SAXSdb — 5ubp

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

Leucine permease transcriptional regulator

Saccharomyces cerevisiae RM11-1a

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Nuclear mRNA export protein THP1 × 1 （Q08231） 26S proteasome complex subunit SEM1 × 1 （O94742） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B3LGC5_YEAS1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–482； UniProt 71–550

Nuclear mRNA export protein THP1

Saccharomyces cerevisiae S288c

UniProt Q08231

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Leucine permease transcriptional regulator × 1 （B3LGC5） 26S proteasome complex subunit SEM1 × 1 （O94742） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THP1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–455； UniProt 1–455

26S proteasome complex subunit SEM1

Saccharomyces cerevisiae S288c

UniProt O94742

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Leucine permease transcriptional regulator × 1 （B3LGC5） Nuclear mRNA export protein THP1 × 1 （Q08231） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEM1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–89； UniProt 1–89

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	5ubp
Deposition date deposition_date	2016-12-21
Structure title title	TREX2 M-region
Keywords keywords	TREX2 complex; TPR repeats, transcription; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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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.

5ubp__assembly_1__model_1

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

Download this curve (.dat)

5ubp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ubp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.29 Å
Rg (electron density)	33.45 Å
Total Rg	34.09 Å
Atom count	15967
Residues	972
Excluded volume	142680 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ubp__assembly_1__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	Leucine permease transcriptional regulator
Molecular weight formula_weight	56163.2 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	16570

SGSPSYTENKPDKKKKYMINDAKTIQLVGPLISSPDNLGFQKRSHKARELPRFLINQEPQLEKRAFVQDPWDKANQEKMISLEESIDDLNELYETLKKMRNTERSIMEEKGLVDKADSAKDLYDAIVFQGTCLDMCPTFERSRRNVEYTVYSYEKNQPNDKKASRTKALKVFARPAAAAAPPLPSDVRPPHILVKTLDYIVDNLLTTLPESEGFLWDRMRSIRQDFTYQNYSGPEAVDCNERIVRIHLLILHIMVKSNVEFSLQQELEQLHKSLITLSEIYDDVRSSGGTCPNEAEFRAYALLSKIRDPQYDENIQRLPKHIFQDKLVQMALCFRRVISNSAYTERGFVKTENCLNFYARFFQLMQSPSLPLLMGFFLQMHLTDIRFYALRALSHTLNKKHKPIPFIYLENMLLFNNRQEIIEFCNYYSIEIINGDAADLKTLQHYSHKLSETQPLKKTYLTCLERRLQKTTYKGLINGGED

Source Source

Source organism organism	Saccharomyces cerevisiae RM11-1a
NCBI taxonomy ID ncbi_taxonomy_id	285006
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nuclear mRNA export protein THP1
Molecular weight formula_weight	52734.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDMANQLLDELAHGNFSHLTLNLSQNGREIAILQKQLTGFDDKQLETFVEQHPAMPNDTRFKIMCTSFLNYARDVDPWSAWSSSDLIFEFYQCLINCLINDNAPHIEMLIPVATRETEFIINLAGKLDSFHLQLHTRSHQFLSHISSILSRLFNSIKPPRGNASSTNIPGKQRILLYLVNKLNNIYFRIESPQLCSNIFKNFQPKSMLAHFNEYQLDQQIEYRYLLGRYYLLNSQVHNAFVQFNEAFQSLLNLPLTNQAITRNGTRILNYMIPTGLILGKMVKWGPLRPFLSQETIDNWSVLYKHVRYGNIQGVSLWLRQNERHLCARQLLIVLLEKLPMVTYRNLIKTVIKSWTTEWGQNKLPYSLIERVLQLSIGPTFEDPGAQEITIYNGIHSPKNVENVLVTLINLGLLRANCFPQLQLCVVKKTTMIQEIVPPVNERITKMFPAHSHVLW

Source Source

Source organism organism	Saccharomyces cerevisiae S288c
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	26S proteasome complex subunit SEM1
Molecular weight formula_weight	10397.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSTDVAAAQAQSKIDLTKKKNEEINKKSLEEDDEFEDFPIDTWANGETIKSNAVTQTNIWEENWDDVEVDDDFTNELKAELDRYKRENQ

Source Source

Source organism organism	Saccharomyces cerevisiae S288c
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	546

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Unit-cell length a length_a	78.368 Å
Unit-cell length b length_b	86.634 Å
Unit-cell length c length_c	168.338 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	19.945 Å
R factor r_factor	0.1803
R_work r_work	0.1783
R_free r_free	0.2171

TREX2 M-region

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

Leucine permease transcriptional regulator

State in the Current Structure

Other States of the Same Protein in the Database

Nuclear mRNA export protein THP1

State in the Current Structure

Other States of the Same Protein in the Database

26S proteasome complex subunit SEM1

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

5ubp__assembly_1__model_1

5ubp__assembly_1__model_1 | I(q)

5ubp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

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 water

7. Citations (1)

TREX2 M-region

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

Leucine permease transcriptional regulator

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nuclear mRNA export protein THP1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

26S proteasome complex subunit SEM1

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

5ubp__assembly_1__model_1

5ubp__assembly_1__model_1 | I(q)

5ubp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

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 water

7. Citations (1)