6k0b

cryo-EM structure of archaeal Ribonuclease P with mature tRNA

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribonuclease P protein component 2

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 4	Ribonuclease P protein component 3 × 2 （Q58539） Ribonuclease P protein component 1 × 2 （Q57903） Ribonuclease P protein component 4 × 2 （Q58372） 50S ribosomal protein L7Ae × 2 （P54066） tRNA × 2 RPR × 2 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNP2_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–134； UniProt 1–134 Author chain B； PDBConstruct 1–134； UniProt 1–134

Ribonuclease P protein component 3

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

UniProt Q58539

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 4	Ribonuclease P protein component 2 × 2 （Q57917） Ribonuclease P protein component 1 × 2 （Q57903） Ribonuclease P protein component 4 × 2 （Q58372） 50S ribosomal protein L7Ae × 2 （P54066） tRNA × 2 RPR × 2 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNP3_METJA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–232； UniProt 1–232 Author chain D； PDBConstruct 1–232； UniProt 1–232

Ribonuclease P protein component 1

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

UniProt Q57903

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 4	Ribonuclease P protein component 2 × 2 （Q57917） Ribonuclease P protein component 3 × 2 （Q58539） Ribonuclease P protein component 4 × 2 （Q58372） 50S ribosomal protein L7Ae × 2 （P54066） tRNA × 2 RPR × 2 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNP1_METJA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–95； UniProt 1–95 Author chain F； PDBConstruct 1–95； UniProt 1–95

Ribonuclease P protein component 4

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

UniProt Q58372

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 4	Ribonuclease P protein component 2 × 2 （Q57917） Ribonuclease P protein component 3 × 2 （Q58539） Ribonuclease P protein component 1 × 2 （Q57903） 50S ribosomal protein L7Ae × 2 （P54066） tRNA × 2 RPR × 2 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNP4_METJA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain G； PDBConstruct 1–128； UniProt 1–128 Author chain H； PDBConstruct 1–128； UniProt 1–128

50S ribosomal protein L7Ae

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

UniProt P54066

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 4	Ribonuclease P protein component 2 × 2 （Q57917） Ribonuclease P protein component 3 × 2 （Q58539） Ribonuclease P protein component 1 × 2 （Q57903） Ribonuclease P protein component 4 × 2 （Q58372） tRNA × 2 RPR × 2 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL7A_METJA
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain I； PDBConstruct 1–117； UniProt 1–117 Author chain J； PDBConstruct 1–117； UniProt 1–117

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_id	6k0b
Deposition date deposition_date	2019-05-05
Structure title title	cryo-EM structure of archaeal Ribonuclease P with mature tRNA
Keywords keywords	Ribonuclease P, RNA-protein complex, RNA BINDING PROTEIN-RNA complex; RNA BINDING PROTEIN/RNA
Experimental Method method	ELECTRON 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.

6k0b__assembly_1__model_1

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

Download this curve (.dat)

6k0b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6k0b__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	63.32 Å
Rg (electron density)	63.57 Å
Total Rg	63.61 Å
Atom count	25908
Residues	2058
Excluded volume	412430 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6k0b__assembly_1__model_1`	tetradecameric （14）	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 (8)

Entity 1 Entity 1 polymer

Description description	Ribonuclease P protein component 2
Molecular weight formula_weight	15972.2 kDa
EC 编号 ec_number	3.1.26.5
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	25908

MIEMLKTLPPTLREKKRYIAFKILYDEELKEGEVVNLIRKAVLEYYGSWGTSKANPWLVYYDFPYGILRCQRDNVDYVKASLILIREFKEKPVNIICLGVSGTIRKAKIKFLGIKKPKRWFVIRRERLKAKKQK

Source Source

Source organism organism	Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
NCBI taxonomy ID ncbi_taxonomy_id	243232
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Ribonuclease P protein component 3
Molecular weight formula_weight	27394.8 kDa
EC 编号 ec_number	3.1.26.5
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MRIDINRIEKEEDIKLLKELKWNGFVFYQYDDEFSKDRYEEVKAIAESYKLKVYSGVKIKTESSKQLRDKVKKFRNKCHIILIEGGVLKINRAAVELHDVDILSTPELGRKDSGIDHVLARLASNHRVAIELNFKTLLNKDGYERARTLLFFRNNLKLAKKFDVPVVISTDAENKYQIKNPYDLRAFLNTLVEPLYAKKIMETAYKICDFRDYLMRDNVVRYGVEIIKEEKE

Source Source

Source organism organism	Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
NCBI taxonomy ID ncbi_taxonomy_id	243232
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Ribonuclease P protein component 1
Molecular weight formula_weight	10910.2 kDa
EC 编号 ec_number	3.1.26.5
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

MITPHNILRHELIGLKVEIVEAKNKAMIGIKGKVVDETRNTLVIEKEDGREVVIPKDIAVFLFQLKGCKVKVDGRLLIGRPEERLKKKIKILYPY

Source Source

Source organism organism	Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
NCBI taxonomy ID ncbi_taxonomy_id	243232
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Ribonuclease P protein component 4
Molecular weight formula_weight	15610.0 kDa
EC 编号 ec_number	3.1.26.5
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H

MKKFLEKKLKKIAYERIDILMSLAEEEAKKGNWDRAKRYVYLARRIAMKMRIRFPKKWKRRICKKCGTFLLYGRNARVRIKSKRYPHVVITCLECGAIYRIPMIREKKEKRRKKLEERLKAKSNSQTS

Source Source

Source organism organism	Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
NCBI taxonomy ID ncbi_taxonomy_id	243232
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	50S ribosomal protein L7Ae
Molecular weight formula_weight	12703.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J

MAVYVKFKVPEEIQKELLDAVAKAQKIKKGANEVTKAVERGIAKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGLEVAASSVAIINEGDAEELKVLIEKVNVLKQ

Source Source

Source organism organism	Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
NCBI taxonomy ID ncbi_taxonomy_id	243232
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 polymer

Description description	tRNA
Molecular weight formula_weight	26613.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	U,V

GGUGGGGUUCCCGAGCGGCCAAAGGGAGCAGACUCUAAAUCUGCCGUCAUCGACUUCGAAGGUUCGAAUCCUUCCCCCACCAC

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	RPR
Molecular weight formula_weight	83581.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	X,Y

GGAGGGGGCUGGUGACUUUCCCCUCUUUAAGAGGGGAGGAAGUUCCGCCCACCCCAUUUAUGGGCAGCGUCCCCUGAGAAGGGGCGGGAGAUGCAGCAGAAACGACACGGCUCCGGAAGAGAUGACGAUGAUAGUGAAAGUUGAGGACUUCCGGAGAACCGGUGAAACGGGCAUCUCCCCUGCCCGGGGUGCAAGCCGGUUUCGGCGCUUAGCCGAAUGUCACCGAAAUUACAGAAGGCGGGCUAUAGCCCCCAUUUU

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.30 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	150000

cryo-EM structure of archaeal Ribonuclease P with mature tRNA

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribonuclease P protein component 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ribonuclease P protein component 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ribonuclease P protein component 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ribonuclease P protein component 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

50S ribosomal protein L7Ae

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6k0b__assembly_1__model_1

6k0b__assembly_1__model_1 | I(q)

6k0b__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 non-polymer

7. Citations (1)