SAXSdb — 9x4h

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

N(6)-L-threonylcarbamoyladenine synthase

Caenorhabditis elegans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 1	non-specific serine/threonine protein kinase × 1 （B5WWL2） EKC/KEOPS complex subunit TPRKB × 1 （O44566） L antigen family member 3 × 2 （Q21019） RNA (76-MER) × 1 POTASSIUM ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9BL28_CAEEL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–337； UniProt 1–337 Author chain F； PDBConstruct 1–337； UniProt 1–337

non-specific serine/threonine protein kinase

Caenorhabditis elegans

UniProt B5WWL2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 1	N(6)-L-threonylcarbamoyladenine synthase × 2 （Q9BL28） EKC/KEOPS complex subunit TPRKB × 1 （O44566） L antigen family member 3 × 2 （Q21019） RNA (76-MER) × 1 POTASSIUM ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B5WWL2_CAEEL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–245； UniProt 1–245

EKC/KEOPS complex subunit TPRKB

Caenorhabditis elegans

UniProt O44566

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 1	N(6)-L-threonylcarbamoyladenine synthase × 2 （Q9BL28） non-specific serine/threonine protein kinase × 1 （B5WWL2） L antigen family member 3 × 2 （Q21019） RNA (76-MER) × 1 POTASSIUM ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O44566_CAEEL
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–183； UniProt 1–183

L antigen family member 3

Caenorhabditis elegans

UniProt Q21019

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 1	N(6)-L-threonylcarbamoyladenine synthase × 2 （Q9BL28） non-specific serine/threonine protein kinase × 1 （B5WWL2） EKC/KEOPS complex subunit TPRKB × 1 （O44566） RNA (76-MER) × 1 POTASSIUM ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q21019_CAEEL
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–123； UniProt 1–123 Author chain E； PDBConstruct 1–123； UniProt 1–123

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	9x4h
Deposition date deposition_date	2025-10-10
Structure title title	Structure Of the KEOPS-tRNA
Keywords keywords	;tRNA modification, t6A, KEOPS-tRNA complex, cryo-EM structure, substrate recognition, catalytic mechanism, regulation principle, TRANSFERASE/RNA, TRANSFERASE-RNA complex ;; TRANSFERASE/RNA
Experimental Method method	ELECTRON MICROSCOPY

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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.

9x4h__assembly_1__model_1

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

Download this curve (.dat)

9x4h__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9x4h__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.14 Å
Rg (electron density)	40.55 Å
Total Rg	40.65 Å
Atom count	10131
Residues	1178
Excluded volume	175770 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9x4h__assembly_1__model_1`	heptameric （7）	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 (6)

Entity 1 Entity 1 polymer

Description description	N(6)-L-threonylcarbamoyladenine synthase
Molecular weight formula_weight	36859.7 kDa
EC 编号 ec_number	2.3.1.234
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F
Atom count atom_count	10131

MVCVIGIEGSANKIGVGIIRDGVVLSNPRATFHAPPGEGFRPTETAQHHRQQIVRLVGEAIKLANIQNPELEIDGIAYTKGPGMGAPLQVGAIVARTLSLTWKKPIIPVNHCVGHIEMGRLITGADNPVVLYVSGGNTQVISYTKKRYRIFGETIDIAVGNCLDRFARVLKLPNAPSPGYNIEQLAKNGKKLMELPYSVKGMDVSLSGILSLIEKKAPKLIESGDFTPEDLCFSLQETVFAMLIEITERAMAHTSSKELLIVGGVGCNLRLQEMASAMCAERGAHLFATDERFCIDNGAMIARAGELMLASGMRFDLRKTTTTQRYRTDQVHVEWRD

Source Source

Source organism organism	Caenorhabditis elegans
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	non-specific serine/threonine protein kinase
Molecular weight formula_weight	27544.5 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MTAATTSSDSEGEMDFETTIETGFGYQIDGLLYQGAEAKVTKCIWLGRQAIIKERFSKGYRHPTLDTQLNKARTKQEIRGLNKARELGIHVPAVYFIDNEKNQLIMEFVPGSTAKNWISQLNPADFDAKTREFGQIFGEKLGKLHRGGLIHGDLTTSNIILRDDDLQKMTFIDFGLSSQGKVTPEEKGVDLYVLERAVISTHDKCAALIEGLMEGYKKADGKQFVAVEKKLNEIRLRGRKRDMIG

Source Source

Source organism organism	Caenorhabditis elegans
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	EKC/KEOPS complex subunit TPRKB
Molecular weight formula_weight	20215.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MKHSHLYELQPDPYDFTQRKTCRVCLFKDVKNAAELSQQLKEGKIDAALIRAELVLEPFVLLAAANRAVHQSAHNRMSCRSLAAELVYSLSPSRNITDSLVTFGIAEHSTAIIAAIFDDDSGKAMKKLAKAIKGTPVPLMEGLPKFANVNMIKKVYQVGNPAFVEEGLSDHIVSRMVSKDFVS

Source Source

Source organism organism	Caenorhabditis elegans
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	L antigen family member 3
Molecular weight formula_weight	13223.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MEVDTSSSSSSEDECDPSSPSTAYIHSASVRLSVGTEEAARTVADVIKIDKEPRRSGARREVCSEGEFVVIKIESKDPKSLSKSIANAVDMIDLSVKTIKLCENLGKSKENGLKRKLSNGSQA

Source Source

Source organism organism	Caenorhabditis elegans
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	RNA (76-MER)
Molecular weight formula_weight	24555.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	T

GCUUCCGUGGCGCAAUAGGCAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGCCCACCCGGGAGCGCCA

Source Source

Source organism organism	Caenorhabditis elegans
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.360 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.36 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	123388

Structure Of the KEOPS-tRNA

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

N(6)-L-threonylcarbamoyladenine synthase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

non-specific serine/threonine protein kinase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

EKC/KEOPS complex subunit TPRKB

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

L antigen family member 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9x4h__assembly_1__model_1

9x4h__assembly_1__model_1 | I(q)

9x4h__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

7. Citations (1)