SAXSdb — 9d85

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

Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein

Methanocaldococcus jannaschii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 1	Regulatory protein Cgi121 × 1 （Q57646） KEOPS complex subunit Pcc1 × 1 （Q8TZI1） tRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KAE1B_METJA
Isoform	—
PDB entities	1, 3
Chains and sequence ranges	Author chain B； PDBConstruct 1–203； UniProt 333–535 Author chain K； PDBConstruct 4–327； UniProt 1–324

Regulatory protein Cgi121

Pyrococcus furiosus DSM 3638

UniProt Q57646

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 1	Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein × 1 （Q58530） Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein × 1 （Q58530） KEOPS complex subunit Pcc1 × 1 （Q8TZI1） tRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CG121_METJA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 4–148； UniProt 1–145

KEOPS complex subunit Pcc1

Pyrococcus furiosus DSM 3638

UniProt Q8TZI1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 1	Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein × 1 （Q58530） Regulatory protein Cgi121 × 1 （Q57646） Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein × 1 （Q58530） tRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8TZI1_PYRFU
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain P； PDBConstruct 1–82； UniProt 1–82

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	9d85
Deposition date deposition_date	2024-08-18
Structure title title	Structure of the KEOPS complex (Cgi121/Bud32/Kae1/Pcc1) bound to tRNA in a distorted tRNA conformation
Keywords keywords	tRNA, modification, t6A, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA complex; RNA BINDING PROTEIN/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.

9d85__assembly_1__model_1

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

Download this curve (.dat)

9d85__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9d85__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.90 Å
Rg (electron density)	34.07 Å
Total Rg	34.42 Å
Atom count	7291
Residues	804
Excluded volume	125620 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9d85__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	Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
Molecular weight formula_weight	23957.5 kDa
Mutation mutation	E152R
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	7291

KIPEHLIGKGAEADIKRDSYLDFDVIIKERVKKGYRDERLDENIRKSRTAREARYLALVKDFGIPAPYIFDVDLDNKRIMMSYINGKLAKDVIEDNLDIAYKIGEIVGKLHKNDVIHNDLTTSNFIFDKDLYIIDFGLGKISNLDRDKAVDLIVFKKAVLSTHHEKFDEIWERFLEGYKSVYDRWEIILELMKDVERRARYVE

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Regulatory protein Cgi121
Molecular weight formula_weight	16963.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MDPMIIRGIRGARINNEIFNLGLKFQILNADVVATKKHVLHAINQAKTKKPIAKSFWMEILVRASGQRQIHEAIKIIGAKDGNVCLICEDEETFRKIYELIGGEIDDSVLEINEDKERLIREIFKIRGFGNVVERVLEKIALIELKKE

Source Source

Source organism organism	Pyrococcus furiosus DSM 3638
NCBI taxonomy ID ncbi_taxonomy_id	186497
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
Molecular weight formula_weight	36115.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MDPMICLGLEGTAEKTGVGIVTSDGEVLFNKTIMYKPPKQGINPREAADHHAETFPKLIKEAFEVVDKNEIDLIAFSQGPGLGPSLRVTATVARTLSLTLKKPIIGVNHCIAHIEIGKLTTEAEDPLTLYVSGGNTQVIAYVSKKYRVFGETLDIAVGNCLDQFARYVNLPHPGGPYIEELARKGKKLVDLPYTVKGMDIAFSGLLTAAMRAYDAGERLEDICYSLQEYAFSMLTEITERALAHTNKGEVMLVGGVAANNRLREMLKAMCEGQNVDFYVPPKEFCGDNGAMIAWLGLLMHKNGRWMSLDETKIIPNYRTDMVEVNWI

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	KEOPS complex subunit Pcc1
Molecular weight formula_weight	9410.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

MKAKRVQAKIEIEFPSEDVAKVVYEAVLYEHLSVPYRRSEIDFKLEGKKIILDIKATDSSALRGTVNSYLRWIKAAIDVIEV

Source Source

Source organism organism	Pyrococcus furiosus DSM 3638
NCBI taxonomy ID ncbi_taxonomy_id	186497
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	tRNA
Molecular weight formula_weight	24758.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	T

GGGCCCGUAGCUCAGUCUGGCAGAGCGCCUGGCUUUUAACCAGGUGGUCGAGGGUUCAAAUCCCUUCGGGCCCGCCA

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	in vitro transcription vector pT7-Fluc(deltai)

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Resolution resolution	3.59 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	83710

Structure of the KEOPS complex (Cgi121/Bud32/Kae1/Pcc1) bound to tRNA in a distorted tRNA conformation

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

Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein

State in the Current Structure

Other States of the Same Protein in the Database

Regulatory protein Cgi121

State in the Current Structure

Other States of the Same Protein in the Database

KEOPS complex subunit Pcc1

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

9d85__assembly_1__model_1

9d85__assembly_1__model_1 | I(q)

9d85__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)

Structure of the KEOPS complex (Cgi121/Bud32/Kae1/Pcc1) bound to tRNA in a distorted tRNA conformation

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

Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Regulatory protein Cgi121

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

KEOPS complex subunit Pcc1

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

9d85__assembly_1__model_1

9d85__assembly_1__model_1 | I(q)

9d85__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)