SAXSdb — 7zrz

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

tRNA-splicing endonuclease subunit Sen34

Homo sapiens

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	tRNA-splicing endonuclease subunit Sen2 × 1 （Q8NCE0） tRNA-splicing endonuclease subunit Sen54 × 1 （Q7Z6J9） tRNA-splicing endonuclease subunit Sen15 × 1 （Q8WW01） pre-tRNA Arg TCT 3-2 × 1	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	1
Chains and sequence ranges	Author chain AP1； PDBConstruct 1–120； UniProt 1–120 Author chain AP1； PDBConstruct 133–263； UniProt 180–310

tRNA-splicing endonuclease subunit Sen2

Homo sapiens

UniProt Q8NCE0

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	tRNA-splicing endonuclease subunit Sen34 × 1 （Q9BSV6） tRNA-splicing endonuclease subunit Sen54 × 1 （Q7Z6J9） tRNA-splicing endonuclease subunit Sen15 × 1 （Q8WW01） pre-tRNA Arg TCT 3-2 × 1	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	2
Chains and sequence ranges	Author chain BP4； PDBConstruct 1–81； UniProt 1–81 Author chain BP4； PDBConstruct 87–260； UniProt 292–465

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 4 RNA 1	tRNA-splicing endonuclease subunit Sen34 × 1 （Q9BSV6） tRNA-splicing endonuclease subunit Sen2 × 1 （Q8NCE0） tRNA-splicing endonuclease subunit Sen15 × 1 （Q8WW01） pre-tRNA Arg TCT 3-2 × 1	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	3
Chains and sequence ranges	Author chain CP1； PDBConstruct 1–178； UniProt 1–178 Author chain CP1； PDBConstruct 192–293； UniProt 425–526

tRNA-splicing endonuclease subunit Sen15

Homo sapiens

UniProt Q8WW01

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	tRNA-splicing endonuclease subunit Sen34 × 1 （Q9BSV6） tRNA-splicing endonuclease subunit Sen2 × 1 （Q8NCE0） tRNA-splicing endonuclease subunit Sen54 × 1 （Q7Z6J9） pre-tRNA Arg TCT 3-2 × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEN15_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain DP1； PDBConstruct 47–217； UniProt 1–171

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	7zrz
Deposition date deposition_date	2022-05-05
Structure title title	Structure of the human tRNA splicing endonuclease defines substrate recognition
Keywords keywords	RNP, endonuclease, tRNA, splicing, 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.

7zrz__assembly_1__model_1

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

Download this curve (.dat)

7zrz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7zrz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.93 Å
Rg (electron density)	31.07 Å
Total Rg	31.75 Å
Atom count	6580
Residues	694
Excluded volume	111560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7zrz__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	tRNA-splicing endonuclease subunit Sen34
Molecular weight formula_weight	28805.8 kDa
EC 编号 ec_number	4.6.1.16,4.6.1.16
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AP1
Atom count atom_count	6580

MLVVEVANGRSLVWGAEAVQALRERLGVGGRTVGALPRGPRQNSRLGLPLLLMPEEARLLAEIGAVTLVSAPRPDSRHHSLALTSFKRQQEESFQEQSALAAEARETRRQELLEKITEGQGGSGGSGGSGGSRSALLVQLATARPRPVKARPLDWRVQSKDWPHAGRPAHELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFFAHYIAQCWAPEDTIPLQDLVAAGRLGTSVRKTLLLCSPQPDGKVVYTSLQWASLQ

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 Sen2
Molecular weight formula_weight	30166.0 kDa
EC 编号 ec_number	4.6.1.16,4.6.1.16
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	BP4

MAEAVFHAPKRKRRVYETYESPLPIPFGQDHGPLKEFKIFRAEMINNNVIVRNAEDIEQLYGKGYFGKGILSRSRPSFTISGGSGGRIFEYLQLSLEEAFFLVYALGCLSIYYEKEPLTIVKLWKAFTVVQPTFRTTYMAYHYFRSKGWVPKVGLKYGTDLLLYRKGPPFYFASYSVIIELVDDHFEGSLRRPLSWKSLAALSRVSVNVSKELMLCYLIKPSTMTDKEMESPECMKRIKVQEVILSRWVSSRERSDQDDL

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	tRNA-splicing endonuclease subunit Sen54
Molecular weight formula_weight	32551.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	CP1

MEPEPEPAAVEVPAGRVLSARELFAARSRSQKLPQRSHGPKDFLPDGSAAQAERLRRCREELWQLLAEQRVERLGSLVAAEWRPEEGFVELKSPAGKFWQTMGFSEQGRQRLHPEEALYLLECGSIHLFHQDLPLSIQEAYQLLLTDHTVTFLQYQVFSHLKRLGYVVRRFQPSSVLSGGSGGSGGSGGSGSVLQTTHLPDGGARLLEKSGGLEIIFDVYQADAVATFRKNNPGKPYARMCISGFDEPVPDLCSLKRLSYQSGDVPLIFALVDHGDISFYSFRDFTLPQDVGH

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 4 Entity 4 polymer

Description description	tRNA-splicing endonuclease subunit Sen15
Molecular weight formula_weight	23860.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	DP1

MDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREPGENLYFQGMEERGDSEPTPGCSGLGPGGVRGFGDGGGAPSWAPEDAWMGTHPKYLEMMELDIGDATQVYVAFLVYLDLMESKSWHEVNCVGLPELQLICLVGTEIEGEGLQTVVPTPITASLSHNRIREILKASRKLQGDPDLPMSFTLAIVESDSTIVYYKLTDGFMLPDPQNISLRR

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	pre-tRNA Arg TCT 3-2
Molecular weight formula_weight	28747.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	ZN1

GGCUCUGUGGCGCAAUGGAUAGCGCAUUGGACUUCUAGAUAGUUAGAGAAAUUCAAAGGUUGUGGGUUCGAGUCCCACCAGAGUCGCCA

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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	triclinic

Resolution resolution	3.09 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	282863

Structure of the human tRNA splicing endonuclease defines substrate recognition

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

tRNA-splicing endonuclease subunit Sen34

State in the Current Structure

Other States of the Same Protein in the Database

tRNA-splicing endonuclease subunit Sen2

State in the Current Structure

Other States of the Same Protein in the Database

tRNA-splicing endonuclease subunit Sen54

State in the Current Structure

Other States of the Same Protein in the Database

tRNA-splicing endonuclease subunit Sen15

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

7zrz__assembly_1__model_1

7zrz__assembly_1__model_1 | I(q)

7zrz__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 (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

7. Citations (1)

Structure of the human tRNA splicing endonuclease defines substrate recognition

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

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 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 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

tRNA-splicing endonuclease subunit Sen15

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

7zrz__assembly_1__model_1

7zrz__assembly_1__model_1 | I(q)

7zrz__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 (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

7. Citations (1)