2ey4

Crystal Structure of a Cbf5-Nop10-Gar1 Complex

Method: X-RAY DIFFRACTION

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

Probable tRNA pseudouridine synthase B

Pyrococcus furiosus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	small nucleolar rnp similar to gar1 × 1 Ribosome biogenesis protein Nop10 × 1 （Q8U1R4） ZINC ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	small nucleolar rnp similar to gar1 × 1 Ribosome biogenesis protein Nop10 × 1 （Q8U1R4） ZINC ION × 1 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	small nucleolar rnp similar to gar1 × 2 Ribosome biogenesis protein Nop10 × 2 （Q8U1R4） ZINC ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRUB_PYRFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–333； UniProt 1–333 Author chain B； PDBConstruct 1–333； UniProt 1–333

Ribosome biogenesis protein Nop10

Pyrococcus furiosus

UniProt Q8U1R4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Probable tRNA pseudouridine synthase B × 1 （Q7LWY0） small nucleolar rnp similar to gar1 × 1 ZINC ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Probable tRNA pseudouridine synthase B × 1 （Q7LWY0） small nucleolar rnp similar to gar1 × 1 ZINC ION × 1 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Probable tRNA pseudouridine synthase B × 2 （Q7LWY0） small nucleolar rnp similar to gar1 × 2 ZINC ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NOP10_PYRFU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–55； UniProt 1–55 Author chain F； PDBConstruct 1–55； UniProt 1–55

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	2ey4
Deposition date deposition_date	2005-11-09
Structure title title	Crystal Structure of a Cbf5-Nop10-Gar1 Complex
Keywords keywords	;Trimeric complex, Structural Genomics, PSI, Protein Structure Initiative, Southeast Collaboratory for Structural Genomics, SECSG, ISOMERASE-BIOSYNTHETIC PROTEIN COMPLEX ;; ISOMERASE/BIOSYNTHETIC 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.

2ey4__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ey4__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ey4__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	39.81 Å
Rg (electron density)	40.34 Å
Total Rg	40.60 Å
Atom count	7280
Residues	907
Excluded volume	131670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ey4__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ey4__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2ey4__assembly_3__model_1`	hexameric （6）	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	Probable tRNA pseudouridine synthase B
Molecular weight formula_weight	37664.0 kDa
EC 编号 ec_number	5.4.99.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7456

MARDEVRRILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKL

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	2261
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	small nucleolar rnp similar to gar1
Molecular weight formula_weight	9505.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MEKQGEKMKRLGKVLHYAKQGFLIVRTNWVPSLNDRVVDKRLQFVGIVKDVFGPVKMPYVAIKPKVSNPEIYVGEVLYVDER

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	186497
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Ribosome biogenesis protein Nop10
Molecular weight formula_weight	6640.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

MRFRIRKCPKCGRYTLKEVCPVCGEKTKVAHPPRFSPEDPYGEYRRRWKREVLGI

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	2261
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2ey4a1
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.1 — PUA domain

Domain ID domain_id	d2ey4a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.265 — Pseudouridine synthase
Superfamily Superfamily superfamily	d.265.1 — Pseudouridine synthase
Family Family family	d.265.1.2 — Pseudouridine synthase II TruB

Domain ID domain_id	d2ey4b1
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.1 — PUA domain

Domain ID domain_id	d2ey4b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.265 — Pseudouridine synthase
Superfamily Superfamily superfamily	d.265.1 — Pseudouridine synthase
Family Family family	d.265.1.2 — Pseudouridine synthase II TruB

Domain ID domain_id	d2ey4c1
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.3 — Translation proteins
Family Family family	b.43.3.5 — Gar1-like SnoRNP

Domain ID domain_id	d2ey4d_
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.3 — Translation proteins
Family Family family	b.43.3.5 — Gar1-like SnoRNP

Domain ID domain_id	d2ey4e1
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

Domain ID domain_id	d2ey4f_
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 (8 domains)

Domain ID domain_id	2ey4A01
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	2ey4A02
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	2ey4B01
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	2ey4B02
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	2ey4C00
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

Domain ID domain_id	2ey4D00
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

Domain ID domain_id	2ey4E00
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	40 — H/ACA ribonucleoprotein complex, subunit Nop10

Domain ID domain_id	2ey4F00
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	40 — H/ACA ribonucleoprotein complex, subunit Nop10

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Unit-cell length a length_a	36.087 Å
Unit-cell length b length_b	75.361 Å
Unit-cell length c length_c	103.240 Å
Unit-cell angle α angle_alpha	95.90 °
Unit-cell angle β angle_beta	96.90 °
Unit-cell angle γ angle_gamma	94.99 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.110 Å
Low-resolution limit resolution_low	39.970 Å
R factor r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.2550

Crystal Structure of a Cbf5-Nop10-Gar1 Complex

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

Probable tRNA pseudouridine synthase B

State in the Current Structure

Other States of the Same Protein in the Database

Ribosome biogenesis protein Nop10

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

2ey4__assembly_3__model_1

2ey4__assembly_3__model_1 | I(q)

2ey4__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of a Cbf5-Nop10-Gar1 Complex

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

Probable tRNA pseudouridine synthase B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ribosome biogenesis protein Nop10

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

2ey4__assembly_3__model_1

2ey4__assembly_3__model_1 | I(q)

2ey4__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)