE × 1 REGULATOR OF NONSENSE TRANSCRIPTS 3B × 1 （Q9BZI7） PROTEIN CASC3 × 1 （O15234） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 5 RNA 1	EUKARYOTIC INITIATION FACTOR 4A-III × 1 （P38919） RNA-BINDING PROTEIN 8A × 1 （Q9Y5S9） RNA POLY-U-RIBONUCLEOTIDE × 1 REGULATOR OF NONSENSE TRANSCRIPTS 3B × 1 （Q9BZI7） 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 Y； 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 5 RNA 1	EUKARYOTIC INITIATION FACTOR 4A-III × 1 （P38919） PROTEIN MAGO NASHI HOMOLOG × 1 （P61326） RNA POLY-U-RIBONUCLEOTIDE × 1 REGULATOR OF NONSENSE TRANSCRIPTS 3B × 1 （Q9BZI7） PROTEIN CASC3 × 1 （O15234） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 5 RNA 1	EUKARYOTIC INITIATION FACTOR 4A-III × 1 （P38919） PROTEIN MAGO NASHI HOMOLOG × 1 （P61326） RNA POLY-U-RIBONUCLEOTIDE × 1 REGULATOR OF NONSENSE TRANSCRIPTS 3B × 1 （Q9BZI7） 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 1–90； UniProt 66–155 Author chain Z； PDBConstruct 1–90； UniProt 66–155

REGULATOR OF NONSENSE TRANSCRIPTS 3B

HOMO SAPIENS

UniProt Q9BZI7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 5 RNA 1	EUKARYOTIC INITIATION FACTOR 4A-III × 1 （P38919） PROTEIN MAGO NASHI HOMOLOG × 1 （P61326） RNA-BINDING PROTEIN 8A × 1 （Q9Y5S9） RNA POLY-U-RIBONUCLEOTIDE × 1 PROTEIN CASC3 × 1 （O15234） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 5 RNA 1	EUKARYOTIC INITIATION FACTOR 4A-III × 1 （P38919） PROTEIN MAGO NASHI HOMOLOG × 1 （P61326） RNA-BINDING PROTEIN 8A × 1 （Q9Y5S9） RNA POLY-U-RIBONUCLEOTIDE × 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	REN3B_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain G； PDBConstruct 1–60； UniProt 411–470 Author chain U； PDBConstruct 1–60； UniProt 411–470

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 5 RNA 1	EUKARYOTIC INITIATION FACTOR 4A-III × 1 （P38919） PROTEIN MAGO NASHI HOMOLOG × 1 （P61326） RNA-BINDING PROTEIN 8A × 1 （Q9Y5S9） RNA POLY-U-RIBONUCLEOTIDE × 1 REGULATOR OF NONSENSE TRANSCRIPTS 3B × 1 （Q9BZI7） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 5 RNA 1	EUKARYOTIC INITIATION FACTOR 4A-III × 1 （P38919） PROTEIN MAGO NASHI HOMOLOG × 1 （P61326） RNA-BINDING PROTEIN 8A × 1 （Q9Y5S9） RNA POLY-U-RIBONUCLEOTIDE × 1 REGULATOR OF NONSENSE TRANSCRIPTS 3B × 1 （Q9BZI7） 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	7
Chains and sequence ranges	Author chain S； 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	2xb2
Deposition date deposition_date	2010-04-03
Structure title title	Crystal structure of the core Mago-Y14-eIF4AIII-Barentsz-UPF3b assembly shows how the EJC is bridged to the NMD machinery
Keywords keywords	EXON JUNCTION COMPLEX, NONSENSE-MEDIATED MRNA DECAY, TRANSLATION, UPF3B, HYDROLASE; 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.

2xb2__assembly_1__model_1

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

Download this curve (.dat)

2xb2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2xb2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.98 Å
Rg (electron density)	26.98 Å
Total Rg	27.67 Å
Atom count	5823
Residues	703
Excluded volume	103020 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2xb2__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2xb2__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2xb2__assembly_3__model_1`	monomeric （1）	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 (9)

Entity 1 Entity 1 polymer

Description description	EUKARYOTIC INITIATION FACTOR 4A-III
Molecular weight formula_weight	46931.0 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	A,X
Atom count atom_count	11710

MATTATMATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI

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,Y

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	10313.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPP

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	RNA POLY-U-RIBONUCLEOTIDE
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,R

UUUUUUUUUUUUUUU

Entity 5 Entity 5 polymer

Description description	PUTATIVE REGULATOR OF NONSENSE TRANSCRIPTS 3B
Molecular weight formula_weight	375.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

AER

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 polymer

Description description	REGULATOR OF NONSENSE TRANSCRIPTS 3B
Molecular weight formula_weight	6809.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

EVVKRDRIRNKDRPAMQLYQPGARSRNRLCPPDDSTKSGDSAAERKQESGISHRKEGGEE

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 7 Entity 7 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	S,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 8 Entity 8 non-polymer

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

Entity 9 Entity 9 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

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2xb2A01
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	2xb2A02
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	2xb2C00
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	2xb2D00
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	2xb2X01
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	2xb2X02
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	2xb2Y00
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	2xb2Z00
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	134.800 Å
Unit-cell length b length_b	134.800 Å
Unit-cell length c length_c	227.250 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	60.000 Å
R factor r_factor	0.2204
R_work r_work	0.2204
R_free r_free	0.2604

Crystal structure of the core Mago-Y14-eIF4AIII-Barentsz-UPF3b assembly shows how the EJC is bridged to the NMD machinery

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

EUKARYOTIC INITIATION FACTOR 4A-III

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

REGULATOR OF NONSENSE TRANSCRIPTS 3B

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

2xb2__assembly_1__model_1

2xb2__assembly_1__model_1 | I(q)

2xb2__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 (9)

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 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)