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4by9

The structure of the Box CD enzyme reveals regulation of rRNA methylation

Method: SOLUTION NMR
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NOP5/NOP56 RELATED PROTEIN

PYROCOCCUS FURIOSUS

UniProt Q8U4M1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 12 RNA 6 SSR26 × 2 50S RIBOSOMAL PROTEIN L7AE × 4 （Q8U160） ;FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE ; × 4 （Q8U4M2） 5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3' × 4 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
2nnw 2nnw 3nmu 3nmu 3nmu 3nvi 3nvi 3nvi 3nvk 3nvm 4by9

11 assemblies

View Construct and Data Evidence
UniProt name Q8U4M1_PYRFU
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–366； UniProt 4–369 Author chain F； PDBConstruct 1–366； UniProt 4–369 Author chain I； PDBConstruct 1–366； UniProt 4–369 Author chain L； PDBConstruct 1–366； UniProt 4–369

50S RIBOSOMAL PROTEIN L7AE

PYROCOCCUS FURIOSUS

UniProt Q8U160

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 12 RNA 6 SSR26 × 2 NOP5/NOP56 RELATED PROTEIN × 4 （Q8U4M1） ;FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE ; × 4 （Q8U4M2） 5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3' × 4 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
2hvy 3hax 3hay 3hjw 3lwo 3lwp 3lwq 3lwr 3lwv 3nmu 3nmu 3nmu

29 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RL7A_PYRFU
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–121； UniProt 3–123 Author chain G； PDBConstruct 1–121； UniProt 3–123 Author chain J； PDBConstruct 1–121； UniProt 3–123 Author chain M； PDBConstruct 1–121； UniProt 3–123

;FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE ;

PYROCOCCUS FURIOSUS

UniProt Q8U4M2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 12 RNA 6 SSR26 × 2 NOP5/NOP56 RELATED PROTEIN × 4 （Q8U4M1） 50S RIBOSOMAL PROTEIN L7AE × 4 （Q8U160） 5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3' × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1pry

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2nnw 2nnw 3nmu 3nmu 3nmu 3nvk 3nvm 4by9

8 assemblies

View Construct and Data Evidence
UniProt name FLPA_PYRFU
Isoform —
PDB entities 4
Chains and sequence ranges Author chain E； PDBConstruct 1–227； UniProt 1–227 Author chain H； PDBConstruct 1–227； UniProt 1–227 Author chain K； PDBConstruct 1–227； UniProt 1–227 Author chain N； PDBConstruct 1–227； UniProt 1–227

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_id4by9
Deposition date deposition_date2013-07-18
Structure title titleThe structure of the Box CD enzyme reveals regulation of rRNA methylation
Keywords keywordsTRANSFERASE-RNA COMPLEX, RRNA MODIFICATION; TRANSFERASE/RNA
Experimental Method methodSOLUTION NMR
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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.

4by9__assembly_1__model_1

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

Download this curve (.dat)

4by9__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4by9__assembly_1__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）60.16 Å
Rg (electron density)61.99 Å
Total Rg61.69 Å
Atom count52476
Residues3044
Excluded volume468800 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4by9__assembly_1__model_1 octadecameric （18） 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)

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id4by9C01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily220 —
Domain ID domain_id4by9C02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily4070 —
Domain ID domain_id4by9C03
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_id4by9D00
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_id4by9E01
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_id4by9E02
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_id4by9F01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily220 —
Domain ID domain_id4by9F02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily4070 —
Domain ID domain_id4by9F03
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_id4by9G00
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_id4by9H01
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_id4by9H02
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_id4by9I01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily220 —
Domain ID domain_id4by9I02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily4070 —
Domain ID domain_id4by9I03
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_id4by9J00
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_id4by9K01
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_id4by9K02
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_id4by9L01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily220 —
Domain ID domain_id4by9L02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily4070 —
Domain ID domain_id4by9L03
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_id4by9M00
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_id4by9N01
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_id4by9N02
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)