5aox

Human Alu RNA retrotransposition complex in the ribosome-stalling conformation

Method: X-RAY DIFFRACTION

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

SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 2 RNA 1	SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN × 1 （P37108） ALU JO CONSENSUS RNA × 1 ACETATE ION × 1 SULFATE ION × 1 DI(HYDROXYETHYL)ETHER × 1 MAGNESIUM ION × 3 water × 3	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 2 RNA 1	SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN × 1 （P37108） ALU JO CONSENSUS RNA × 1 ACETATE ION × 1 SULFATE ION × 1 MAGNESIUM ION × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SRP09_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–85； UniProt 2–86 Author chain D； PDBConstruct 1–85； UniProt 2–86

SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN

HOMO SAPIENS

UniProt P37108

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 2 RNA 1	SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN × 1 （P49458） ALU JO CONSENSUS RNA × 1 ACETATE ION × 1 SULFATE ION × 1 DI(HYDROXYETHYL)ETHER × 1 MAGNESIUM ION × 3 water × 3	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 2 RNA 1	SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN × 1 （P49458） ALU JO CONSENSUS RNA × 1 ACETATE ION × 1 SULFATE ION × 1 MAGNESIUM ION × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SRP14_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–94； UniProt 2–95 Author chain E； PDBConstruct 1–94； UniProt 2–95

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	5aox
Deposition date deposition_date	2015-09-12
Structure title title	Human Alu RNA retrotransposition complex in the ribosome-stalling conformation
Keywords keywords	;TRANSLATION, RETROTRANSPOSITION, PROTEIN TARGETING, RNA, MOBILE DNA, SINE, LINE, RIBONUCLEOPROTEIN PARTICLE, SIGNAL RECOGNITION PARTICLE ;; TRANSLATION
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.

5aox__assembly_1__model_1

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

Download this curve (.dat)

5aox__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5aox__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.11 Å
Rg (electron density)	21.48 Å
Total Rg	22.17 Å
Atom count	5398
Residues	248
Excluded volume	49454 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5aox__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5aox__assembly_2__model_1`	trimeric （3）	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	SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
Molecular weight formula_weight	9980.5 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	11120

PQYQTWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVSLVYKTDQAQDVKKIEKFHSQLMRLMVAKEARNVTMETE

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	SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
Molecular weight formula_weight	10555.3 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GAMESEQFLTELTRLFQKCRTSGSVYITLKKYDGRTKPIPKKGTVEGFEPADNKCLLRATDGKKKISTVVSSKEVNKFQMAYSNLLRANMDGLK

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	ALU JO CONSENSUS RNA
Molecular weight formula_weight	28238.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C,F

GGCCGGGCGCGGUGGCUCACGCCUGUAAUCCCAGCACUUUGGGAGGCCGAGGCGGGAGGAUCGCGAACACGCGAGACCCCGUCUCUA

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	381

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5aoxA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	720 — Signal recognition particle alu RNA binding heterodimer, srp9/1
Homologous superfamily homologous superfamily	10 — Signal recognition particle alu RNA binding heterodimer, srp9/1

Domain ID domain_id	5aoxB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	720 — Signal recognition particle alu RNA binding heterodimer, srp9/1
Homologous superfamily homologous superfamily	10 — Signal recognition particle alu RNA binding heterodimer, srp9/1

Domain ID domain_id	5aoxD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	720 — Signal recognition particle alu RNA binding heterodimer, srp9/1
Homologous superfamily homologous superfamily	10 — Signal recognition particle alu RNA binding heterodimer, srp9/1

Domain ID domain_id	5aoxE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	720 — Signal recognition particle alu RNA binding heterodimer, srp9/1
Homologous superfamily homologous superfamily	10 — Signal recognition particle alu RNA binding heterodimer, srp9/1

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Unit-cell length a length_a	81.480 Å
Unit-cell length b length_b	56.730 Å
Unit-cell length c length_c	170.590 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.69 °
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	2.040 Å
Low-resolution limit resolution_low	56.746 Å
R factor r_factor	0.1866
R_work r_work	0.1855
R_free r_free	0.2220

Human Alu RNA retrotransposition complex in the ribosome-stalling conformation

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

SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN

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

5aox__assembly_1__model_1

5aox__assembly_1__model_1 | I(q)

5aox__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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Human Alu RNA retrotransposition complex in the ribosome-stalling conformation

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

SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN

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

5aox__assembly_1__model_1

5aox__assembly_1__model_1 | I(q)

5aox__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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)