SAXSdb — 2vdu

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

TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82

SACCHAROMYCES CEREVISIAE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE × 2 （Q12009） PHOSPHATE ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE × 1 （Q12009） PHOSPHATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE × 1 （Q12009） PHOSPHATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRM82_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–444； UniProt 1–444 Author chain D； PDBConstruct 1–444； UniProt 1–444

TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE

SACCHAROMYCES CEREVISIAE

UniProt Q12009

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82 × 2 （Q03774） PHOSPHATE ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82 × 1 （Q03774） PHOSPHATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82 × 1 （Q03774） PHOSPHATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRM8_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–248； UniProt 39–286 Author chain F； PDBConstruct 1–248； UniProt 39–286

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	2vdu
Deposition date deposition_date	2007-10-11
Structure title title	Structure of trm8-trm82, THE YEAST TRNA m7G methylation complex
Keywords keywords	S-ADENOSYL-L-METHIONINE, TRNA PROCESSING, PHOSPHORYLATION, METHYLTRANSFERASE, M7G, TRNA, SPOUT MT, WD REPEAT, TRANSFERASE; TRANSFERASE
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.

2vdu__assembly_1__model_1

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

Download this curve (.dat)

2vdu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vdu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.37 Å
Rg (electron density)	40.56 Å
Total Rg	40.61 Å
Atom count	9312
Residues	1152
Excluded volume	166790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vdu__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vdu__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2vdu__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Description description	TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82
Molecular weight formula_weight	51383.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D
Atom count atom_count	9571

MSVIHPLQNLLTSRDGSLVFAIIKNCILSFKYQSPNHWEFAGKWSDDFDKIQESRNTTAKEQQGQSSENENENKKLKSNKGDSIKRTAAKVPSPGLGAPPIYSYIRNLRLTSDESRLIACADSDKSLLVFDVDKTSKNVLKLRKRFCFSKRPNAISIAEDDTTVIIADKFGDVYSIDINSIPEEKFTQEPILGHVSMLTDVHLIKDSDGHQFIITSDRDEHIKISHYPQCFIVDKWLFGHKHFVSSICCGKDYLLLSAGGDDKIFAWDWKTGKNLSTFDYNSLIKPYLNDQHLAPPRFQNENNDIIEFAVSKIIKSKNLPFVAFFVEATKCIIILEMSEKQKGDLALKQIITFPYNVISLSAHNDEFQVTLDNKESSGVQKNFAKFIEYNLNENSFVVNNEKSNEFDSAIIQSVQGDSNLVTKKEEIYPLYNVSSLRKHGEHYSHHHHHH

Source Source

Source organism organism	SACCHAROMYCES CEREVISIAE
Common name common_name	;BAKER'S YEAST ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE
Molecular weight formula_weight	29796.2 kDa
EC 编号 ec_number	2.1.1.33
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

VQEGQKIDLPKKRYYRQRAHSNPFSDHQLEYPVSPQDMDWSKLYPYYKNAENGQMTKKVTIADIGCGFGGLMIDLSPAFPEDLILGMEIRVQVTNYVEDRIIALRNNTASKHGFQNINVLRGNAMKFLPNFFEKGQLSKMFFCFPDPHFKQRKHKARIITNTLLSEYAYVLKEGGVVYTITDVKDLHEWMVKHLEEHPLFERLSKEWEENDECVKIMRNATEEGKKVERKKGDKFVACFTRLPTPAILHHHHHH

Source Source

Source organism organism	SACCHAROMYCES CEREVISIAE
Common name common_name	;BAKER'S YEAST ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	259

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2vduE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	2vduF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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Unit-cell length a length_a	53.376 Å
Unit-cell length b length_b	107.676 Å
Unit-cell length c length_c	127.749 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.53 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2280
R_free r_free	0.2764

Structure of trm8-trm82, THE YEAST TRNA m7G methylation complex

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

TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82

State in the Current Structure

Other States of the Same Protein in the Database

TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE

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

2vdu__assembly_1__model_1

2vdu__assembly_1__model_1 | I(q)

2vdu__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 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure of trm8-trm82, THE YEAST TRNA m7G methylation complex

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

TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE

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

2vdu__assembly_1__model_1

2vdu__assembly_1__model_1 | I(q)

2vdu__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 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)