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3pla

Crystal structure of a catalytically active substrate-bound box C/D RNP from Sulfolobus solfataricus

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pre mRNA splicing protein

Sulfolobus solfataricus

UniProt Q97ZH3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 6 RNA 4 50S ribosomal protein L7Ae × 2 （D0KRE2） ;Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ; × 2 （P58032） C/D guide RNA × 2 ;RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3') ; × 2 S-ADENOSYL-L-HOMOCYSTEINE × 2 Consistent with all polymers
2 Protein–RNA Heteromer Protein 6 RNA 4 50S ribosomal protein L7Ae × 2 （D0KRE2） ;Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ; × 2 （P58032） C/D guide RNA × 2 ;RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3') ; × 2 S-ADENOSYL-L-HOMOCYSTEINE × 2 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer
3icx 3icx

2 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3id5 3id6 3pla 3pla

4 assemblies

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 B； PDBConstruct 1–380； UniProt 1–380 Author chain K； PDBConstruct 1–380； UniProt 1–380

50S ribosomal protein L7Ae

Sulfolobus solfataricus

UniProt D0KRE2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 6 RNA 4 Pre mRNA splicing protein × 2 （Q97ZH3） ;Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ; × 2 （P58032） C/D guide RNA × 2 ;RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3') ; × 2 S-ADENOSYL-L-HOMOCYSTEINE × 2 Consistent with all polymers
2 Protein–RNA Heteromer Protein 6 RNA 4 Pre mRNA splicing protein × 2 （Q97ZH3） ;Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase ; × 2 （P58032） C/D guide RNA × 2 ;RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3') ; × 2 S-ADENOSYL-L-HOMOCYSTEINE × 2 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3pla 3pla

2 assemblies

View Construct and Data Evidence
UniProt name D0KRE2_SULS9
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–130； UniProt 1–130 Author chain D； PDBConstruct 1–130； UniProt 1–130 Author chain L； PDBConstruct 1–130； UniProt 1–130

;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 4 Pre mRNA splicing protein × 2 （Q97ZH3） 50S ribosomal protein L7Ae × 2 （D0KRE2） C/D guide RNA × 2 ;RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3') ; × 2 S-ADENOSYL-L-HOMOCYSTEINE × 2 Consistent with all polymers
2 Protein–RNA Heteromer Protein 6 RNA 4 Pre mRNA splicing protein × 2 （Q97ZH3） 50S ribosomal protein L7Ae × 2 （D0KRE2） C/D guide RNA × 2 ;RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3') ; × 2 S-ADENOSYL-L-HOMOCYSTEINE × 2 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3id5 3id6 3pla 3pla

4 assemblies

View Construct and Data Evidence
UniProt name FLPA_SULSO
Isoform —
PDB entities 3
Chains and sequence ranges Author chain E； PDBConstruct 1–232； UniProt 1–232 Author chain F； PDBConstruct 1–232； UniProt 1–232 Author chain M； 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_id3pla
Deposition date deposition_date2010-11-15
Structure title titleCrystal structure of a catalytically active substrate-bound box C/D RNP from Sulfolobus solfataricus
Keywords keywordsRNA-binding, METHYLTRANSFERASE, SAM, Box C/D RNA, Guide RNA, RNA-Protein complex, TRANSFERASE-RNA complex; TRANSFERASE/RNA
Experimental Method methodX-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.

3pla__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3pla__assembly_2__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3pla__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）39.00 Å
Rg (electron density)39.64 Å
Total Rg39.84 Å
Atom count13288
Residues1530
Excluded volume232030 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3pla__assembly_1__model_1 decameric （10） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3pla__assembly_2__model_1 decameric （10） 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 (6)

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6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id3plaA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily220 —
Domain ID domain_id3plaA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily4070 —
Domain ID domain_id3plaA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily90 — Nop domain
Domain ID domain_id3plaB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily220 —
Domain ID domain_id3plaB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily4070 —
Domain ID domain_id3plaB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily90 — Nop domain
Domain ID domain_id3plaC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily30 — Ribosomal protein L30/S12
Domain ID domain_id3plaD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily30 — Ribosomal protein L30/S12
Domain ID domain_id3plaE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id3plaE02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id3plaF01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id3plaF02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id3plaK01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily220 —
Domain ID domain_id3plaK02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily4070 —
Domain ID domain_id3plaK03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily90 — Nop domain
Domain ID domain_id3plaL00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily30 — Ribosomal protein L30/S12
Domain ID domain_id3plaM01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id3plaM02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
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7. Citations (1)