8hmy

Cryo-EM structure of the human pre-catalytic TSEN/pre-tRNA complex

Method: ELECTRON MICROSCOPY

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

tRNA-splicing endonuclease subunit Sen2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 5 RNA 1	tRNA-splicing endonuclease subunit Sen34 × 1 （Q9BSV6） Pre-tRNA × 1 tRNA-splicing endonuclease subunit Sen54 × 1 （Q7Z6J9） Chromosome 1 open reading frame 19, isoform CRA_a × 1 （A0A2U3TZM3） ;Polyribonucleotide 5'-hydroxyl-kinase Clp1 ; × 1 （Q92989） MAGNESIUM ION × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEN2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–485； UniProt 1–465

tRNA-splicing endonuclease subunit Sen34

Homo sapiens

UniProt Q9BSV6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 5 RNA 1	tRNA-splicing endonuclease subunit Sen2 × 1 （Q8NCE0） Pre-tRNA × 1 tRNA-splicing endonuclease subunit Sen54 × 1 （Q7Z6J9） Chromosome 1 open reading frame 19, isoform CRA_a × 1 （A0A2U3TZM3） ;Polyribonucleotide 5'-hydroxyl-kinase Clp1 ; × 1 （Q92989） MAGNESIUM ION × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEN34_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 21–330； UniProt 1–310

tRNA-splicing endonuclease subunit Sen54

Homo sapiens

UniProt Q7Z6J9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 5 RNA 1	tRNA-splicing endonuclease subunit Sen2 × 1 （Q8NCE0） tRNA-splicing endonuclease subunit Sen34 × 1 （Q9BSV6） Pre-tRNA × 1 Chromosome 1 open reading frame 19, isoform CRA_a × 1 （A0A2U3TZM3） ;Polyribonucleotide 5'-hydroxyl-kinase Clp1 ; × 1 （Q92989） MAGNESIUM ION × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEN54_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain C； PDBConstruct 21–546； UniProt 1–526

Chromosome 1 open reading frame 19, isoform CRA_a

Homo sapiens

UniProt A0A2U3TZM3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 5 RNA 1	tRNA-splicing endonuclease subunit Sen2 × 1 （Q8NCE0） tRNA-splicing endonuclease subunit Sen34 × 1 （Q9BSV6） Pre-tRNA × 1 tRNA-splicing endonuclease subunit Sen54 × 1 （Q7Z6J9） ;Polyribonucleotide 5'-hydroxyl-kinase Clp1 ; × 1 （Q92989） MAGNESIUM ION × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2U3TZM3_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain D； PDBConstruct 39–213； UniProt 1–175

;Polyribonucleotide 5'-hydroxyl-kinase Clp1 ;

Homo sapiens

UniProt Q92989

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 5 RNA 1	tRNA-splicing endonuclease subunit Sen2 × 1 （Q8NCE0） tRNA-splicing endonuclease subunit Sen34 × 1 （Q9BSV6） Pre-tRNA × 1 tRNA-splicing endonuclease subunit Sen54 × 1 （Q7Z6J9） Chromosome 1 open reading frame 19, isoform CRA_a × 1 （A0A2U3TZM3） MAGNESIUM ION × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CLP1_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain E； PDBConstruct 21–445； UniProt 1–425

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	8hmy
Deposition date deposition_date	2022-12-06
Structure title title	Cryo-EM structure of the human pre-catalytic TSEN/pre-tRNA complex
Keywords keywords	pre-tRNA splicing, TSEN, pre-tRNA, RNA BINDING PROTEIN/RNA, 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.

8hmy__assembly_1__model_1

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

Download this curve (.dat)

8hmy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8hmy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.35 Å
Rg (electron density)	44.80 Å
Total Rg	44.56 Å
Atom count	11675
Residues	1458
Excluded volume	198090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8hmy__assembly_1__model_1`	hexameric （6）	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 (7)

Entity 1 Entity 1 polymer

Description description	tRNA-splicing endonuclease subunit Sen2
Molecular weight formula_weight	55391.9 kDa
EC 编号 ec_number	4.6.1.16
Mutation mutation	H377A
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	11675

MASDYKDDDDKASDEVDAGTMAEAVFHAPKRKRRVYETYESPLPIPFGQDHGPLKEFKIFRAEMINNNVIVRNAEDIEQLYGKGYFGKGILSRSRPSFTISDPKLVAKWKDMKTNMPIITSKRYQHSVEWAAELMRRQGQDESTVRRILKDYTKPLEHPPVKRNEEAQVHDKLNSGMVSNMEGTAGGERPSVVNGDSGKSGGVGDPREPLGCLQEGSGCHPTTESFEKSVREDASPLPHVCCCKQDALILQRGLHHEDGSQHIGLLHPGDRGPDHEYVLVEEAECAMSEREAAPNEELVQRNRLICRRNPYRIFEYLQLSLEEAFFLVYALGCLSIYYEKEPLTIVKLWKAFTVVQPTFRTTYMAYHYFRSKGWVPKVGLKYGTDLLLYRKGPPFYAASYSVIIELVDDHFEGSLRRPLSWKSLAALSRVSVNVSKELMLCYLIKPSTMTDKEMESPECMKRIKVQEVILSRWVSSRERSDQDDL

