SAXSdb — 5aff

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

SYMPORTIN 1

CHAETOMIUM THERMOPHILUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	RIBOSOMAL PROTEIN L5 × 1 （G0SEG2） RIBOSOMAL PROTEIN L11 × 1 （G0SHQ2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G0S5S6_CHATD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–654； UniProt 24–676

RIBOSOMAL PROTEIN L5

CHAETOMIUM THERMOPHILUM

UniProt G0SEG2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	SYMPORTIN 1 × 1 （G0S5S6） RIBOSOMAL PROTEIN L11 × 1 （G0SHQ2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G0SEG2_CHATD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 8–48； UniProt 1–41

RIBOSOMAL PROTEIN L11

CHAETOMIUM THERMOPHILUM

UniProt G0SHQ2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	SYMPORTIN 1 × 1 （G0S5S6） RIBOSOMAL PROTEIN L5 × 1 （G0SEG2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G0SHQ2_CHATD
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–173； UniProt 1–173

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	5aff
Deposition date deposition_date	2015-01-21
Structure title title	Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA binding site
Keywords keywords	CHAPERONE, RIBOSOME BIOGENESIS, ALPHA SOLENOID.; CHAPERONE
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.

5aff__assembly_1__model_1

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

Download this curve (.dat)

5aff__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5aff__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.75 Å
Rg (electron density)	31.30 Å
Total Rg	31.91 Å
Atom count	5606
Residues	712
Excluded volume	100390 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5aff__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	SYMPORTIN 1
Molecular weight formula_weight	72162.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5606

MTDPELAKLREDKILPVLKDLKSPDAKSRTTAAGAIANIVQDAKCRKLLLREQVVHIVLTETLTDNNIDSRAAGWEILKVLAQEEEADFCVHLYRLDVLTAIEHAAKAVLETLTTSEPPFSKLLKAQQRLVWDITGSLLVLIGLLALARDEIHEAVATKQTILRLLFRLISADIAPQDIYEEAISCLTTLSEDNLKVGQAITDDQETHVYDVLLKLATGTDPRAVMACGVLHNVFTSLQWMDHSPGKDGACDAILIPTLTRALEHVVPGGAKFNGDARYANITLLALVTLASIGTDFQETLVKGNQGSRESPISAADEEWNGFDDADGDAMDVDQKSSSGEDQEEDYEEIDVKEDDEDDDDDSITSEMQADMERVVGADGTDDGDLEDLPTLRELIQTAVPQLIRLSNLPIDSDESLTIQSHALSALNNISWTISCLEFANGENANIHNAWYPTAKKIWRKTILPILEADSADLKLATQVTSLAWAVARVLHGETPTDGNPHRKFISLYHSSKQQAGGNSNSIEEPEDPFQGLGVKCIGVVGSLAHDPAPIEVNREVGVFLVTLLRQSNNVPPAEIVEALNQLFDIYGDEELACDKEVFWKDGFLKHLEEFLPKMRTLTKGIDKRTQPELRTRADEALLNLGRFVQYKKKHAPK

Source Source

Source organism organism	CHAETOMIUM THERMOPHILUM
NCBI taxonomy ID ncbi_taxonomy_id	209285
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	RIBOSOMAL PROTEIN L5
Molecular weight formula_weight	6060.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MHHHHHHMAFHKLVKNSAYYSRFQTKFKRRRQGKTDYYARKRLITQAK

Source Source

Source organism organism	CHAETOMIUM THERMOPHILUM
NCBI taxonomy ID ncbi_taxonomy_id	209285
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 polymer

Description description	RIBOSOMAL PROTEIN L11
Molecular weight formula_weight	20119.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSSEKAQNPMRELRIQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVYSKARYTVRQFGIRRNEKIAVHVTVRGPKAEEILERGLKVKEYELRRRNFSETGNFGFGISEHIDLGIKYDPSIGIYGMDFYCCMTRPGERVAKRRRCKSRIGASHRITREETIRWFKQRFDGIVR

Source Source

Source organism organism	CHAETOMIUM THERMOPHILUM
NCBI taxonomy ID ncbi_taxonomy_id	209285
Host organism host_organism	ESCHERICHIA COLI

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5affA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

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Unit-cell length a length_a	60.087 Å
Unit-cell length b length_b	105.959 Å
Unit-cell length c length_c	147.234 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.398 Å
Low-resolution limit resolution_low	49.256 Å
R factor r_factor	0.2391
R_work r_work	0.2361
R_free r_free	0.2998

Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA binding site

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

SYMPORTIN 1

State in the Current Structure

Other States of the Same Protein in the Database

RIBOSOMAL PROTEIN L5

State in the Current Structure

Other States of the Same Protein in the Database

RIBOSOMAL PROTEIN L11

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

5aff__assembly_1__model_1

5aff__assembly_1__model_1 | I(q)

5aff__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 (3)

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

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA binding site

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

SYMPORTIN 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RIBOSOMAL PROTEIN L5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RIBOSOMAL PROTEIN L11

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

5aff__assembly_1__model_1

5aff__assembly_1__model_1 | I(q)

5aff__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 (3)

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

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)