SAXSdb — 3iab

▼

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

Ribonucleases P/MRP protein subunit POP6

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 2 RNA 1	Ribonucleases P/MRP protein subunit POP7 × 1 （P38291） P3 domain of the RNA component of RNase MRP × 1 ZINC ION × 3 water × 3	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 4 RNA 2	Ribonucleases P/MRP protein subunit POP7 × 2 （P38291） P3 domain of the RNA component of RNase MRP × 2 ZINC ION × 6 water × 6	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–158； UniProt 1–158

Ribonucleases P/MRP protein subunit POP7

Saccharomyces cerevisiae

UniProt P38291

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 2 RNA 1	Ribonucleases P/MRP protein subunit POP6 × 1 （P53218） P3 domain of the RNA component of RNase MRP × 1 ZINC ION × 3 water × 3	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 4 RNA 2	Ribonucleases P/MRP protein subunit POP6 × 2 （P53218） P3 domain of the RNA component of RNase MRP × 2 ZINC ION × 6 water × 6	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–140； UniProt 1–140

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3iab
Deposition date deposition_date	2009-07-13
Structure title title	Crystal structure of RNase P /RNase MRP proteins Pop6, Pop7 in a complex with the P3 domain of RNase MRP RNA
Keywords keywords	;RNase P, RNase MRP, Ribonuclease P, Ribonuclease MRP, Pop6, Pop6p, Pop7, Pop7p, P3, NME1, yeast, tRNA, pre-tRNA, rRNA, Ribozyme, PROTEIN-RNA COMPLEX, ALBA, heterodimer, Coiled coil, Hydrolase, Nucleus, rRNA processing, tRNA processing, Phosphoprotein, HYDROLASE-RNA COMPLEX ;; HYDROLASE/RNA
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3iab__assembly_2__model_1

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

Download this curve (.dat)

3iab__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3iab__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	30.38 Å
Rg (electron density)	30.33 Å
Total Rg	30.67 Å
Atom count	6073
Residues	594
Excluded volume	102200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3iab__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3iab__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Ribonucleases P/MRP protein subunit POP6
Molecular weight formula_weight	18440.6 kDa
EC 编号 ec_number	3.1.26.5
Mutation mutation	L141M
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3087

MINGVYYNEISRDLDISSSTQCLRFLKETVIPSLANNGNNSTSIQYHGISKNDNIKKSVNKLDKQINMADRSLGLQQVVCIFSYGPHIQKMLSILEIFKKGYIKNNKKIYQWNKLTSFDIKREGRNELQEERLKVPILVTMVSDSEIIDLNLHSFTKQ

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ribonucleases P/MRP protein subunit POP7
Molecular weight formula_weight	15985.0 kDa
EC 编号 ec_number	3.1.26.5
Mutation mutation	none
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MALKKNTHNKSTKRVTKHPSLKTLTHKQIHTTIFVKSTTPYVSALKRINKFLDSVHKQGSSYVAVLGMGKAVEKTLALGCHFQDQKNKKIEVYTKTIEVLDEVITEGQADIDMESDVEDDDKETQLKKRAVSGVELRIYV

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	P3 domain of the RNA component of RNase MRP
Molecular weight formula_weight	14828.9 kDa
EC 编号 ec_number	3.1.26.5
Mutation mutation	;circular permutation; A49C, A50C, U59G, U60G (yeast sequence numbering). See important note regarging nucleotide numbering in the model. ;
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	R

GGACUCAGUAAUAUGCUUUGGAAACGAAGCUUACAAAAUGGAGUCC

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	50

▼

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3iabB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	20 — Alba-like domain

▶

Unit-cell length a length_a	126.514 Å
Unit-cell length b length_b	126.514 Å
Unit-cell length c length_c	76.766 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	8

Space group space_group	P 42 2 2
Space-group number int_tables_number	93
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2500
R_work r_work	0.2500
R_free r_free	0.2650

Crystal structure of RNase P /RNase MRP proteins Pop6, Pop7 in a complex with the P3 domain of RNase MRP RNA

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

Ribonucleases P/MRP protein subunit POP6

State in the Current Structure

Other States of the Same Protein in the Database

Ribonucleases P/MRP protein subunit POP7

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3iab__assembly_2__model_1

3iab__assembly_2__model_1 | I(q)

3iab__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of RNase P /RNase MRP proteins Pop6, Pop7 in a complex with the P3 domain of RNase MRP RNA

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

Ribonucleases P/MRP protein subunit POP6

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ribonucleases P/MRP protein subunit POP7

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

3iab__assembly_2__model_1

3iab__assembly_2__model_1 | I(q)

3iab__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)