SAXSdb — 6yle

▼

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

Pre-rRNA-processing protein IPI3

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Pre-rRNA-processing protein RIX1 × 2 （P38883） Pre-rRNA-processing protein IPI1 × 1 （A6ZSZ4）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IPI3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–555； UniProt 1–555 Author chain B； PDBConstruct 1–555； UniProt 1–555

Pre-rRNA-processing protein RIX1

OrganismNot specified

UniProt P38883

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Pre-rRNA-processing protein IPI3 × 2 （P53877） Pre-rRNA-processing protein IPI1 × 1 （A6ZSZ4）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIX1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–763； UniProt 1–763 Author chain D； PDBConstruct 1–763； UniProt 1–763

Pre-rRNA-processing protein IPI1

OrganismNot specified

UniProt A6ZSZ4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Pre-rRNA-processing protein IPI3 × 2 （P53877） Pre-rRNA-processing protein RIX1 × 2 （P38883）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IPI1_YEAS7
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain K； PDBConstruct 1–334； UniProt 1–334

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	6yle
Deposition date deposition_date	2020-04-07
Structure title title	Rix1-Rea1 pre-60S particle - Rix1-subcomplex, body 3 (rigid body refinement)
Keywords keywords	pre-60S, Biogenesis, LSU, Large subunit, ribosome assembly, RIBOSOME; RIBOSOME
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

6yle__assembly_1__model_1

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

Download this curve (.dat)

6yle__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6yle__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.97 Å
Rg (electron density)	37.87 Å
Total Rg	38.51 Å
Atom count	15345
Residues	1930
Excluded volume	278130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6yle__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Pre-rRNA-processing protein IPI3
Molecular weight formula_weight	61836.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	15345

MDEQVIFTTNTSGTIASVHSFEQINLRQCSTQSRNSCVQVGNKYLFIAQAQKALINVYNLSGSFKRESVEQRLPLPEILKCLEVVENDGVQYDRIQGVNHNLPDFNLPYLLLGSTESGKLYIWELNSGILLNVKPMAHYQSITKIKSILNGKYIITSGNDSRVIIWQTVDLVSASNDDPKPLCILHDHTLPVTDFQVSSSQGKFLSCTDTKLFTVSQDATIRCYDLSLIGSKKKQKANENDVSIGKTPVLLATFTTPYSIKSIVLDPADRACYIGTAEGCFSLNLFYKLKGNAIVNLLQSAGVNTVQKGRVFSLVQRNSLTGGENEDLDALYAMGQLVCENVLNSNVSCLEISMDGTLLLIGDTEGKVSIAEIYSKQIIRTIQTLTTSQDSVGEVTNLLTNPYRLERGNLLFEGESKGKQPSNNNGHNFMKIPNLQRVIFDGKNKGHLHDIWYQIGEPEAETDPNLALPLNDFNAYLEQVKTQESIFSHIGKVSSNVKVIDNKIDATSSLDSNAAKDEEITELKTNIEALTHAYKELRDMHEKLYEEHQQMLDKQ

Entity 2 Entity 2 polymer

Description description	Pre-rRNA-processing protein RIX1
Molecular weight formula_weight	86839.8 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MSEEFIAVSTLARNLEIAKGNEFHTILATLRSPVYINEQLLKSELSFLVTKILKLIRSGNDFDLWKGCHTSVVTCAYNPLVLSTHGGQLLAAIYSRLEQKTGFYSSVISSSHGKQLFNTLISSVAIIIDLMKNKPTLSREALVPKLKAIIPTLITLSQYEPELVLPVLQRILKRNTTTFKPFTNKFRTVLINLIISDYASLGTKTQRLVCENFAYLHLLKIQVSDTSDDETQAHHKIYADSNWRTGLMSILSQFKPIIQLCGEILDFEQDNELYKLIKSLPVIDESNNKEEFLPSLKLDFNAPLTLWEIPQRLSLLADMLVAFISLPTPFPIRVPLGGINSLCEVLLGVSNKYLPLKKELRHDNELNGVINTILPQIQFQGIRLWEIMVSKYGKCGLSFFEGILSSIELFIPLKKKSNNEIDFNVVGSLKFEFATVFRLVNMILSHLGHQLNIISVISQLIEVALFLSHDKTLIDSLFKNRKSIMKQQTKTKQSKRSKSAEGAFSDIYTHPELFVCKNSMNWFNEINDFFITALNNWILPSTPHIQILKYSITQSLRLKERFGYIPESFVNLLRCEVLHPGSERVSILPIAISLLKNINDDMFELLCHPKVPVGMVYQLHKPLDLGEDGEVRDDINKKEVETNESSSNANTGLETLKALENLENVTIPEPKHEVPKVVDDTAIFKKRSVEEVIERESTSSHKKVKFVEETTVDNGEELIVKKAVSQTKEEEKPMEDSEDEEQEEFEIPAIELSDDEEEEEEEE

Entity 3 Entity 3 polymer

Description description	Pre-rRNA-processing protein IPI1
Molecular weight formula_weight	37928.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MTKSRKQKQKKQDFLRKKLKVGKPKEKARNATDTSFVSKTISIRNQHLDQNPHDLTKRLTLLKHHNINVRKETLTTFQKSIPSIIKSRLMTPLLTQSIPLICDESQQVRQGLIDLVDEIGSHDAEILKLHCNIFVLYINMAMTHIVTQIQADSTKFLSHLLKYCGDEVVRKSWVKLLNGVFGVLGWGQVGKNDSASIVQTKKRNAKYVTIHLNALYTLVEYGCQDERARSDGDTAETTEDSGTLRNPYLIPDYPQPFEHLKLFTRELKVQDATSSGVNATLLSLATQDIDTRKAVFIEQFLPIVRKKIEVIIKEGGECGKSANKLKTLLAKIFD

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6yleA01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	6yleB01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

▶

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	—

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

Resolution resolution	3.30 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	114398

Rix1-Rea1 pre-60S particle - Rix1-subcomplex, body 3 (rigid body refinement)

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

Pre-rRNA-processing protein IPI3

State in the Current Structure

Other States of the Same Protein in the Database

Pre-rRNA-processing protein RIX1

State in the Current Structure

Other States of the Same Protein in the Database

Pre-rRNA-processing protein IPI1

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

6yle__assembly_1__model_1

6yle__assembly_1__model_1 | I(q)

6yle__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Rix1-Rea1 pre-60S particle - Rix1-subcomplex, body 3 (rigid body refinement)

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

Pre-rRNA-processing protein IPI3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Pre-rRNA-processing protein RIX1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Pre-rRNA-processing protein IPI1

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

6yle__assembly_1__model_1

6yle__assembly_1__model_1 | I(q)

6yle__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)