4gwq

Structure of the Mediator Head Module from S. cerevisiae in complex with the carboxy-terminal domain (CTD) of RNA Polymerase II Rpb1 subunit

Method: X-RAY DIFFRACTION

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

Mediator of RNA polymerase II transcription subunit 11

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	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） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MED11_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–115； UniProt 1–115

Mediator of RNA polymerase II transcription subunit 17

OrganismNot specified

UniProt P32569

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Mediator of RNA polymerase II transcription subunit 11 × 1 （Q99278） 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） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050）	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 B； PDBConstruct 1–687； UniProt 1–687

Mediator of RNA polymerase II transcription subunit 8

OrganismNot specified

UniProt P38304

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Mediator of RNA polymerase II transcription subunit 11 × 1 （Q99278） 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） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050）	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 C； PDBConstruct 1–223； UniProt 1–223

Mediator of RNA polymerase II transcription subunit 22

OrganismNot specified

UniProt P32570

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Mediator of RNA polymerase II transcription subunit 11 × 1 （Q99278） 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） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050）	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 D； PDBConstruct 1–121； UniProt 1–121

Mediator of RNA polymerase II transcription subunit 18

OrganismNot specified

UniProt P32585

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Mediator of RNA polymerase II transcription subunit 11 × 1 （Q99278） 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） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050）	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 E； PDBConstruct 1–307； UniProt 1–307

Mediator of RNA polymerase II transcription subunit 20

OrganismNot specified

UniProt P34162

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Mediator of RNA polymerase II transcription subunit 11 × 1 （Q99278） 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） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050）	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 F； PDBConstruct 1–210； UniProt 1–210

Mediator of RNA polymerase II transcription subunit 6

OrganismNot specified

UniProt P38782

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Mediator of RNA polymerase II transcription subunit 11 × 1 （Q99278） 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） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050）	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 G； PDBConstruct 1–295； UniProt 1–295

DNA-directed RNA polymerase II subunit RPB1

OrganismNot specified

UniProt P04050

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Mediator of RNA polymerase II transcription subunit 11 × 1 （Q99278） 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	RPB1_YEAST
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain H； PDBConstruct 1–35； UniProt 1556–1590

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	4gwq
Deposition date deposition_date	2012-09-03
Structure title title	Structure of the Mediator Head Module from S. cerevisiae in complex with the carboxy-terminal domain (CTD) of RNA Polymerase II Rpb1 subunit
Keywords keywords	;Binding Sites, Mediator Complex, Models, Molecular, Phosphorylation, Protein Structure, Tertiary, Protein Subunits, RNA Polymerase II, Saccharomyces cerevisiae, Structure-Activity Relationship, 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.

4gwq__assembly_1__model_1

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

Download this curve (.dat)

4gwq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4gwq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.59 Å
Rg (electron density)	49.71 Å
Total Rg	49.37 Å
Atom count	9217
Residues	1566
Excluded volume	155460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4gwq__assembly_1__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 (8)

Entity 1 Entity 1 polymer

Description description	Mediator of RNA polymerase II transcription subunit 11
Molecular weight formula_weight	13324.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9217

MQPPYIQERLKSLNDIETQLCSMLQEASQVTFIFGELKRGNESVKPQFENHVKQFYERLDKSTTQLRKEIQLLDENVGTRLLPINVNKKALGQDTEKMEEQLDLLSAILDPSKSK

Entity 2 Entity 2 polymer

Description description	Mediator of RNA polymerase II transcription subunit 17
Molecular weight formula_weight	78582.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MTTEDPDSNHLSSETGIKLALDPNLITLALSSNPNSSLHSPTSDEPVPESAGKADTSIRLEGDELENKTKKDNDKNLKFLKNKDSLVSNPHEIYGSMPLEQLIPIILRQRGPGFKFVDLNEKELQNEIKQLGSDSSDGHNSEKKDTDGADENVQIGEDFMEVDYEDKDNPVDSRNETDHKTNENGETDDNIETVMTQEQFVKRRRDMLEHINLAMNESSLALEFVSLLLSSVKESTGMSSMSPFLRKVVKPSSLNSDKIPYVAPTKKEYIELDILNKGWKLQSLNESKDLLRASFNKLSSILQNEHDYWNKIMQSISNKDVIFKIRDRTSGQKLLAIKYGYEDSGSTYKHDRGIANIRNNIESQNLDLIPHSSSVFKGTDFVHSVKKFLRVRIFTKIESEDDYILSGESVMDRDSESEEAETKDIRKQIQLLKKIIFEKELMYQIKKECALLISYGVSIENENKVIIELPNEKFEIELLSLDDDSIVNHEQDLPKINDKRANLMLVMLRLLLVVIFKKTLRSRISSPHGLINLNVDDDILIIRPILGKVRFANYKLLLKKIIKDYVLDIVPGSSITETEVEREQPQENKNIDDENITKLNKEIRAFDKLLNIPRRELKINLPLTEHKSPNLSLMLESPNYCNALIHIKFSAGTEANAVSFDTTFSDFKEVEDFLHFIVAEYIQQKKV

