SAXSdb — 5t16

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

Ribonuclease 3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 6 RNA 2	RNA substrate analog × 2 1,2-ETHANEDIOL × 4 water × 8	Consistent with all polymers
2	Protein–RNA	Homooligomer	Protein 6 RNA 2	RNA substrate analog × 2 1,2-ETHANEDIOL × 6 water × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNT1_YEAST
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–276； UniProt 184–459 Author chain B； PDBConstruct 1–276； UniProt 184–459 Author chain I； PDBConstruct 1–276； UniProt 184–459 Author chain J； PDBConstruct 1–276； UniProt 184–459 Author chain C； PDBConstruct 1–119； UniProt 41–159 Author chain D； PDBConstruct 1–119； UniProt 41–159 Author chain E； PDBConstruct 1–119； UniProt 41–159 Author chain F； PDBConstruct 1–119； UniProt 41–159 Author chain K； PDBConstruct 1–119； UniProt 41–159 Author chain L； PDBConstruct 1–119； UniProt 41–159 Author chain M； PDBConstruct 1–119； UniProt 41–159 Author chain N； PDBConstruct 1–119； UniProt 41–159

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	5t16
Deposition date deposition_date	2016-08-18
Structure title title	Crystal structure of yeast RNase III (Rnt1p) complexed with a non-hydrolyzable RNA substrate analog
Keywords keywords	Rnt1p, RNase III, substrate-loaded complex, hydrolase-rna complex; hydrolase/rna
Experimental Method method	X-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.

5t16__assembly_2__model_1

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

Download this curve (.dat)

5t16__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5t16__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	41.60 Å
Rg (electron density)	43.09 Å
Total Rg	42.99 Å
Atom count	9599
Residues	1068
Excluded volume	167090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5t16__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5t16__assembly_2__model_1`	octameric （8）	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 (5)

Entity 1 Entity 1 polymer

Description description	Ribonuclease 3
Molecular weight formula_weight	31481.3 kDa
EC 编号 ec_number	3.1.26.3
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,I,J
Atom count atom_count	19568

YDPTKAGDIVKATKWPPKLPEIQDLAIRARVFIHKSTIKDKVYLSGSEMINAHNERLEFLGDSILNSVMTLIIYNKFPDYSEGQLSTLRMNLVSNEQIKQWSIMYNFHEKLKTNFDLKDENSNFQNGKLKLYADVFEAYIGGLMEDDPRNNLPKIRKWLRKLAKPVIEEATRNQVALEKTDKLDMNAKRQLYSLIGYASLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIRAAENALRDKKMLDFYAKQRAAIPRSESVLKDPS

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ribonuclease 3
Molecular weight formula_weight	13975.9 kDa
EC 编号 ec_number	3.1.26.3
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,E,F,K,L,M,N

ISNYKYLEVIQLEHAVTKLVESYNKIIELSPNLVAYNEAVNNQDRVPVQILPSLSRYQLKLAAELKTLHDLKKDAILTEITDYENEFDTEQKQPILQEISKADMEKLEKLEQVKREKRE

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	RNA substrate analog
Molecular weight formula_weight	10940.6 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	G,H,O,P

GCXAUGUCAUGUCAUGAGUCCAUGGCAUGGCAUG

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	358

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Unit-cell length a length_a	62.037 Å
Unit-cell length b length_b	164.065 Å
Unit-cell length c length_c	176.855 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.78 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.783 Å
Low-resolution limit resolution_low	38.985 Å
R factor r_factor	0.2263
R_work r_work	0.2259
R_free r_free	0.2653

Crystal structure of yeast RNase III (Rnt1p) complexed with a non-hydrolyzable RNA substrate analog

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

Ribonuclease 3

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

5t16__assembly_2__model_1

5t16__assembly_2__model_1 | I(q)

5t16__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

7. Citations (2)

Crystal structure of yeast RNase III (Rnt1p) complexed with a non-hydrolyzable RNA substrate analog

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

Ribonuclease 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5t16__assembly_2__model_1

5t16__assembly_2__model_1 | I(q)

5t16__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

7. Citations (2)