Source Source

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

Entity 2 Entity 2 polymer

Description description	tRNA-splicing endonuclease subunit Sen34
Molecular weight formula_weight	35759.9 kDa
EC 编号 ec_number	4.6.1.16
Mutation mutation	H255A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MASDYKDDDDKASDEVDAGTMLVVEVANGRSLVWGAEAVQALRERLGVGGRTVGALPRGPRQNSRLGLPLLLMPEEARLLAEIGAVTLVSAPRPDSRHHSLALTSFKRQQEESFQEQSALAAEARETRRQELLEKITEGQAAKKQKLEQASGASSSQEAGSSQAAKEDETSDGQASGEQEEAGPSSSQAGPSNGVAPLPRSALLVQLATARPRPVKARPLDWRVQSKDWPHAGRPAHELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFAAHYIAQCWAPEDTIPLQDLVAAGRLGTSVRKTLLLCSPQPDGKVVYTSLQWASLQ

Source Source

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

Entity 3 Entity 3 polymer

Description description	Pre-tRNA
Molecular weight formula_weight	36798.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	T

UAAUACGACUCACUAUAGGGGGCUCUGUGGCGCAAUGGAUAGCGCAUUGGACUUCUAGUGACGAAUAGAGCAAUUCAAAGGUUGUGGGUUCGAAUCCCACCAGAGUCGGAUAUC

Entity 4 Entity 4 polymer

Description description	tRNA-splicing endonuclease subunit Sen54
Molecular weight formula_weight	61032.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MASDYKDDDDKASDEVDAGTMEPEPEPAAVEVPAGRVLSARELFAARSRSQKLPQRSHGPKDFLPDGSAAQAERLRRCREELWQLLAEQRVERLGSLVAAEWRPEEGFVELKSPAGKFWQTMGFSEQGRQRLHPEEALYLLECGSIHLFHQDLPLSIQEAYQLLLTDHTVTFLQYQVFSHLKRLGYVVRRFQPSSVLSPYERQLNLDASVQHLEDGDGKRKRSSSSPRSINKKAKALDNSLQPKSLAASSPPPCSQPSQCPEEKPQESSPMKGPGGPFQLLGSLGPSPGPAREGVGCSWESGRAENGVTGAGKRRWNFEQISFPNMASDSRHTLLRAPAPELLPANVAGRETDAESWCQKLNQRKEKLSRREREHHAEAAQFQEDVNADPEVQRCSSWREYKELLQRRQVQRSQRRAPHLWGQPVTPLLSPGQASSPAVVLQHISVLQTTHLPDGGARLLEKSGGLEIIFDVYQADAVATFRKNNPGKPYARMCISGFDEPVPDLCSLKRLSYQSGDVPLIFALVDHGDISFYSFRDFTLPQDVGH

Source Source

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

Entity 5 Entity 5 polymer

Description description	Chromosome 1 open reading frame 19, isoform CRA_a
Molecular weight formula_weight	22796.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MASSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKGSAAAMEERGDSEPTPGCSGLGPGGVRGFGDGGGAPSWAPEDAWMGTHPKYLEMMELDIGDATQVYVAFLVYLDLMESKSWHEVNCVGLPELQLICLVGTEIEGEGLQTVVPTPITASLSHNRIREILKASRKLQGDPDLPMSFTLAIVESDSTIVYYKLTDGFMLPDPQVSFENISLRR

Source Source

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

Entity 6 Entity 6 polymer

Description description	;Polyribonucleotide 5'-hydroxyl-kinase Clp1 ;
Molecular weight formula_weight	49837.5 kDa
EC 编号 ec_number	2.7.1.78
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MASDYKDDDDKASDEVDAGTMGEEANDDKKPTTKFELERETELRFEVEASQSVQLELLTGMAEIFGTELTRNKKFTFDAGAKVAVFTWHGCSVQLSGRTEVAYVSKDTPMLLYLNTHTALEQMRRQAEKEEERGPRVMVVGPTDVGKSTVCRLLLNYAVRLGRRPTYVELDVGQGSVSIPGTMGALYIERPADVEEGFSIQAPLVYHFGSTTPGTNIKLYNKITSRLADVFNQRCEVNRRASVSGCVINTCGWVKGSGYQALVHAASAFEVDVVVVLDQERLYNELKRDLPHFVRTVLLPKSGGVVERSKDFRRECRDERIREYFYGFRGCFYPHAFNVKFSDVKIYKVGAPTIPDSCLPLGMSQEDNQLKLVPVTPGRDMVHHLLSVSTAEGTEENLSETSVAGFIVVTSVDLEHQVFTVLSPAPRPLPKNFLLIMDIRFMDLK

Source Source

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

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

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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	2.94 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	199001

Cryo-EM structure of the human pre-catalytic TSEN/pre-tRNA complex

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

tRNA-splicing endonuclease subunit Sen2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

tRNA-splicing endonuclease subunit Sen34

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

tRNA-splicing endonuclease subunit Sen54

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Chromosome 1 open reading frame 19, isoform CRA_a

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;Polyribonucleotide 5'-hydroxyl-kinase Clp1 ;

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

8hmy__assembly_1__model_1

8hmy__assembly_1__model_1 | I(q)

8hmy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

7. Citations (1)