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3cjq

Ribosomal protein L11 methyltransferase (PrmA) in complex with dimethylated ribosomal protein L11 in space group P212121

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

Ribosomal protein L11 methyltransferase

Thermus thermophilus

UniProt Q84BQ9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 50S ribosomal protein L11 × 1 （P36238） S-ADENOSYL-L-HOMOCYSTEINE × 1 IODIDE ION × 1 N,N-dimethyl-L-methionine × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 50S ribosomal protein L11 × 1 （P36238） S-ADENOSYL-L-HOMOCYSTEINE × 1 N,N-dimethyl-L-methionine × 1 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 50S ribosomal protein L11 × 1 （P36238） S-ADENOSYL-L-HOMOCYSTEINE × 1 IODIDE ION × 1 N,N-dimethyl-L-methionine × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1ufk 2nxc 2nxe 2nxe 2nxj 2nxj 2zbp 2zbq 2zbr

9 assemblies

Homodimer
2zbp 2zbq 2zbr

3 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2nxn 3cjq 3cjq 3cjq 3cjr 3cjs 3cjt 3cjt 3cjt 3cjt 3cjt 3cjt

15 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name PRMA_THET8
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–254； UniProt 1–254 Author chain D； PDBConstruct 1–254； UniProt 1–254 Author chain G； PDBConstruct 1–254； UniProt 1–254

50S ribosomal protein L11

Thermus thermophilus

UniProt P36238

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Ribosomal protein L11 methyltransferase × 1 （Q84BQ9） S-ADENOSYL-L-HOMOCYSTEINE × 1 IODIDE ION × 1 N,N-dimethyl-L-methionine × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Ribosomal protein L11 methyltransferase × 1 （Q84BQ9） S-ADENOSYL-L-HOMOCYSTEINE × 1 N,N-dimethyl-L-methionine × 1 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Ribosomal protein L11 methyltransferase × 1 （Q84BQ9） S-ADENOSYL-L-HOMOCYSTEINE × 1 IODIDE ION × 1 N,N-dimethyl-L-methionine × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2e34 2e35 2e36 2h8w 2klm 3cjs

6 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2nxn 3cjq 3cjq 3cjq 3cjr 3cjs 3cjt 3cjt 3cjt 3cjt 3cjt 3cjt

22 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RL11_THETH
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–146； UniProt 2–147 Author chain E； PDBConstruct 1–146； UniProt 2–147 Author chain H； PDBConstruct 1–146； UniProt 2–147

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_id3cjq
Deposition date deposition_date2008-03-13
Structure title titleRibosomal protein L11 methyltransferase (PrmA) in complex with dimethylated ribosomal protein L11 in space group P212121
Keywords keywords;S-Adenosyl-L-Methionine dependent methyltransferase, post-translational modification, multi-specific trimethylation, Ribonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding, Transferase-Ribosomal protein COMPLEX ;; Transferase/Ribosomal protein
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.

3cjq__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3cjq__assembly_3__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3cjq__assembly_3__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）25.66 Å
Rg (electron density)24.97 Å
Total Rg25.63 Å
Atom count2862
Residues373
Excluded volume51443 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3cjq__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3cjq__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3cjq__assembly_3__model_1 dimeric （2） 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) 21 domains

SCOP 2.08 (9 domains)

Domain ID domain_idd3cjqa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.39 — Ribosomal protein L11 methyltransferase PrmA
Domain ID domain_idd3cjqb1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.7 — Ribosomal protein L11, C-terminal domain
Family Family familya.4.7.1 — Ribosomal protein L11, C-terminal domain
Domain ID domain_idd3cjqb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.47 — Ribosomal L11/L12e N-terminal domain
Superfamily Superfamily superfamilyd.47.1 — Ribosomal L11/L12e N-terminal domain
Family Family familyd.47.1.1 — Ribosomal L11/L12e N-terminal domain
Domain ID domain_idd3cjqd1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.39 — Ribosomal protein L11 methyltransferase PrmA
Domain ID domain_idd3cjqe1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.7 — Ribosomal protein L11, C-terminal domain
Family Family familya.4.7.1 — Ribosomal protein L11, C-terminal domain
Domain ID domain_idd3cjqe2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.47 — Ribosomal L11/L12e N-terminal domain
Superfamily Superfamily superfamilyd.47.1 — Ribosomal L11/L12e N-terminal domain
Family Family familyd.47.1.1 — Ribosomal L11/L12e N-terminal domain
Domain ID domain_idd3cjqg1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.39 — Ribosomal protein L11 methyltransferase PrmA
Domain ID domain_idd3cjqh1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.7 — Ribosomal protein L11, C-terminal domain
Family Family familya.4.7.1 — Ribosomal protein L11, C-terminal domain
Domain ID domain_idd3cjqh2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.47 — Ribosomal L11/L12e N-terminal domain
Superfamily Superfamily superfamilyd.47.1 — Ribosomal L11/L12e N-terminal domain
Family Family familyd.47.1.1 — Ribosomal L11/L12e N-terminal domain

CATH v4.4 (12 domains)

Domain ID domain_id3cjqA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1170 — Sun protein; domain 3
Domain ID domain_id3cjqA02
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_id3cjqB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1550 — Ribosomal protein L11, N-terminal domain
Homologous superfamily homologous superfamily10 — Ribosomal protein L11/L12, N-terminal domain
Domain ID domain_id3cjqB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily250 — Ribosomal protein L11/L12, C-terminal domain
Domain ID domain_id3cjqD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1170 — Sun protein; domain 3
Domain ID domain_id3cjqD02
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_id3cjqE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1550 — Ribosomal protein L11, N-terminal domain
Homologous superfamily homologous superfamily10 — Ribosomal protein L11/L12, N-terminal domain
Domain ID domain_id3cjqE02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily250 — Ribosomal protein L11/L12, C-terminal domain
Domain ID domain_id3cjqG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1170 — Sun protein; domain 3
Domain ID domain_id3cjqG02
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_id3cjqH01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1550 — Ribosomal protein L11, N-terminal domain
Homologous superfamily homologous superfamily10 — Ribosomal protein L11/L12, N-terminal domain
Domain ID domain_id3cjqH02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily250 — Ribosomal protein L11/L12, C-terminal domain
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7. Citations (1)