SAXSdb — 6jp6

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

;tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734 ;

Saccharomyces cerevisiae S288c

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	;tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase ; × 1 （P38238） SULFATE ION × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	;tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase ; × 1 （P38238） SULFATE ION × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	WDR6_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1013； UniProt 1–1013 Author chain C； PDBConstruct 1–1013； UniProt 1–1013

;tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase ;

Saccharomyces cerevisiae S288c

UniProt P38238

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	;tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734 ; × 1 （Q08924） SULFATE ION × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	;tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734 ; × 1 （Q08924） SULFATE ION × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRM7_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–310； UniProt 1–310 Author chain D； PDBConstruct 1–310； UniProt 1–310

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	6jp6
Deposition date deposition_date	2019-03-26
Structure title title	The X-ray structure of yeast tRNA methyltransferase complex of Trm7 and Trm734 essential for 2'-O-methylation at the first position of anticodon in specific tRNAs
Keywords keywords	tRNA methyltransferase, tRNA maturation, 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.

6jp6__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6jp6__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6jp6__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	35.08 Å
Rg (electron density)	34.61 Å
Total Rg	35.13 Å
Atom count	9805
Residues	1229
Excluded volume	175050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6jp6__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6jp6__assembly_2__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	;tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734 ;
Molecular weight formula_weight	116391.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	19867

MKDLSHYGPALCVKFYNDYVLAGYGPFIHVYDYHSATLINKCRLFHYNKVHGLSLSSEGKILAYGARSVTIVELEDVLKKESLVDFERINSDWITGATFSFDNLQIYLLTCYNKVLICDLNCEVLFRKSLGGERSILYSGIIKVFGPDKVYVNAGTVMGGVIIWDLFSETKIHNLLGHEGSIFYVNLSNNGRYVASCSDDRSIRLWDLETGKQLSVGWSHTARIWNLMFFDNDSKLISVSEDCTCRVWNIIESRENVAELSISNVYEVHLIKSIWGVDVKDDEMIAVTSGNDGRLKLIDLLQLKRHGDEETSFSLDDIAKQCGDIFEKNESIKGFQWFSFGVIAITSLGKILKYSDVTKQWKLLLTNEKFNSYPITNGIQTQNIAVFSNNKSDILLIKFSKDSADIIETEEFHLDELSKTNNCLVTEYDDDSFLLTLQSPNPREKFVCLEISLQNLKIKSKHCFNKPENFSSSCLTSFRNHILVGSRFSTLVIYNLLDESEEPFIIRRLSPGDTTTSIEFVEDKDNSAVFSVTNRDGYYVFIELTKNSLEEGPYRLSYKVLHSNKMMKGFLEGAFFNSKGEYITYGFKSSLFYLYNETNCYELASEVCGGSHRLWNLAKITDGHVLMYIKASRFHLRKIYNSIVPETLENGVHGREIRDISICPVSNTNTNDNFKDGHIFCTASEDTTIKLGYFNNRTGKVQNFWTQRKHVSGLQRCQFINHKLMISSSAREELFLWELNDKYNKRPYMTIRQALPVSTNNSDLRIMDFDVKFISQSGDFLLVTVYSDSTIKIWHYRENQNKFDLIMQGRYKTCCLFNVVFIALKEELLVVISPTDGHLVVYNITEYVPFSVDPISGDLVDHKLDATISNLPAPVAQLPVHQSGVKSLDYVANATRTSATILTGGDDNGLGLSNLKLDDSNKVTLKTSDFIAAAASSTITSGMLINGGKEVITTSVDQVIRAWEITAGKLSLVDKKRTTVADTGSLEIISNDEDADSEKTLLIGGVGLSIWKKLEVLFQGPSHHHHHH

Source Source

Source organism organism	Saccharomyces cerevisiae S288c
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase ;
Molecular weight formula_weight	36546.5 kDa
EC 编号 ec_number	2.1.1.205
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MGKSSKDKRDLYYRKAKEQGYRARSAFKLLQLNDQFHFLDDPNLKRVVDLCAAPGSWSQVLSRKLFDESPSSDKEDRKIVSVDLQPMSPIPHVTTLQADITHPKTLARILKLFGNEKADFVCSDGAPDVTGLHDLDEYVQQQLIMSALQLTACILKKGGTFVAKIFRGRDIDMLYSQLGYLFDKIVCAKPRSSRGTSLEAFIVCLGYNPPSNWTPKLDVNTSVDEFFQGCFLNKLCISDKLSHWNEEERNIAEFMACGSLQSFDSDATYHDLPSSVAGTSSSLDPVQSPTNPPYKKALELKRSGKLTRSVLEVLFQGPSHHHHHH

Source Source

Source organism organism	Saccharomyces cerevisiae S288c
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

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	4

Entity 4 Entity 4 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 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	257

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6jp6D01
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	253.643 Å
Unit-cell length b length_b	110.351 Å
Unit-cell length c length_c	133.503 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.02 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.699 Å
Low-resolution limit resolution_low	36.433 Å
R factor r_factor	0.1962
R_work r_work	0.1939
R_free r_free	0.2387

The X-ray structure of yeast tRNA methyltransferase complex of Trm7 and Trm734 essential for 2'-O-methylation at the first position of anticodon in specific tRNAs

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

;tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734 ;

State in the Current Structure

Other States of the Same Protein in the Database

;tRNA (cytidine(34)/guanosine(34)-2'-O)-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

6jp6__assembly_2__model_1

6jp6__assembly_2__model_1 | I(q)

6jp6__assembly_2__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

The X-ray structure of yeast tRNA methyltransferase complex of Trm7 and Trm734 essential for 2'-O-methylation at the first position of anticodon in specific tRNAs

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

;tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734 ;

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 (cytidine(34)/guanosine(34)-2'-O)-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

6jp6__assembly_2__model_1

6jp6__assembly_2__model_1 | I(q)

6jp6__assembly_2__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)