SAXSdb — 1p27

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

Mago nashi protein homolog

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	RNA-binding protein 8A × 2 （Q9Y5S9） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	RNA-binding protein 8A × 1 （Q9Y5S9） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	RNA-binding protein 8A × 1 （Q9Y5S9） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MGN_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–144； UniProt 2–145 Author chain C； PDBConstruct 1–144； UniProt 2–145

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 heterocomplex	Heteromer	Protein 4	Mago nashi protein homolog × 2 （P61326） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Mago nashi protein homolog × 1 （P61326） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Mago nashi protein homolog × 1 （P61326） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBM8A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–106； UniProt 50–155 Author chain D； PDBConstruct 1–106； UniProt 50–155

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	1p27
Deposition date deposition_date	2003-04-14
Structure title title	Crystal Structure of the Human Y14/Magoh complex
Keywords keywords	RNA-binding, Nuclear protein, mRNA splicing, RNA binding protein; RNA BINDING PROTEIN
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.

1p27__assembly_1__model_1

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

Download this curve (.dat)

1p27__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1p27__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.22 Å
Rg (electron density)	25.27 Å
Total Rg	26.06 Å
Atom count	3866
Residues	472
Excluded volume	68627 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1p27__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1p27__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1p27__assembly_3__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	Mago nashi protein homolog
Molecular weight formula_weight	16945.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	3966

ESDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIGLHFKIKP

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	RNA-binding protein 8A
Molecular weight formula_weight	12138.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MREDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPP

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 BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	100

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1p27a_
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	d1p27b_
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	d1p27c_
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	d1p27d_
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 (4 domains)

Domain ID domain_id	1p27A00
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	1p27B00
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	1p27C00
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	1p27D00
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	47.150 Å
Unit-cell length b length_b	108.455 Å
Unit-cell length c length_c	50.942 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.24 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	46.110 Å
R factor r_factor	0.2223
R_work r_work	0.2198
R_free r_free	0.2683

Crystal Structure of the Human Y14/Magoh complex

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

Mago nashi protein homolog

State in the Current Structure

Other States of the Same Protein in the Database

RNA-binding protein 8A

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

1p27__assembly_1__model_1

1p27__assembly_1__model_1 | I(q)

1p27__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of the Human Y14/Magoh complex

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

Mago nashi protein 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1p27__assembly_1__model_1

1p27__assembly_1__model_1 | I(q)

1p27__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)