7znj

Structure of an ALYREF-exon junction complex hexamer

Method: ELECTRON MICROSCOPY

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

Eukaryotic initiation factor 4A-III, N-terminally processed

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 24 RNA 6	Protein mago nashi homolog × 6 （P61326） RNA-binding protein 8A × 6 （Q9Y5S9） Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4 × 6 （P0AEY0,Q86V81） RNA × 6 MAGNESIUM ION × 6 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6	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 1–382； UniProt 23–404 Author chain F； PDBConstruct 1–382； UniProt 23–404 Author chain K； PDBConstruct 1–382； UniProt 23–404 Author chain a； PDBConstruct 1–382； UniProt 23–404 Author chain f； PDBConstruct 1–382； UniProt 23–404 Author chain k； PDBConstruct 1–382； UniProt 23–404

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	Insufficient information	Heteromer	Protein 24 RNA 6	Eukaryotic initiation factor 4A-III, N-terminally processed × 6 （P38919） RNA-binding protein 8A × 6 （Q9Y5S9） Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4 × 6 （P0AEY0,Q86V81） RNA × 6 MAGNESIUM ION × 6 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6	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 B； PDBConstruct 1–146； UniProt 1–146 Author chain G； PDBConstruct 1–146； UniProt 1–146 Author chain L； PDBConstruct 1–146； UniProt 1–146 Author chain b； PDBConstruct 1–146； UniProt 1–146 Author chain g； PDBConstruct 1–146； UniProt 1–146 Author chain l； 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	Insufficient information	Heteromer	Protein 24 RNA 6	Eukaryotic initiation factor 4A-III, N-terminally processed × 6 （P38919） Protein mago nashi homolog × 6 （P61326） Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4 × 6 （P0AEY0,Q86V81） RNA × 6 MAGNESIUM ION × 6 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6	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 C； PDBConstruct 1–91； UniProt 65–155 Author chain H； PDBConstruct 1–91； UniProt 65–155 Author chain M； PDBConstruct 1–91； UniProt 65–155 Author chain c； PDBConstruct 1–91； UniProt 65–155 Author chain h； PDBConstruct 1–91； UniProt 65–155 Author chain m； PDBConstruct 1–91； UniProt 65–155

Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4

Homo sapiens

UniProt P0AEY0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 24 RNA 6	Eukaryotic initiation factor 4A-III, N-terminally processed × 6 （P38919） Protein mago nashi homolog × 6 （P61326） RNA-binding protein 8A × 6 （Q9Y5S9） RNA × 6 MAGNESIUM ION × 6 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MALE_ECO57
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 15–384； UniProt 23–392 Author chain I； PDBConstruct 15–384； UniProt 23–392 Author chain N； PDBConstruct 15–384； UniProt 23–392 Author chain d； PDBConstruct 15–384； UniProt 23–392 Author chain i； PDBConstruct 15–384； UniProt 23–392 Author chain n； PDBConstruct 15–384； UniProt 23–392

Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4

Homo sapiens

UniProt Q86V81

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 24 RNA 6	Eukaryotic initiation factor 4A-III, N-terminally processed × 6 （P38919） Protein mago nashi homolog × 6 （P61326） RNA-binding protein 8A × 6 （Q9Y5S9） RNA × 6 MAGNESIUM ION × 6 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THOC4_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 401–527； UniProt 56–182 Author chain I； PDBConstruct 401–527； UniProt 56–182 Author chain N； PDBConstruct 401–527； UniProt 56–182 Author chain d； PDBConstruct 401–527； UniProt 56–182 Author chain i； PDBConstruct 401–527； UniProt 56–182 Author chain n； PDBConstruct 401–527； UniProt 56–182

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	7znj
Deposition date deposition_date	2022-04-21
Structure title title	Structure of an ALYREF-exon junction complex hexamer
Keywords keywords	transcription-exort complex, TREX, splicing, exon junction complex, EJC, RNA export, RNA binding proteins, GENE REGULATION; GENE REGULATION
Experimental Method method	ELECTRON MICROSCOPY

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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.

7znj__assembly_1__model_1

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

Download this curve (.dat)

7znj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7znj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	60.85 Å
Rg (electron density)	60.01 Å
Total Rg	60.17 Å
Atom count	35088
Residues	4278
Excluded volume	622270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7znj__assembly_1__model_1`	30-meric （30）	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 (7)

Entity 1 Entity 1 polymer

Description description	Eukaryotic initiation factor 4A-III, N-terminally processed
Molecular weight formula_weight	43819.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,a,F,f,K,k
Atom count atom_count	35088

MTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMP

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	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,b,G,g,L,l

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	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,c,H,h,M,m

GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPP

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	Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4
Molecular weight formula_weight	57598.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,d,I,i,N,n

MQLSHHHHHHHHHHSSGMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTSSGLEVLFQGPGSSGIRNRPAIARGAAGGGGRNRPAPYSRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT

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	RNA
Molecular weight formula_weight	1792.0 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E,e,J,j,O,o

UUUUUU

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	6

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	6

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	7znjA01
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	7znjA02
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	7znjF01
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	7znjF02
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	7znjK01
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	7znjK02
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	7znja01
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	7znja02
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	7znjf01
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	7znjf02
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	7znjk01
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	7znjk02
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	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	1564602

Structure of an ALYREF-exon junction complex hexamer

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

Eukaryotic initiation factor 4A-III, N-terminally processed

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

Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4

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

7znj__assembly_1__model_1

7znj__assembly_1__model_1 | I(q)

7znj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

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

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)