SAXSdb — 3u28

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

H/ACA ribonucleoprotein complex subunit 4

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	H/ACA ribonucleoprotein complex subunit 3 × 1 （Q6Q547） H/ACA ribonucleoprotein complex subunit 1 × 1 （P28007） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CBF5_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–394； UniProt 3–394

H/ACA ribonucleoprotein complex subunit 3

Saccharomyces cerevisiae

UniProt Q6Q547

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	H/ACA ribonucleoprotein complex subunit 4 × 1 （P33322） H/ACA ribonucleoprotein complex subunit 1 × 1 （P28007） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NOP10_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–58； UniProt 1–58

H/ACA ribonucleoprotein complex subunit 1

Saccharomyces cerevisiae

UniProt P28007

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	H/ACA ribonucleoprotein complex subunit 4 × 1 （P33322） H/ACA ribonucleoprotein complex subunit 3 × 1 （Q6Q547） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GAR1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 22–114； UniProt 32–124

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	3u28
Deposition date deposition_date	2011-10-02
Structure title title	Crystal structure of a Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae
Keywords keywords	pseudouridine synthase, pseudouridylation, H/ACA RNA, Nucleolus, ISOMERASE-PROTEIN BINDING complex; ISOMERASE/PROTEIN BINDING
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.

3u28__assembly_1__model_1

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

Download this curve (.dat)

3u28__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3u28__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.02 Å
Rg (electron density)	27.48 Å
Total Rg	28.06 Å
Atom count	3749
Residues	475
Excluded volume	67247 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3u28__assembly_1__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	H/ACA ribonucleoprotein complex subunit 4
Molecular weight formula_weight	44981.8 kDa
EC 编号 ec_number	5.4.99.-
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	4028

MAKEDFVIKPEAAGASTDTSEWPLLLKNFDKLLVRSGHYTPIPAGSSPLKRDLKSYISSGVINLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQGAGKEYVCIVRLHDALKDEKDLGRSLENLTGALFQRPPLISAVKRQLRVRTIYESNLIEFDNKRNLGVFWASCEAGTYMRTLCVHLGMLLGVGGHMQELRRVRSGALSENDNMVTLHDVMDAQWVYDNTRDESYLRSIIQPLETLLVGYKRIVVKDSAVNAVCYGAKLMIPGLLRYEEGIELYDEIVLITTKGEAIAVAIAQMSTVDLASCDHGVVASVKRCIMERDLYPRRWGLGPVAQKKKQMKADGKLDKYGRVNENTPEQWKKEYVPLDNAEQHHHHHH

Source Source

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

Entity 2 Entity 2 polymer

Description description	H/ACA ribonucleoprotein complex subunit 3
Molecular weight formula_weight	6649.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MHLMYTLGPDGKRIYTLKKVTESGEITKSAHPARFSPDDKYSRQRVTLKKRFGLVPGQ

Source Source

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

Entity 3 Entity 3 polymer

Description description	H/ACA ribonucleoprotein complex subunit 1
Molecular weight formula_weight	12618.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGSSHHHHHHSSGLVPRGSHMGPPDTVLEMGAFLHPCEGDIVCRSINTKIPYFNAPIYLENKTQVGKVDEILGPLNEVFFTIKCGDGVQATSFKEGDKFYIAADKLLPIERFLP

Source Source

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	279

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3u28b_
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.16 — Nop10-like SnoRNP
Family Family family	g.41.16.1 — Nucleolar RNA-binding protein Nop10-like

CATH v4.4 (4 domains)

Domain ID domain_id	3u28A01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
Homologous superfamily homologous superfamily	10 — PUA domain

Domain ID domain_id	3u28A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2350 — Pseudouridine synthase
Homologous superfamily homologous superfamily	10 — Pseudouridine synthase

Domain ID domain_id	3u28B01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	3u28C00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	230 — Probable tRNA pseudouridine synthase domain

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Unit-cell length a length_a	54.413 Å
Unit-cell length b length_b	59.386 Å
Unit-cell length c length_c	169.212 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	19.920 Å
R factor r_factor	0.2051
R_work r_work	0.2036
R_free r_free	0.2334

Crystal structure of a Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae

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

H/ACA ribonucleoprotein complex subunit 4

State in the Current Structure

Other States of the Same Protein in the Database

H/ACA ribonucleoprotein complex subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

H/ACA ribonucleoprotein complex subunit 1

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

3u28__assembly_1__model_1

3u28__assembly_1__model_1 | I(q)

3u28__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae

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

H/ACA ribonucleoprotein complex subunit 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

H/ACA ribonucleoprotein complex subunit 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

H/ACA ribonucleoprotein complex subunit 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3u28__assembly_1__model_1

3u28__assembly_1__model_1 | I(q)

3u28__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (1)