Entity 3 Entity 3 polymer

Description description	Mediator of RNA polymerase II transcription subunit 8
Molecular weight formula_weight	45930.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSQSTASLVPEGNQGSLQEDVSFDFNGVPGQALDAVRMRLAQLTHSLRRIRDEMSKAELPQWYTLQSQLNVTLSQLVSVTSTLQHFQETLDSTVVYPLPKFPTTSHESLVTTLLRKKNIPEVDEWMKYVRETSGVTTALLKDEEIEKLLQQDREITNWARTTFRNEYGKHDFKNEESLSEEHASLLVRDSKPSKPFNVDDVLKFTFTGEKPIITGSTSTSSSNSMEKRRWKKNFIAVSAANRFKKISSSGALDYDIPTTASENLYFQGELKTAALAQHDEAVDNKFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAPKVDNKFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNGAQAPKVDANSAGKST

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	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MSNQALYEKLEQTRTILSVKLAELINMTTIADRNDDDEGSFAQENSELAVATTSVMMVNNQTMQLIKNVQDLLILTRSIKEKWLLNQIPVTEHSKVTRFDEKQIEELLDNCIETFVAEKTT

Entity 5 Entity 5 polymer

Description description	Mediator of RNA polymerase II transcription subunit 18
Molecular weight formula_weight	34316.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MVQQLSLFGSIGDDGYDLLISTLTTISGNPPLLYNSLCTVWKPNPSYDVENVNSRNQLVEPNRIKLSKEVPFSYLIDETMMDKPLNFRILKSFTNDKIPLNYAMTRNILHNTVPQVTNFNSTNEDQNNSKHTEDTVNESRNSDDIIDVDMDASPAPSNESCSPWSLQISDIPAAGNNRSVSMQTIAETIILSSAGKNSSVSSLMNGLGYVFEFQYLTIGVKFFMKHGLILELQKIWQIEEAGNSQITSGGFLLKAYINVSRGTDIDRINYTETALMNLKKELQGYIELSVPDRQSMDSRVAHGNILI

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	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MGKSAVIFVERATPATLTELKDALSNSILSVRDPWSIDFRTYRCSIKNLPADVSKLMYSITFHHHGRQTVLIKDNSAMVTTAAAADIPPALVFNGSSTGVPESIDTILSSKLSNIWMQRQLIKGDAGETLILDGLTVRLVNLFSSTGFKGLLIELQADEAGEFETKIAGIEGHLAEIRAKEYKTSSDSLGPDTSNEICDLAYQYVRALEL

Entity 7 Entity 7 polymer

Description description	Mediator of RNA polymerase II transcription subunit 6
Molecular weight formula_weight	32844.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MNVTPLDELQWKSPEWIQVFGLRTENVLDYFAESPFFDKTSNNQVIKMQRQFSQLNDPNAAVNMTQNIMTLPDGKNGNLEEEFAYVDPARRQILFKYPMYMQLEEELMKLDGTEYVLSSVREPDFWVIRKQRRTNNSGVGSAKGPEIIPLQDYYIIGANIYQSPTIFKIVQSRLMSTSYHLNSTLESLYDLIEFQPSQGVHYKVPTDTSTTATAATNGNNAGGGSNKSSVRPTGGANMATVPSTTNVNMTVNTMGTGGQTIDNGTGRTGNGNMGITTEMLDKLMVTSIRSTPNYI

Entity 8 Entity 8 polymer

Description description	DNA-directed RNA polymerase II subunit RPB1
Molecular weight formula_weight	3616.7 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS

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Unit-cell length a length_a	142.449 Å
Unit-cell length b length_b	142.449 Å
Unit-cell length c length_c	305.641 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	4.500 Å
Low-resolution limit resolution_low	45.000 Å
R factor r_factor	0.2890
R_work r_work	0.2860
R_free r_free	0.3450

Structure of the Mediator Head Module from S. cerevisiae in complex with the carboxy-terminal domain (CTD) of RNA Polymerase II Rpb1 subunit

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

DNA-directed RNA polymerase II subunit RPB1

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

4gwq__assembly_1__model_1

4gwq__assembly_1__model_1 | I(q)

4gwq__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer