SAXSdb — 3fbn

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

Mediator of RNA polymerase II transcription subunit 7

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Mediator of RNA polymerase II transcription subunit 31 × 1 （P38633） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Mediator of RNA polymerase II transcription subunit 31 × 1 （P38633） water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 8	Mediator of RNA polymerase II transcription subunit 31 × 4 （P38633） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MED7_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–84； UniProt 2–83 Author chain C； PDBConstruct 3–84； UniProt 2–83

Mediator of RNA polymerase II transcription subunit 31

Saccharomyces cerevisiae

UniProt P38633

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Mediator of RNA polymerase II transcription subunit 7 × 1 （Q08278） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Mediator of RNA polymerase II transcription subunit 7 × 1 （Q08278） water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 8	Mediator of RNA polymerase II transcription subunit 7 × 4 （Q08278） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MED31_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–130； UniProt 1–127 Author chain D； PDBConstruct 4–130； UniProt 1–127

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	3fbn
Deposition date deposition_date	2008-11-19
Structure title title	Structure of the Mediator submodule Med7N/31
Keywords keywords	;proline-rich stretches, right-handed four-helix bundle, protein-protein complex, nucleus, transcription, transcription regulation, Activator ;; 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.

3fbn__assembly_1__model_1

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

Download this curve (.dat)

3fbn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fbn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.03 Å
Rg (electron density)	16.58 Å
Total Rg	17.75 Å
Atom count	1226
Residues	148
Excluded volume	22148 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fbn__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fbn__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3fbn__assembly_3__model_1`	octameric （8）	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 (3)

Entity 1 Entity 1 polymer

Description description	Mediator of RNA polymerase II transcription subunit 7
Molecular weight formula_weight	9286.3 kDa
Mutation mutation	L13Y, Y14S, P16T, P17S, P19S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	2402

MASNDPGNEVSSYSPTSPSYVKFFTQSNLEKLPKYKEKKAASAKQTAPNNSNGGSEEEITCALDYLIPPPMPKNQQYRAFGSIW

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Mediator of RNA polymerase II transcription subunit 31
Molecular weight formula_weight	15030.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GSHMSSTNGNAPATPSSDQNPLPTRFEVELEFIQSLANIQYVTYLLTQQQIWKSPNFKNYLKYLEYWCNPPYSQCIVYPNCLFILKLLNGFMESAIVNEDGLLEGLDELPKIIQLQGPQWMNEMVERWAN

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3fbnA00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1520 —

Domain ID domain_id	3fbnB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1340 — Mediator of RNA polymerase II, submodule Med31 (Soh1)

Domain ID domain_id	3fbnC00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1520 —

Domain ID domain_id	3fbnD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1340 — Mediator of RNA polymerase II, submodule Med31 (Soh1)

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Unit-cell length a length_a	174.620 Å
Unit-cell length b length_b	174.620 Å
Unit-cell length c length_c	117.840 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	36

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	3.007 Å
Low-resolution limit resolution_low	43.655 Å
R factor r_factor	0.1810
R_work r_work	0.1780
R_free r_free	0.2310

Structure of the Mediator submodule Med7N/31

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

Mediator of RNA polymerase II transcription subunit 7

State in the Current Structure

Other States of the Same Protein in the Database

Mediator of RNA polymerase II transcription subunit 31

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

3fbn__assembly_1__model_1

3fbn__assembly_1__model_1 | I(q)

3fbn__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of the Mediator submodule Med7N/31

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

Mediator of RNA polymerase II transcription subunit 7

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Mediator of RNA polymerase II transcription subunit 31

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

3fbn__assembly_1__model_1

3fbn__assembly_1__model_1 | I(q)

3fbn__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)