SAXSdb — 7ewm

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

Protein THP3

Saccharomyces cerevisiae S288C

UniProt Q12049

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Cop9 signalosome complex subunit 12 × 1 （P47130） 26S proteasome complex subunit SEM1 × 1 （O94742） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THP3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–289； UniProt 186–470

Cop9 signalosome complex subunit 12

Saccharomyces cerevisiae S288C

UniProt P47130

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Protein THP3 × 1 （Q12049） 26S proteasome complex subunit SEM1 × 1 （O94742） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CSN12_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–423； UniProt 1–423

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	Protein THP3 × 1 （Q12049） Cop9 signalosome complex subunit 12 × 1 （P47130） water × 2	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	7ewm
Deposition date deposition_date	2021-05-25
Structure title title	Native crystal structure of S. cerevisiae Csn12 in complex with Thp3 and Sem1
Keywords keywords	Complex, Nucleic acid binding, Transcription, mRNA splicing; 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.

7ewm__assembly_1__model_1

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

Download this curve (.dat)

7ewm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7ewm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.55 Å
Rg (electron density)	31.70 Å
Total Rg	32.41 Å
Atom count	6106
Residues	739
Excluded volume	109330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7ewm__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	Protein THP3
Molecular weight formula_weight	33959.3 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	6110

GSHMKIHVVGRCQTLEKSYLRLTSEPNPDLIRPPNILQKMYCLLMDKYQSKTATYTYLCDQFKSMRQDLRVQMIENSFTIKVYQTHARIALENGDLGEFNQCQNRIMALFENPTIPKKSYSEFICYSVLYSMLTEDYPSISHLKLKLIDDGSSEILEDEHVKMIFELSDMKLVGNYHYFMKNYLKLHKFEKCLINSFLNLEKLIFLTIICKSYNQVNLDFVKSEFNFNSIEETTNFLNEQNLTEFILNKQITDSNGKSSNIKILNTKGCRVQLIQNYMKSKKIDIKGQK

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Cop9 signalosome complex subunit 12
Molecular weight formula_weight	49558.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDVDIGCYFEEKRYDDKLLDFIRYDVKTPKKTKYILQRPTATDEESVRLQRFYQLGVDLKLKYSKRRSLKKQGRIKNATEELLRLANEQLKLFNRIVERETNWIIYPLWVMAKQLIRLANESSELNKDSIEECGRTIHRSFTICLNDRNPRLNENKKIGCYMFANLEFSIYHRLSNKDMIKNLVKVLESRVNARDIPPLNKSLAMEHKSQVVLYNYYLGQYYGCLENDHERGFFHLNEALLQCPMLYVESTGKFVLQGQMEKIMILLVPLALLTKRLYPHWDHPVIAGVITRSKRLSQVYPTLVRSVISGNLSLYEATAASHERFFLSQGLHVVITLLREVVFTRLVQRCWQWGNDRKSIMPLKILLATKQHDSSANEDEEEQLDALECRLASAIASGLLRAYLSHSNRCIVFSKKEPFPHSK

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

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 BL21(DE3)

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7ewmA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	990 —

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Unit-cell length a length_a	115.575 Å
Unit-cell length b length_b	115.575 Å
Unit-cell length c length_c	126.825 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	32.290 Å
R factor r_factor	0.2236
R_work r_work	0.2220
R_free r_free	0.2510

Native crystal structure of S. cerevisiae Csn12 in complex with Thp3 and Sem1

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

Protein THP3

State in the Current Structure

Other States of the Same Protein in the Database

Cop9 signalosome complex subunit 12

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

7ewm__assembly_1__model_1

7ewm__assembly_1__model_1 | I(q)

7ewm__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

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Native crystal structure of S. cerevisiae Csn12 in complex with Thp3 and Sem1

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

Protein THP3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cop9 signalosome complex subunit 12

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

7ewm__assembly_1__model_1

7ewm__assembly_1__model_1 | I(q)

7ewm__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

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)