6w6v

Structure of yeast RNase MRP holoenzyme

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribonucleases P/MRP protein subunit POP1

OrganismNot specified

UniProt P41812

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 10 RNA 1 RNA component of RNase MRP NME1 × 1 RNases MRP/P 32.9 kDa subunit × 1 (P38336) Ribonuclease P/MRP protein subunit POP5 × 1 (P28005) Ribonucleases P/MRP protein subunit POP6 × 1 (P53218) Ribonucleases P/MRP protein subunit POP7 × 1 (P38291) Ribonucleases P/MRP protein subunit POP8 × 1 (P38208) Ribonuclease P/MRP protein subunit RPP1 × 2 (P38786) Ribonuclease MRP protein subunit SNM1 × 1 (P40993) Ribonuclease MRP protein subunit RMP1 × 1 (Q12530) Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name POP1_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–875; UniProt 1–875

RNases MRP/P 32.9 kDa subunit

OrganismNot specified

UniProt P38336

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 10 RNA 1 RNA component of RNase MRP NME1 × 1 Ribonucleases P/MRP protein subunit POP1 × 1 (P41812) Ribonuclease P/MRP protein subunit POP5 × 1 (P28005) Ribonucleases P/MRP protein subunit POP6 × 1 (P53218) Ribonucleases P/MRP protein subunit POP7 × 1 (P38291) Ribonucleases P/MRP protein subunit POP8 × 1 (P38208) Ribonuclease P/MRP protein subunit RPP1 × 2 (P38786) Ribonuclease MRP protein subunit SNM1 × 1 (P40993) Ribonuclease MRP protein subunit RMP1 × 1 (Q12530) Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name POP4_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 1–279; UniProt 1–279

Ribonuclease P/MRP protein subunit POP5

OrganismNot specified

UniProt P28005

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 10 RNA 1 RNA component of RNase MRP NME1 × 1 Ribonucleases P/MRP protein subunit POP1 × 1 (P41812) RNases MRP/P 32.9 kDa subunit × 1 (P38336) Ribonucleases P/MRP protein subunit POP6 × 1 (P53218) Ribonucleases P/MRP protein subunit POP7 × 1 (P38291) Ribonucleases P/MRP protein subunit POP8 × 1 (P38208) Ribonuclease P/MRP protein subunit RPP1 × 2 (P38786) Ribonuclease MRP protein subunit SNM1 × 1 (P40993) Ribonuclease MRP protein subunit RMP1 × 1 (Q12530) Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name POP5_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain E; PDBConstruct 1–173; UniProt 1–173

Ribonucleases P/MRP protein subunit POP6

OrganismNot specified

UniProt P53218

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 10 RNA 1 RNA component of RNase MRP NME1 × 1 Ribonucleases P/MRP protein subunit POP1 × 1 (P41812) RNases MRP/P 32.9 kDa subunit × 1 (P38336) Ribonuclease P/MRP protein subunit POP5 × 1 (P28005) Ribonucleases P/MRP protein subunit POP7 × 1 (P38291) Ribonucleases P/MRP protein subunit POP8 × 1 (P38208) Ribonuclease P/MRP protein subunit RPP1 × 2 (P38786) Ribonuclease MRP protein subunit SNM1 × 1 (P40993) Ribonuclease MRP protein subunit RMP1 × 1 (Q12530) Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name POP6_YEAST
Isoform —
PDB entities 5
Chains and sequence ranges Author chain F; PDBConstruct 1–158; UniProt 1–158

Ribonucleases P/MRP protein subunit POP7

OrganismNot specified

UniProt P38291

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 10 RNA 1 RNA component of RNase MRP NME1 × 1 Ribonucleases P/MRP protein subunit POP1 × 1 (P41812) RNases MRP/P 32.9 kDa subunit × 1 (P38336) Ribonuclease P/MRP protein subunit POP5 × 1 (P28005) Ribonucleases P/MRP protein subunit POP6 × 1 (P53218) Ribonucleases P/MRP protein subunit POP8 × 1 (P38208) Ribonuclease P/MRP protein subunit RPP1 × 2 (P38786) Ribonuclease MRP protein subunit SNM1 × 1 (P40993) Ribonuclease MRP protein subunit RMP1 × 1 (Q12530) Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name POP7_YEAST
Isoform —
PDB entities 6
Chains and sequence ranges Author chain G; PDBConstruct 1–140; UniProt 1–140

