SAXSdb — 9x4h

▼

1. Structure Basics

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

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	39.14 Å
rg_electron	40.55 Å
i0	400330000.00
molecular_weight	146020.0 kDa
excluded_volume	175770 Å³
envelope_volume	242790 Å³
shell_volume	52434 Å³
envelope_diameter	152.5 Å
shell_rg	43.54 Å
envelope_rg	40.44 Å
shape_rg	40.56 Å
total_rg	40.65 Å
total_atoms	10131
n_residues	1178
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	139.6 Å
rg_real	39.46 Å
rg_real_error	1.52 Å
i0_real	4.0030e+08
i0_real_error	6.9180e+06
rg_reciprocal	39.26 Å
i0_reciprocal	400200000.0000
total_estimate	0.6246
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	41.9 Å
skewness	0.554
kurtosis	-0.028
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	37500000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.750; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.876; Smooth: 0.804

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	N(6)-L-threonylcarbamoyladenine synthase
formula_weight	36859.7 kDa
ec_number	2.3.1.234
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,F
atom_count	10131

MVCVIGIEGSANKIGVGIIRDGVVLSNPRATFHAPPGEGFRPTETAQHHRQQIVRLVGEAIKLANIQNPELEIDGIAYTKGPGMGAPLQVGAIVARTLSLTWKKPIIPVNHCVGHIEMGRLITGADNPVVLYVSGGNTQVISYTKKRYRIFGETIDIAVGNCLDRFARVLKLPNAPSPGYNIEQLAKNGKKLMELPYSVKGMDVSLSGILSLIEKKAPKLIESGDFTPEDLCFSLQETVFAMLIEITERAMAHTSSKELLIVGGVGCNLRLQEMASAMCAERGAHLFATDERFCIDNGAMIARAGELMLASGMRFDLRKTTTTQRYRTDQVHVEWRD

Source

organism	Caenorhabditis elegans
ncbi_taxonomy_id	6239
host_organism	Escherichia coli

Entity 2 polymer

description	non-specific serine/threonine protein kinase
formula_weight	27544.5 kDa
ec_number	2.7.11.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MTAATTSSDSEGEMDFETTIETGFGYQIDGLLYQGAEAKVTKCIWLGRQAIIKERFSKGYRHPTLDTQLNKARTKQEIRGLNKARELGIHVPAVYFIDNEKNQLIMEFVPGSTAKNWISQLNPADFDAKTREFGQIFGEKLGKLHRGGLIHGDLTTSNIILRDDDLQKMTFIDFGLSSQGKVTPEEKGVDLYVLERAVISTHDKCAALIEGLMEGYKKADGKQFVAVEKKLNEIRLRGRKRDMIG

Source

organism	Caenorhabditis elegans
ncbi_taxonomy_id	6239
host_organism	Escherichia coli

Entity 3 polymer

description	EKC/KEOPS complex subunit TPRKB
formula_weight	20215.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MKHSHLYELQPDPYDFTQRKTCRVCLFKDVKNAAELSQQLKEGKIDAALIRAELVLEPFVLLAAANRAVHQSAHNRMSCRSLAAELVYSLSPSRNITDSLVTFGIAEHSTAIIAAIFDDDSGKAMKKLAKAIKGTPVPLMEGLPKFANVNMIKKVYQVGNPAFVEEGLSDHIVSRMVSKDFVS

Source

organism	Caenorhabditis elegans
ncbi_taxonomy_id	6239
host_organism	Escherichia coli

Entity 4 polymer

description	L antigen family member 3
formula_weight	13223.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,E

MEVDTSSSSSSEDECDPSSPSTAYIHSASVRLSVGTEEAARTVADVIKIDKEPRRSGARREVCSEGEFVVIKIESKDPKSLSKSIANAVDMIDLSVKTIKLCENLGKSKENGLKRKLSNGSQA

Source

organism	Caenorhabditis elegans
ncbi_taxonomy_id	6239
host_organism	Escherichia coli

Entity 5 polymer

description	RNA (76-MER)
formula_weight	24555.6 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	T

GCUUCCGUGGCGCAAUAGGCAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGCCCACCCGGGAGCGCCA

Source

organism	Caenorhabditis elegans
ncbi_taxonomy_id	6239
host_organism	Escherichia coli

Entity 6 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	2

▶

6. Citations (1)

▶

length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.360 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.36 Å
resolution_method	—
num_particles	123388

fit	/app/data/saxs_computation/x4/9x4h/9x4h.fit
pddf	/app/data/pr_computation/x4/9x4h/9x4h.pr.out
profile	/app/data/saxs_computation/x4/9x4h/9x4h.dat

Structure Of the KEOPS-tRNA

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)