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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 6 RNA 1 PDB declaration: heptameric（7） Consistent with all polymer counts	Chain A； UniProt 1–337 Chain F； UniProt 1–337	Not recorded	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 K POTASSIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.36 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9X4H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9X4G Structure Of the KEOPS dimer Deposited 2025-10-10	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–337（337 aa） Chain E 1–337（337 aa）	Not recorded	K POTASSIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 6 RNA 1 PDB declaration: heptameric（7） Consistent with all polymer counts	Chain B； UniProt 1–245	Not recorded	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 K POTASSIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.36 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9X4H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9X4G Structure Of the KEOPS dimer Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–245（245 aa） Chain F 1–245（245 aa）	Not recorded	K POTASSIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 6 RNA 1 PDB declaration: heptameric（7） Consistent with all polymer counts	Chain C； UniProt 1–183	Not recorded	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 K POTASSIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.36 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9X4H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9X4G Structure Of the KEOPS dimer Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 1–183（183 aa） Chain G 1–183（183 aa）	Not recorded	K POTASSIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 6 RNA 1 PDB declaration: heptameric（7） Consistent with all polymer counts	Chain D； UniProt 1–123 Chain E； UniProt 1–123	Not recorded	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 K POTASSIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.36 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9X4H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9X4G Structure Of the KEOPS dimer Deposited 2025-10-10	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–123（123 aa） Chain H 1–123（123 aa）	Not recorded	K POTASSIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	39.14 Å
Radius of gyration Rg (electron density) rg_electron	40.55 Å
Forward intensity I(0) i0	400330000.00
Molecular weight molecular_weight	146020.0 kDa
Excluded volume excluded_volume	175770 Å³
Envelope volume envelope_volume	242790 Å³
Hydration-shell volume shell_volume	52434 Å³
Envelope diameter envelope_diameter	152.5 Å
Shell Rg shell_rg	43.54 Å
Envelope Rg envelope_rg	40.44 Å
Shape Rg shape_rg	40.56 Å
Total Rg total_rg	40.65 Å
Total atoms total_atoms	10131
Residues n_residues	1178
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	139.6 Å
Rg (real space) rg_real	39.46 Å
Rg uncertainty (real space) rg_real_error	1.52 Å
I(0) (real space) i0_real	4.0030e+08
I(0) uncertainty (real space) i0_real_error	6.9180e+06
Rg (reciprocal space) rg_reciprocal	39.26 Å
I(0) (reciprocal space) i0_reciprocal	400200000.0000
Solution quality estimate total_estimate	0.6246
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.9 Å
Skewness Skewness skewness	0.554
Kurtosis Kurtosis kurtosis	-0.028
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	37500000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.750; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.876; Smooth: 0.804

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Caenorhabditis elegans
NCBI Class编号 ncbi_taxonomy_id	6239
宿主生物 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

来源 Source

来源生物 organism	Caenorhabditis elegans
NCBI Class编号 ncbi_taxonomy_id	6239
宿主生物 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

来源 Source

来源生物 organism	Caenorhabditis elegans
NCBI Class编号 ncbi_taxonomy_id	6239
宿主生物 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

来源 Source

来源生物 organism	Caenorhabditis elegans
NCBI Class编号 ncbi_taxonomy_id	6239
宿主生物 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

来源 Source

来源生物 organism	Caenorhabditis elegans
NCBI Class编号 ncbi_taxonomy_id	6239
宿主生物 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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8. Citations (1)

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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测定方法 resolution_method	—
颗粒数 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

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

non-specific serine/threonine protein kinase

State in the Current Structure

Other States of the Same Protein in the Database

EKC/KEOPS complex subunit TPRKB

State in the Current Structure

Other States of the Same Protein in the Database

L antigen family member 3

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)