3j1o

Cryo-EM map of a yeast minimal preinitiation complex interacting with the Mediator Head module

Method: ELECTRON MICROSCOPY

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

Mediator of RNA polymerase II transcription subunit 11

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Mediator of RNA polymerase II transcription subunit 17 × 1 （P32569） Mediator of RNA polymerase II transcription subunit 8 × 1 （P38304） Mediator of RNA polymerase II transcription subunit 22 × 1 （P32570） Mediator of RNA polymerase II transcription subunit 18 × 1 （P32585） Mediator of RNA polymerase II transcription subunit 20 × 1 （P34162） Mediator of RNA polymerase II transcription subunit 6 × 1 （P38782）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0D3YMY9_YEASX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain H； PDBConstruct 1–131； UniProt 1–131

Mediator of RNA polymerase II transcription subunit 17

Saccharomyces cerevisiae

UniProt P32569

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Mediator of RNA polymerase II transcription subunit 11 × 1 （A0A0D3YMY9） Mediator of RNA polymerase II transcription subunit 8 × 1 （P38304） Mediator of RNA polymerase II transcription subunit 22 × 1 （P32570） Mediator of RNA polymerase II transcription subunit 18 × 1 （P32585） Mediator of RNA polymerase II transcription subunit 20 × 1 （P34162） Mediator of RNA polymerase II transcription subunit 6 × 1 （P38782）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MED17_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–420； UniProt 197–616 Author chain I； PDBConstruct 466–484； UniProt 669–687

Mediator of RNA polymerase II transcription subunit 8

Saccharomyces cerevisiae

UniProt P38304

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Mediator of RNA polymerase II transcription subunit 11 × 1 （A0A0D3YMY9） Mediator of RNA polymerase II transcription subunit 17 × 1 （P32569） Mediator of RNA polymerase II transcription subunit 22 × 1 （P32570） Mediator of RNA polymerase II transcription subunit 18 × 1 （P32585） Mediator of RNA polymerase II transcription subunit 20 × 1 （P34162） Mediator of RNA polymerase II transcription subunit 6 × 1 （P38782）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MED8_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain J； PDBConstruct 1–223； UniProt 1–223

Mediator of RNA polymerase II transcription subunit 22

Saccharomyces cerevisiae

UniProt P32570

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Mediator of RNA polymerase II transcription subunit 11 × 1 （A0A0D3YMY9） Mediator of RNA polymerase II transcription subunit 17 × 1 （P32569） Mediator of RNA polymerase II transcription subunit 8 × 1 （P38304） Mediator of RNA polymerase II transcription subunit 18 × 1 （P32585） Mediator of RNA polymerase II transcription subunit 20 × 1 （P34162） Mediator of RNA polymerase II transcription subunit 6 × 1 （P38782）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MED22_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain K； PDBConstruct 1–121； UniProt 1–121

Mediator of RNA polymerase II transcription subunit 18

Saccharomyces cerevisiae

UniProt P32585

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Mediator of RNA polymerase II transcription subunit 11 × 1 （A0A0D3YMY9） Mediator of RNA polymerase II transcription subunit 17 × 1 （P32569） Mediator of RNA polymerase II transcription subunit 8 × 1 （P38304） Mediator of RNA polymerase II transcription subunit 22 × 1 （P32570） Mediator of RNA polymerase II transcription subunit 20 × 1 （P34162） Mediator of RNA polymerase II transcription subunit 6 × 1 （P38782）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MED18_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain L； PDBConstruct 1–108； UniProt 1–108 Author chain L； PDBConstruct 109–275； UniProt 141–307

Mediator of RNA polymerase II transcription subunit 20

Saccharomyces cerevisiae

UniProt P34162

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Mediator of RNA polymerase II transcription subunit 11 × 1 （A0A0D3YMY9） Mediator of RNA polymerase II transcription subunit 17 × 1 （P32569） Mediator of RNA polymerase II transcription subunit 8 × 1 （P38304） Mediator of RNA polymerase II transcription subunit 22 × 1 （P32570） Mediator of RNA polymerase II transcription subunit 18 × 1 （P32585） Mediator of RNA polymerase II transcription subunit 6 × 1 （P38782）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MED20_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain M； PDBConstruct 1–210； UniProt 1–210

Mediator of RNA polymerase II transcription subunit 6

Saccharomyces cerevisiae

UniProt P38782

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Mediator of RNA polymerase II transcription subunit 11 × 1 （A0A0D3YMY9） Mediator of RNA polymerase II transcription subunit 17 × 1 （P32569） Mediator of RNA polymerase II transcription subunit 8 × 1 （P38304） Mediator of RNA polymerase II transcription subunit 22 × 1 （P32570） Mediator of RNA polymerase II transcription subunit 18 × 1 （P32585） Mediator of RNA polymerase II transcription subunit 20 × 1 （P34162）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MED6_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain N； PDBConstruct 1–25； UniProt 166–190

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	3j1o
Deposition date deposition_date	2012-03-29
Structure title title	Cryo-EM map of a yeast minimal preinitiation complex interacting with the Mediator Head module
Keywords keywords	RNA polymerase II, mediator head module, preinitiation complex, TRANSCRIPTION; TRANSCRIPTION
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.

