SAXSdb — 3id6

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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 heterocomplex	Heteromer	Protein 4	;Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ; × 2 （P58032） S-ADENOSYLMETHIONINE × 2	Consistent with protein count

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 1–262； UniProt 1–262

;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 heterocomplex	Heteromer	Protein 4	Pre mRNA splicing protein × 2 （Q97ZH3） S-ADENOSYLMETHIONINE × 2	Consistent with protein count

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 C； PDBConstruct 1–232； UniProt 1–232

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	3id6
Deposition date deposition_date	2009-07-20
Structure title title	Crystal structure of Sulfolobus solfataricus Nop5 (1-262) and fibrillarin complex
Keywords keywords	;C/D guide RNA, 2'-O-methylation, coiled-coil, Methyltransferase, RNA-binding, rRNA processing, Transferase, tRNA processing ;; TRANSFERASE
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.

3id6__assembly_1__model_1

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

Download this curve (.dat)

3id6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3id6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.51 Å
Rg (electron density)	46.06 Å
Total Rg	46.10 Å
Atom count	7816
Residues	956
Excluded volume	139950 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3id6__assembly_1__model_1`	tetrameric （4）	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	Pre mRNA splicing protein
Molecular weight formula_weight	31136.3 kDa
Mutation mutation	M2V
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	3908

MVKIYLIEHVIGAVAYDENGNIVDYITNPRDLGKITEELLNNEKGIPFSATVELLKKVNPQEVVVENEAEVPKLQALGYRVSYEPYSKVSRIFRESLPKVAIDIKFASNEEDYYNFLHELSLEYTRRKLRSAAQKRDLLAIQAVRAMDDIDKTINLFSERLREWYSIHFPELDKLIEDHEEYATIVSRFGDRGFLTIDSLKELGFNEQRINRILDAAKKSIGADISEDDLSAMRMIANTILDLYNIRRNLNNYLEGVMKEVAHHHHHH

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

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 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3id6c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3id6A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	220 —

Domain ID domain_id	3id6A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	4070 —

Domain ID domain_id	3id6C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3id6C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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Unit-cell length a length_a	75.517 Å
Unit-cell length b length_b	182.364 Å
Unit-cell length c length_c	79.140 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2350
R_work r_work	0.2320
R_free r_free	0.2850

Crystal structure of Sulfolobus solfataricus Nop5 (1-262) and fibrillarin complex

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3id6__assembly_1__model_1

3id6__assembly_1__model_1 | I(q)

3id6__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 non-polymer

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Sulfolobus solfataricus Nop5 (1-262) and fibrillarin complex

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3id6__assembly_1__model_1

3id6__assembly_1__model_1 | I(q)

3id6__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 non-polymer

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (1)