SAXSdb — 3id5

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

Pre mRNA splicing protein

Sulfolobus solfataricus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 2	;Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ; × 2 （P58032） 50S ribosomal protein L7Ae × 2 （P55858） half C/D RNA × 2 S-ADENOSYLMETHIONINE × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q97ZH3_SULSO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–380； UniProt 1–380 Author chain E； PDBConstruct 1–380； UniProt 1–380

;Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ;

Sulfolobus solfataricus

UniProt P58032

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 2	Pre mRNA splicing protein × 2 （Q97ZH3） 50S ribosomal protein L7Ae × 2 （P55858） half C/D RNA × 2 S-ADENOSYLMETHIONINE × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FLPA_SULSO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–232； UniProt 1–232 Author chain F； PDBConstruct 1–232； UniProt 1–232

50S ribosomal protein L7Ae

Sulfolobus solfataricus

UniProt P55858

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 2	Pre mRNA splicing protein × 2 （Q97ZH3） ;Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ; × 2 （P58032） half C/D RNA × 2 S-ADENOSYLMETHIONINE × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL7A_SULSO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 4–130； UniProt 1–127 Author chain G； PDBConstruct 4–130； UniProt 1–127

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	3id5
Deposition date deposition_date	2009-07-20
Structure title title	Crystal structure of Sulfolobus solfataricus C/D RNP assembled with Nop5, fibrillarin, L7Ae and a split half C/D RNA
Keywords keywords	;C/D guide RNA, 2'-O-methylation, coiled-coil, Methyltransferase, RNA-binding, rRNA processing, Transferase, tRNA processing, Ribonucleoprotein, Ribosomal protein, SPLICING-TRANSFERASE-RIBOSOMAL PROTEIN-RNA COMPLEX, TRANSFERASE-RIBOSOMAL PROTEIN-RNA complex ;; TRANSFERASE/RIBOSOMAL PROTEIN/RNA
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.

3id5__assembly_1__model_1

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

Download this curve (.dat)

3id5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3id5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.60 Å
Rg (electron density)	43.93 Å
Total Rg	44.24 Å
Atom count	12730
Residues	1496
Excluded volume	223200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3id5__assembly_1__model_1`	octameric （8）	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 (5)

Entity 1 Entity 1 polymer

Description description	Pre mRNA splicing protein
Molecular weight formula_weight	44168.5 kDa
Mutation mutation	M2V
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	12730

MVKIYLIEHVIGAVAYDENGNIVDYITNPRDLGKITEELLNNEKGIPFSATVELLKKVNPQEVVVENEAEVPKLQALGYRVSYEPYSKVSRIFRESLPKVAIDIKFASNEEDYYNFLHELSLEYTRRKLRSAAQKRDLLAIQAVRAMDDIDKTINLFSERLREWYSIHFPELDKLIEDHEEYATIVSRFGDRGFLTIDSLKELGFNEQRINRILDAAKKSIGADISEDDLSAMRMIANTILDLYNIRRNLNNYLEGVMKEVAPNVTALVGPALGARLLSIAGSLDELAKMPASTIQVLGAEKALFRALRSGGRPPKHGIIFQYPAIHTSPRWQRGKIARALAAKLAIAARVDAFSGRFIGDQLNEQLKKRIDEIKEKFAQHHHHHHHH

Source Source

Source organism organism	Sulfolobus solfataricus
NCBI taxonomy ID ncbi_taxonomy_id	2287
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ;
Molecular weight formula_weight	26439.4 kDa
EC 编号 ec_number	2.1.1.-
Mutation mutation	S2A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MAEVITVKQTNMENIYECEFNDGSFRLCTRNLVPNFNVYGERLIKYEGVEYREWNAFRSKLAGAILKGLKTNPIRKGTKVLYLGAASGTTISHVSDIIELNGKAYGVEFSPRVVRELLLVAQRRPNIFPLLADARFPQSYKSVVENVDVLYVDIAQPDQTDIAIYNAKFFLKVNGDMLLVIKARSIDVTKDPKEIYKTEVEKLENSNFETIQIINLDPYDKDHAIVLSKYKG

Source Source

Source organism organism	Sulfolobus solfataricus
NCBI taxonomy ID ncbi_taxonomy_id	2287
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	50S ribosomal protein L7Ae
Molecular weight formula_weight	14075.3 kDa
Mutation mutation	N2D
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MDAMSKASYVKFEVPQDLADKVLEAVRKAKESGKIKKGTNETTKAVERGQAKLVIIAEDVQPEEIVAHLPLLCDEKKIPYVYVSSKKALGEACGLQVATASAAILEPGEAKDLVDEIIKRVNEIKGKTSS

Source Source

Source organism organism	Sulfolobus solfataricus
NCBI taxonomy ID ncbi_taxonomy_id	2287
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	half C/D RNA
Molecular weight formula_weight	11261.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D,H

GGGGCGCCCUCUGAGCGUUCGCGCUGUGAUGAAUU

Entity 5 Entity 5 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	2

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Unit-cell length a length_a	265.485 Å
Unit-cell length b length_b	265.485 Å
Unit-cell length c length_c	129.434 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	4.010 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2860
R_work r_work	0.2850
R_free r_free	0.3040

Crystal structure of Sulfolobus solfataricus C/D RNP assembled with Nop5, fibrillarin, L7Ae and a split half C/D RNA

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

Pre mRNA splicing protein

State in the Current Structure

Other States of the Same Protein in the Database

;Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ;

State in the Current Structure

Other States of the Same Protein in the Database

50S ribosomal protein L7Ae

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

3id5__assembly_1__model_1

3id5__assembly_1__model_1 | I(q)

3id5__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 (5)

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 non-polymer

7. Citations (1)

Crystal structure of Sulfolobus solfataricus C/D RNP assembled with Nop5, fibrillarin, L7Ae and a split half C/D RNA

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

Pre mRNA splicing 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

;Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

50S ribosomal protein L7Ae

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

3id5__assembly_1__model_1

3id5__assembly_1__model_1 | I(q)

3id5__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 (5)

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 non-polymer

7. Citations (1)