3j1o__assembly_1__model_1

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

Download this curve (.dat)

3j1o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3j1o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.60 Å
Rg (electron density)	48.10 Å
Total Rg	47.96 Å
Atom count	5560
Residues	1120
Excluded volume	89544 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3j1o__assembly_1__model_1`	heptameric （7）	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	Mediator of RNA polymerase II transcription subunit 11
Molecular weight formula_weight	15100.1 kDa
Mutation mutation	T16G, M17S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	5560

MQVLNTKSETKQENEGSQPPYIQERLKSLNDIETQLCSMLQEASQVTFIFGELKRGNESVKPQFENHVKQFYERLDKSTTQLRKEIQLLDENVGTRLLPINVNKKALGQDTEKMEEQLDLLSAILDPSKSK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Mediator of RNA polymerase II transcription subunit 17
Molecular weight formula_weight	54893.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

QEQFVKRRRDMLEHINLAMNESSLALEFVSLLLSSVKESTGMSSMSPFLRKVVKPSSLNSDKIPYVAPTKKEYIELDILNKGWKLQSLNESKDLLRASFNKLSSILQNEHDYWNKIMQSISNKDVIFKIRDRTSGQKLLAIKYGYEDSGSTYKHDRGIANIRNNIESQNLDLIPHSSSVFKGTDFVHSVKKFLRVRIFTKIESEDDYILSGESVMDRDSESEEAETKDIRKQIQLLKKIIFEKELMYQIKKECALLISYGVSIENENKVIIELPNEKFEIELLSLDDDSIVNHEQDLPKINDKRANLMLVMLRLLLVVIFKKTLRSRISSPHGLINLNVDDDILIIRPILGKVRFANYKLLLKKIIKDYVLDIVPGSSITETEVEREQPQENKNIDDENITKLNKEIRAFDKLLNIPRREXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEVEDFLHFIVAEYIQQKKV

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	Mediator of RNA polymerase II transcription subunit 8
Molecular weight formula_weight	25297.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MSQSTASLVPEGNQGSLQEDVSFDFNGVPGQALDAVRMRLAQLTHSLRRIRDEMSKAELPQWYTLQSQLNVTLSQLVSVTSTLQHFQETLDSTVVYPLPKFPTTSHESLVTTLLRKKNIPEVDEWMKYVRETSGVTTALLKDEEIEKLLQQDREITNWARTTFRNEYGKHDFKNEESLSEEHASLLVRDSKPSKPFNVDDVLKFTFTGEKPIITGSTSTSSSN

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 4 Entity 4 polymer

Description description	Mediator of RNA polymerase II transcription subunit 22
Molecular weight formula_weight	13875.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MSNQALYEKLEQTRTILSVKLAELINMTTIADRNDDDEGSFAQENSELAVATTSVMMVNNQTMQLIKNVQDLLILTRSIKEKWLLNQIPVTEHSKVTRFDEKQIEELLDNCIETFVAEKTT

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 5 Entity 5 polymer

Description description	Mediator of RNA polymerase II transcription subunit 18
Molecular weight formula_weight	30659.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MVQQLSLFGSIGDDGYDLLISTLTTISGNPPLLYNSLCTVWKPNPSYDVENVNSRNQLVEPNRIKLSKEVPFSYLIDETMMDKPLNFRILKSFTNDKIPLNYAMTRNINSDDIIDVDMDASPAPSNESCSPWSLQISDIPAAGNNRSVSMQTIAETIILSSAGKNSSVSSLMNGLGYVFEFQYLTIGVKFFMKHGLILELQKIWQIEEAGNSQITSGGFLLKAYINVSRGTDIDRINYTETALMNLKKELQGYIELSVPDRQSMDSRVAHGNILI

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 6 Entity 6 polymer

Description description	Mediator of RNA polymerase II transcription subunit 20
Molecular weight formula_weight	22918.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MGKSAVIFVERATPATLTELKDALSNSILSVRDPWSIDFRTYRCSIKNLPADVSKLMYSITFHHHGRQTVLIKDNSAMVTTAAAADIPPALVFNGSSTGVPESIDTILSSKLSNIWMQRQLIKGDAGETLILDGLTVRLVNLFSSTGFKGLLIELQADEAGEFETKIAGIEGHLAEIRAKEYKTSSDSLGPDTSNEICDLAYQYVRALEL

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 7 Entity 7 polymer

Description description	Mediator of RNA polymerase II transcription subunit 6
Molecular weight formula_weight	2949.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

IFKIVQSRLMSTSYHLNSTLESLYD

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

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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	1

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

Resolution resolution	16.00 Å
Resolution测定Method resolution_method	projection matching
颗粒数 num_particles	51000

Cryo-EM map of a yeast minimal preinitiation complex interacting with the Mediator Head module

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

Mediator of RNA polymerase II transcription subunit 11

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 17

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 8

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 22

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 18

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 20

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 6

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

3j1o__assembly_1__model_1

3j1o__assembly_1__model_1 | I(q)

3j1o__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

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source