SAXSdb — 9fl9

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

EKC/KEOPS complex subunit TPRKB

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	EKC/KEOPS complex subunit TP53RK × 1 （Q96S44） Probable tRNA N6-adenosine threonylcarbamoyltransferase × 1 （Q9NPF4） EKC/KEOPS complex subunit LAGE3 × 1 （Q14657） EKC/KEOPS complex subunit GON7 × 1 （Q9BXV9）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TPRKB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–188； UniProt 2–175

EKC/KEOPS complex subunit TP53RK

Homo sapiens

UniProt Q96S44

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	EKC/KEOPS complex subunit TPRKB × 1 （Q9Y3C4） Probable tRNA N6-adenosine threonylcarbamoyltransferase × 1 （Q9NPF4） EKC/KEOPS complex subunit LAGE3 × 1 （Q14657） EKC/KEOPS complex subunit GON7 × 1 （Q9BXV9）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRPK_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 15–266； UniProt 2–253

Probable tRNA N6-adenosine threonylcarbamoyltransferase

Homo sapiens

UniProt Q9NPF4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	EKC/KEOPS complex subunit TPRKB × 1 （Q9Y3C4） EKC/KEOPS complex subunit TP53RK × 1 （Q96S44） EKC/KEOPS complex subunit LAGE3 × 1 （Q14657） EKC/KEOPS complex subunit GON7 × 1 （Q9BXV9）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OSGEP_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–335； UniProt 1–335

EKC/KEOPS complex subunit LAGE3

Homo sapiens

UniProt Q14657

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	EKC/KEOPS complex subunit TPRKB × 1 （Q9Y3C4） EKC/KEOPS complex subunit TP53RK × 1 （Q96S44） Probable tRNA N6-adenosine threonylcarbamoyltransferase × 1 （Q9NPF4） EKC/KEOPS complex subunit GON7 × 1 （Q9BXV9）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LAGE3_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–143； UniProt 1–143

EKC/KEOPS complex subunit GON7

Homo sapiens

UniProt Q9BXV9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	EKC/KEOPS complex subunit TPRKB × 1 （Q9Y3C4） EKC/KEOPS complex subunit TP53RK × 1 （Q96S44） Probable tRNA N6-adenosine threonylcarbamoyltransferase × 1 （Q9NPF4） EKC/KEOPS complex subunit LAGE3 × 1 （Q14657）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GON7_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–100； UniProt 1–100

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	9fl9
Deposition date deposition_date	2024-06-04
Structure title title	Cryo-EM structure of the human KEOPS complex
Keywords keywords	Complex t6A modification tRNA KEOPS Galloway-Mowat, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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.

9fl9__assembly_1__model_1

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

Download this curve (.dat)

9fl9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9fl9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.19 Å
Rg (electron density)	37.75 Å
Total Rg	37.84 Å
Atom count	6769
Residues	872
Excluded volume	121090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9fl9__assembly_1__model_1`	pentameric （5）	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	EKC/KEOPS complex subunit TPRKB
Molecular weight formula_weight	21364.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6769

MHHHHHHENLYFQGQLTHQLDLFPECRVTLLLFKDVKNAGDLRRKAMEGTIDGSLINPTVIVDPFQILVAANKAVHLYKLGKMKTRTLSTEIIFNLSPNNNISEALKKFGISANDTSILIVYIEEGEKQINQEYLISQVEGHQVSLKNLPEIMNITEVKKIYKLSSQEESIGTLLDAIICRMSTKDVL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	EKC/KEOPS complex subunit TP53RK
Molecular weight formula_weight	29885.3 kDa
EC 编号 ec_number	3.6.-.-,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

MHHHHHHENLYFQGAAARATTPADGEEPAPEAEALAAARERSSRFLSGLELVKQGAEARVFRGRFQGRAAVIKHRFPKGYRHPALEARLGRRRTVQEARALLRCRRAGISAPVVFFVDYASNCLYMEEIEGSVTVRDYIQSTMETEKTPQGLSNLAKTIGQVLARMHDEDLIHGDLTTSNMLLKPPLEQLNIVLIDFGLSFISALPEDKGVDLYVLEKAFLSTHPNTETVFEAFLKSYSTSSKKARPVLKKLDEVRLRGRKRSMVG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Probable tRNA N6-adenosine threonylcarbamoyltransferase
Molecular weight formula_weight	36466.8 kDa
EC 编号 ec_number	2.3.1.234
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MPAVLGFEGSANKIGVGVVRDGKVLANPRRTYVTPPGTGFLPGDTARHHRAVILDLLQEALTESGLTSQDIDCIAYTKGPGMGAPLVSVAVVARTVAQLWNKPLVGVNHCIGHIEMGRLITGATSPTVLYVSGGNTQVIAYSEHRYRIFGETIDIAVGNCLDRFARVLKISNDPSPGYNIEQMAKRGKKLVELPYTVKGMDVSFSGILSFIEDVAHRMLATGECTPEDLCFSLQETVFAMLVEITERAMAHCGSQEALIVGGVGCNVRLQEMMATMCQERGARLFATDERFCIDNGAMIAQAGWEMFRAGHRTPLSDSGVTQRYRTDEVEVTWRD

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	EKC/KEOPS complex subunit LAGE3
Molecular weight formula_weight	14825.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MRDADADAGGGADGGDGRGGHSCRGGVDTAAAPAGGAPPAHAPGPGRDAASAARGSRMRPHIFTLSVPFPTPLEAEIAHGSLAPDAEPHQRVVGKDLTVSGRILVVRWKAEDCRLLRISVINFLDQLSLVVRTMQRFGPPVSR

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	EKC/KEOPS complex subunit GON7
Molecular weight formula_weight	11697.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MELLGEYVGQEGKPQKLRVSCEAPGDGDPFQGLLSGVAQMKDMVTELFDPLVQGEVQHRVAAAPDEDLDGDDEDDAEDENNIDNRTNFDGPSAKRPKTPSHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

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Resolution resolution	3.74 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	214527

Cryo-EM structure of the human KEOPS complex

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

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

EKC/KEOPS complex subunit TP53RK

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Probable tRNA N6-adenosine threonylcarbamoyltransferase

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 LAGE3

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 GON7

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

9fl9__assembly_1__model_1

9fl9__assembly_1__model_1 | I(q)

9fl9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

7. Citations (1)