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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 3–394	Fragment：UNP residues 3-394	H/ACA ribonucleoprotein complex subunit 3 × 1 （Q6Q547） H/ACA ribonucleoprotein complex subunit 1 × 1 （P28007）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.04；293 K；0.2M sodium malonate, 7%(w/v) polyethylene glycol 3350, pH 8.04, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.233

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3U28	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3UAI Structure of the Shq1-Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae Deposited 2011-10-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 3–394（392 aa） Fragment：Core domain, UNP residues 3-394	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；297 K；0.1M Bis-Tris, 20%(w/v) polyethylene glycol monomethyl ether 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 3.06 Å R-free 0.275
3ZV0 Structure of the SHQ1P-CBF5P complex Deposited 2011-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–60（60 aa） Fragment：DCAT DOMAIN, RESIDUES 1-60,258-386 Chain C 258–386（129 aa） Fragment：DCAT DOMAIN, RESIDUES 1-60,258-386 Chain D 1–60（60 aa） Fragment：DCAT DOMAIN, RESIDUES 1-60,258-386 Chain D 258–386（129 aa） Fragment：DCAT DOMAIN, RESIDUES 1-60,258-386	Not recorded	GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；CRYSTALLIZED AT 291 KELVIN BY THE HANGING DROP VAPOR DIFFUSION METHOD FROM A 1:1 UL OF PROTEIN AND PRECIPITANT CONTAINING 4 TO 8 % PEG 2000	Resolution 2.80 Å R-free 0.208
9G25 snR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 Deposited 2024-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain A 1–483（483 aa） Chain E 1–483（483 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.89 Å
9G28 snR30 snoRNP - State 2 - Utp23-Krr1-deltaC3 Deposited 2024-07-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain A 1–483（483 aa） Chain E 1–483（483 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–58	Not recorded	H/ACA ribonucleoprotein complex subunit 4 × 1 （P33322） H/ACA ribonucleoprotein complex subunit 1 × 1 （P28007）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.04；293 K；0.2M sodium malonate, 7%(w/v) polyethylene glycol 3350, pH 8.04, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.233

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3U28	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Y2Y Structural Characterization of Nop10p using Nuclear Magnetic Resonance Spectroscopy Deposited 2004-11-23	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–58（58 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；288 K；Ionic strength (raw mmCIF value) 110 mM；Pressure ambient NMR sample composition 1.5 mM 15N/13C Nop1p0p; 10 mM potassium phosphate buffer, pH 6.5; 100 mM potassium chloride; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.5 mM 15N/13C Nop1p0p; 10 mM potassium phosphate buffer, pH 6.5; 100 mM potassium chloride; 100% D2O \| 100% D2O	Resolution not provided
2AQA NMR structural analysis of Nop10p from Saccharomyces cerevisiae Deposited 2005-08-17	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–58（57 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；298 K；Ionic strength (raw mmCIF value) 50mM; 100mM；Pressure 1 NMR sample composition 1mM yNop10p unlabelled; Sodium Acetate, KCl \| 90% H2O/10% D2O NMR sample composition 1mM yNop10p unlabelled; Sodium Acetate, KCl \| 100% D2O NMR sample composition 1mM yNop10p 15N-labelled; Sodium Acetate, KCl \| 90% H2O/10% D2O NMR sample composition 1mM yNop10p 15N,13C-labelled; Sodium Acetate, KCl \| 90% H2O/10% D2O	Resolution not provided
3UAI Structure of the Shq1-Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae Deposited 2011-10-21	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–58（58 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；297 K；0.1M Bis-Tris, 20%(w/v) polyethylene glycol monomethyl ether 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 3.06 Å R-free 0.275
9G25 snR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 Deposited 2024-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain B 1–58（58 aa） Chain F 1–58（58 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.89 Å
9G28 snR30 snoRNP - State 2 - Utp23-Krr1-deltaC3 Deposited 2024-07-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain B 1–58（58 aa） Chain F 1–58（58 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 32–124	Fragment：UNP residues 32-124	H/ACA ribonucleoprotein complex subunit 4 × 1 （P33322） H/ACA ribonucleoprotein complex subunit 3 × 1 （Q6Q547）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.04；293 K；0.2M sodium malonate, 7%(w/v) polyethylene glycol 3350, pH 8.04, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.233

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3U28	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3UAI Structure of the Shq1-Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae Deposited 2011-10-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 32–124（93 aa） Fragment：Core domain, UNP residues 32-124	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；297 K；0.1M Bis-Tris, 20%(w/v) polyethylene glycol monomethyl ether 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 3.06 Å R-free 0.275
9G25 snR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 Deposited 2024-07-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain C 1–205（205 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.89 Å
9G28 snR30 snoRNP - State 2 - Utp23-Krr1-deltaC3 Deposited 2024-07-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain C 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.02 Å
Radius of gyration Rg (electron density) rg_electron	27.48 Å
Forward intensity I(0) i0	46000400.00
Molecular weight molecular_weight	53402.0 kDa
Excluded volume excluded_volume	67247 Å³
Envelope volume envelope_volume	84948 Å³
Hydration-shell volume shell_volume	26599 Å³
Envelope diameter envelope_diameter	91.0 Å
Shell Rg shell_rg	33.59 Å
Envelope Rg envelope_rg	27.58 Å
Shape Rg shape_rg	27.51 Å
Total Rg total_rg	28.06 Å
Total atoms total_atoms	3749
Residues n_residues	475
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	89.1 Å
Rg (real space) rg_real	28.10 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	4.6000e+07
I(0) uncertainty (real space) i0_real_error	6.7480e+05
Rg (reciprocal space) rg_reciprocal	28.08 Å
I(0) (reciprocal space) i0_reciprocal	46000000.0000
Solution quality estimate total_estimate	0.8903
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	26.6 Å
Skewness Skewness skewness	0.330
Kurtosis Kurtosis kurtosis	-0.565
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13240000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.821

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	yeast
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 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

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	yeast
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 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

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	yeast
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 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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7. 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/u2/3u28/3u28.fit
pddf	/app/data/pr_computation/u2/3u28/3u28.pr.out
profile	/app/data/saxs_computation/u2/3u28/3u28.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)