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3nvi

Structure of N-terminal truncated Nop56/58 bound with L7Ae and box C/D RNA

Method: X-RAY DIFFRACTION
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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 4 RNA 2 50S ribosomal protein L7Ae × 2 （Q8U160） ;RNA (5'-R(*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*AP*AP*GP*GP*CP*GP*UP*GP*AP*UP*GP*AP*GP*C)-3') ; × 2 water × 5 Consistent with all polymers
2 Protein–RNA Heteromer Protein 2 RNA 1 50S ribosomal protein L7Ae × 1 （Q8U160） ;RNA (5'-R(*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*AP*AP*GP*GP*CP*GP*UP*GP*AP*UP*GP*AP*GP*C)-3') ; × 1 water × 2 Consistent with all polymers
3 Protein–RNA Heteromer Protein 2 RNA 1 50S ribosomal protein L7Ae × 1 （Q8U160） ;RNA (5'-R(*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*AP*AP*GP*GP*CP*GP*UP*GP*AP*UP*GP*AP*GP*C)-3') ; × 1 water × 3 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 1
Chains and sequence ranges Author chain A； PDBConstruct 11–379； UniProt 1–369 Author chain C； PDBConstruct 11–379； UniProt 1–369

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 4 RNA 2 NOP5/NOP56 related protein × 2 （Q8U4M1） ;RNA (5'-R(*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*AP*AP*GP*GP*CP*GP*UP*GP*AP*UP*GP*AP*GP*C)-3') ; × 2 water × 5 Consistent with all polymers
2 Protein–RNA Heteromer Protein 2 RNA 1 NOP5/NOP56 related protein × 1 （Q8U4M1） ;RNA (5'-R(*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*AP*AP*GP*GP*CP*GP*UP*GP*AP*UP*GP*AP*GP*C)-3') ; × 1 water × 2 Consistent with all polymers
3 Protein–RNA Heteromer Protein 2 RNA 1 NOP5/NOP56 related protein × 1 （Q8U4M1） ;RNA (5'-R(*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*AP*AP*GP*GP*CP*GP*UP*GP*AP*UP*GP*AP*GP*C)-3') ; × 1 water × 3 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 2
Chains and sequence ranges Author chain B； PDBConstruct 8–129； UniProt 2–123 Author chain D； PDBConstruct 8–129； UniProt 2–123

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_id3nvi
Deposition date deposition_date2010-07-08
Structure title titleStructure of N-terminal truncated Nop56/58 bound with L7Ae and box C/D RNA
Keywords keywordsKink turn, ribosome biogenesis, 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.

3nvi__assembly_2__model_1

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

Download this curve (.dat)

3nvi__assembly_2__model_1 | I(q)

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

3nvi__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）27.93 Å
Rg (electron density)28.56 Å
Total Rg28.83 Å
Atom count3429
Residues392
Excluded volume59894 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3nvi__assembly_1__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3nvi__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3nvi__assembly_3__model_1 trimeric （3） 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 (4)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3nvia_
Class classa — All alpha proteins
Fold Fold folda.183 — Nop domain
Superfamily Superfamily superfamilya.183.1 — Nop domain
Family Family familya.183.1.0 — automated matches
Domain ID domain_idd3nvic_
Class classa — All alpha proteins
Fold Fold folda.183 — Nop domain
Superfamily Superfamily superfamilya.183.1 — Nop domain
Family Family familya.183.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id3nviA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily4070 —
Domain ID domain_id3nviA02
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_id3nviB00
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_id3nviC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily4070 —
Domain ID domain_id3nviC02
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_id3nviD00
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
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7. Citations (1)