SAXSdb — 4m5d

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

U3 small nucleolar RNA-associated protein 22

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ribosomal RNA-processing protein 7 × 1 （P25368） SULFATE ION × 11 TRIETHYLENE GLYCOL × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UTP22_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1237； UniProt 1–1237

Ribosomal RNA-processing protein 7

Saccharomyces cerevisiae

UniProt P25368

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	U3 small nucleolar RNA-associated protein 22 × 1 （P53254） SULFATE ION × 11 TRIETHYLENE GLYCOL × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RRP7_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–297； UniProt 1–297

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	4m5d
Deposition date deposition_date	2013-08-08
Structure title title	Crystal structure of the Utp22 and Rrp7 complex from Saccharomyces cerevisiae
Keywords keywords	Nucleolus, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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.

4m5d__assembly_1__model_1

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

Download this curve (.dat)

4m5d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4m5d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.54 Å
Rg (electron density)	39.41 Å
Total Rg	39.71 Å
Atom count	10316
Residues	1267
Excluded volume	185540 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4m5d__assembly_1__model_1`	dimeric （2）	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	U3 small nucleolar RNA-associated protein 22
Molecular weight formula_weight	140660.1 kDa
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	11079

MATSVKRKASETSDQNIVKVQKKHSTQDSTTDNGSKENDHSSQAINERTVPEQENDESDTSPESNEVATNTAATRHNGKVTATESYDIHIARETAELFKSNIFKLQIDELLEQVKLKQKHVLKVEKFLHKLYDILQEIPDWEEKSLAEVDSFFKNKIVSVPFVDPKPIPQNTNYKFNYKKPDISLIGSFALKAGIYQPNGSSIDTLLTMPKELFEKKDFLNFRCLHKRSVYLAYLTHHLLILLKKDKLDSFLQLEYSYFDNDPLLPILRISCSKPTGDSLSDYNFYKTRFSINLLIGFPYKVFEPKKLLPNRNCIRIAQESKEQSLPATPLYNFSVLSSSTHENYLKYLYKTKKQTESFVEATVLGRLWLQQRGFSSNMSHSGSLGGFGTFEFTILMAALLNGGGINSNKILLHGFSSYQLFKGVIKYLATMDLCHDGHLQFHSNPENSSSSPASKYIDEGFQTPTLFDKSTKVNILTKMTVSSYQILKEYAGETLRMLNNVVQDQFSNIFLTNISRFDNLKYDLCYDVQLPLGKYNNLETSLAATFGSMERVKFITLENFLAHKITNVARYALGDRIKYIQIEMVGQKSDFPITKRKVYSNTGGNHFNFDFVRVKLIVNPSECDKLVTKGPAHSETMSTEAAVFKNFWGIKSSLRRFKDGSITHCCVWSTSSSEPIISSIVNFALQKHVSKKAQISNETIKKFHNFLPLPNLPSSAKTSVLNLSSFFNLKKSFDDLYKIIFQMKLPLSVKSILPVGSAFRYTSLCQPVPFAYSDPDFFQDVILEFETSPKWPDEITSLEKAKTAFLLKIQEELSANSSTYRSFFSRDESIPYNLEIVTLNILTPEGYGFKFRVLTERDEILYLRAIANARNELKPELEATFLKFTAKYLASVRHTRTLENISHSYQFYSPVVRLFKRWLDTHLLLGHITDELAELIAIKPFVDPAPYFIPGSLENGFLKVLKFISQWNWKDDPLILDLVKPEDDIRDTFETSIGAGSELDSKTMKKLSERLTLAQYKGIQMNFTNLRNSDPNGTHLQFFVASKNDPSGILYSSGIPLPIATRLTALAKVAVNLLQTHGLNQQTINLLFTPGLKDYDFVVDLRTPIGLKSSCGILSATEFKNITNDQAPSNFPENLNDLSEKMDPTYQLVKYLNLKYKNSLILSSRKYIGVNGGEKGDKNVITGLIKPLFKGAHKFRVNLDCNVKPVDDENVILNKEAIFHEIAAFGNDMVINFETD

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	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Ribosomal RNA-processing protein 7
Molecular weight formula_weight	34526.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGIEDISAMKNGFIVVPFKLPDHKALPKSQEASLHFMFAKRHQSSNSNESDCLFLVNLPLLSNIEHMKKFVGQLCGKYDTVSHVEELLYNDEFGLHEVDLSALTSDLMSSTDVNEKRYTPRNTALLKFVDAASINNCWNALKKYSNLHAKHPNELFEWTYTTPSFTTFVNFYKPLDIDYLKEDIHTHMAIFEQREAQAQEDVQSSIVDEDGFTLVVGKNTKSLNSIRKKILNKNPLSKHENKAKPISNIDKKAKKDFYRFQVRERKKQEINQLLSKFKEDQERIKVMKAKRKFNPYT

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	Spodoptera frugiperda

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 4 Entity 4 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 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	763

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4m5dA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1410 — Poly(a)-polymerase, middle domain
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4m5dA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3020 —

Domain ID domain_id	4m5dA05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3030 —

Domain ID domain_id	4m5dB02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2760 —

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Unit-cell length a length_a	126.257 Å
Unit-cell length b length_b	129.560 Å
Unit-cell length c length_c	214.440 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.970 Å
Low-resolution limit resolution_low	19.940 Å
R factor r_factor	0.2099
R_work r_work	0.2084
R_free r_free	0.2385

Crystal structure of the Utp22 and Rrp7 complex from Saccharomyces cerevisiae

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

U3 small nucleolar RNA-associated protein 22

State in the Current Structure

Other States of the Same Protein in the Database

Ribosomal RNA-processing protein 7

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

4m5d__assembly_1__model_1

4m5d__assembly_1__model_1 | I(q)

4m5d__assembly_1__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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the Utp22 and Rrp7 complex from Saccharomyces cerevisiae

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

U3 small nucleolar RNA-associated protein 22

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ribosomal RNA-processing protein 7

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

4m5d__assembly_1__model_1

4m5d__assembly_1__model_1 | I(q)

4m5d__assembly_1__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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)