Ribonucleases P/MRP protein subunit POP8

OrganismNot specified

UniProt P38208

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 10 RNA 1 RNA component of RNase MRP NME1 × 1 Ribonucleases P/MRP protein subunit POP1 × 1 (P41812) RNases MRP/P 32.9 kDa subunit × 1 (P38336) Ribonuclease P/MRP protein subunit POP5 × 1 (P28005) Ribonucleases P/MRP protein subunit POP6 × 1 (P53218) Ribonucleases P/MRP protein subunit POP7 × 1 (P38291) Ribonuclease P/MRP protein subunit RPP1 × 2 (P38786) Ribonuclease MRP protein subunit SNM1 × 1 (P40993) Ribonuclease MRP protein subunit RMP1 × 1 (Q12530) Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name POP8_YEAST
Isoform —
PDB entities 7
Chains and sequence ranges Author chain H; PDBConstruct 1–133; UniProt 1–133

Ribonuclease P/MRP protein subunit RPP1

OrganismNot specified

UniProt P38786

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 10 RNA 1 RNA component of RNase MRP NME1 × 1 Ribonucleases P/MRP protein subunit POP1 × 1 (P41812) RNases MRP/P 32.9 kDa subunit × 1 (P38336) Ribonuclease P/MRP protein subunit POP5 × 1 (P28005) Ribonucleases P/MRP protein subunit POP6 × 1 (P53218) Ribonucleases P/MRP protein subunit POP7 × 1 (P38291) Ribonucleases P/MRP protein subunit POP8 × 1 (P38208) Ribonuclease MRP protein subunit SNM1 × 1 (P40993) Ribonuclease MRP protein subunit RMP1 × 1 (Q12530) Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPP1_YEAST
Isoform —
PDB entities 8
Chains and sequence ranges Author chain I; PDBConstruct 1–293; UniProt 1–293 Author chain J; PDBConstruct 1–293; UniProt 1–293

Ribonuclease MRP protein subunit SNM1

OrganismNot specified

UniProt P40993

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 10 RNA 1 RNA component of RNase MRP NME1 × 1 Ribonucleases P/MRP protein subunit POP1 × 1 (P41812) RNases MRP/P 32.9 kDa subunit × 1 (P38336) Ribonuclease P/MRP protein subunit POP5 × 1 (P28005) Ribonucleases P/MRP protein subunit POP6 × 1 (P53218) Ribonucleases P/MRP protein subunit POP7 × 1 (P38291) Ribonucleases P/MRP protein subunit POP8 × 1 (P38208) Ribonuclease P/MRP protein subunit RPP1 × 2 (P38786) Ribonuclease MRP protein subunit RMP1 × 1 (Q12530) Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RMRP_YEAST
Isoform —
PDB entities 9
Chains and sequence ranges Author chain K; PDBConstruct 1–198; UniProt 1–198

Ribonuclease MRP protein subunit RMP1

OrganismNot specified

UniProt Q12530

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 10 RNA 1 RNA component of RNase MRP NME1 × 1 Ribonucleases P/MRP protein subunit POP1 × 1 (P41812) RNases MRP/P 32.9 kDa subunit × 1 (P38336) Ribonuclease P/MRP protein subunit POP5 × 1 (P28005) Ribonucleases P/MRP protein subunit POP6 × 1 (P53218) Ribonucleases P/MRP protein subunit POP7 × 1 (P38291) Ribonucleases P/MRP protein subunit POP8 × 1 (P38208) Ribonuclease P/MRP protein subunit RPP1 × 2 (P38786) Ribonuclease MRP protein subunit SNM1 × 1 (P40993) Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RMP1_YEAST
Isoform —
PDB entities 10
Chains and sequence ranges Author chain L; PDBConstruct 1–201; UniProt 1–201

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_id6w6v
Deposition date deposition_date2020-03-17
Structure title titleStructure of yeast RNase MRP holoenzyme
Keywords keywordsribozyme, RNP, ribonucleoprotein, HYDROLASE; HYDROLASE
Experimental Method methodELECTRON MICROSCOPY
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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.

6w6v__assembly_1__model_1

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

Download this curve (.dat)

6w6v__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.

6w6v__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)48.38 Å
Rg (electron density)48.71 Å
Total Rg48.84 Å
Atom count24828
Residues2600
Excluded volume421260 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6w6v__assembly_1__model_1 undecameric (11) 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 (10)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id6w6vE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily3250 — Ribonuclease P, Pop5 subunit
Domain ID domain_id6w6vG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily20 — Alba-like domain
Domain ID domain_id6w6vI01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily140 — Metal-dependent hydrolases
Domain ID domain_id6w6vJ01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily140 — Metal-dependent hydrolases
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7. Citations (1)