2hzm

Structure of the Mediator head subcomplex Med18/20

Method: X-RAY DIFFRACTION Dmax: 161.9 Å Quality: GOOD

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

RNA polymerase II mediator complex subunit 20

Saccharomyces cerevisiae

UniProt P34162

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–210 Not recorded RNA polymerase II mediator complex subunit 18 × 1 (P32585) PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;100 mM Tris, 1.8 M Na/K phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.264
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–210 Not recorded RNA polymerase II mediator complex subunit 18 × 1 (P32585) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;100 mM Tris, 1.8 M Na/K phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.264
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 1–210 Not recorded RNA polymerase II mediator complex subunit 18 × 1 (P32585) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;100 mM Tris, 1.8 M Na/K phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.264
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 1–210 Not recorded RNA polymerase II mediator complex subunit 18 × 1 (P32585) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;100 mM Tris, 1.8 M Na/K phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.264

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

13 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MED20_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–212; UniProt 1–210 Author chain C; PDBConstruct 3–212; UniProt 1–210 Author chain E; PDBConstruct 3–212; UniProt 1–210 Author chain G; PDBConstruct 3–212; UniProt 1–210

RNA polymerase II mediator complex subunit 18

Saccharomyces cerevisiae

UniProt P32585

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 2–307 Fragment:residues 2-307 RNA polymerase II mediator complex subunit 20 × 1 (P34162) PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;100 mM Tris, 1.8 M Na/K phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.264
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 2–307 Fragment:residues 2-307 RNA polymerase II mediator complex subunit 20 × 1 (P34162) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;100 mM Tris, 1.8 M Na/K phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.264
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 2–307 Fragment:residues 2-307 RNA polymerase II mediator complex subunit 20 × 1 (P34162) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;100 mM Tris, 1.8 M Na/K phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.264
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain H; UniProt 2–307 Fragment:residues 2-307 RNA polymerase II mediator complex subunit 20 × 1 (P34162) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;100 mM Tris, 1.8 M Na/K phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.264

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

12 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MED18_YEAST
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–306; UniProt 2–307 Author chain D; PDBConstruct 1–306; UniProt 2–307 Author chain F; PDBConstruct 1–306; UniProt 2–307 Author chain H; PDBConstruct 1–306; UniProt 2–307

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2hzm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2hzm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2hzm
Deposition date deposition_date2006-08-09
Structure title titleStructure of the Mediator head subcomplex Med18/20
Keywords keywordsbeta barrel, channel, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier46.39
Radius of gyration Rg (electron density) rg_electron46.36
Forward intensity I(0) i0505890000.00
Molecular weight molecular_weight189900.0 kDa
Excluded volume excluded_volume239880 ų
Envelope volume envelope_volume341640 ų
Hydration-shell volume shell_volume64840 ų
Envelope diameter envelope_diameter166.7
Shell Rg shell_rg47.43
Envelope Rg envelope_rg46.17
Shape Rg shape_rg46.35
Total Rg total_rg46.45
Total atoms total_atoms13358
Residues n_residues1717
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax161.9
Rg (real space) rg_real46.59
Rg uncertainty (real space) rg_real_error1.85
I(0) (real space) i0_real5.0590e+08
I(0) uncertainty (real space) i0_real_error1.0100e+07
Rg (reciprocal space) rg_reciprocal46.39
I(0) (reciprocal space) i0_reciprocal505800000.0000
Solution quality estimate total_estimate0.8568
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary52.4
Skewness Skewness skewness0.448
Kurtosis Kurtosis kurtosis-0.194
Angular range angular_range— – 0.1700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30470000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.713

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id2hzmA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily180
Domain ID domain_id2hzmA02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology140 — q64v53_bacfr protein fold
Homologous superfamily homologous superfamily20
Domain ID domain_id2hzmB00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology320 — Hypothetical Protein Pfu-838710-001
Homologous superfamily homologous superfamily10 — Hypothetical Protein Pfu-838710-001
Domain ID domain_id2hzmC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily180
Domain ID domain_id2hzmC02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology140 — q64v53_bacfr protein fold
Homologous superfamily homologous superfamily20
Domain ID domain_id2hzmD00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology320 — Hypothetical Protein Pfu-838710-001
Homologous superfamily homologous superfamily10 — Hypothetical Protein Pfu-838710-001
Domain ID domain_id2hzmE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily180
Domain ID domain_id2hzmE02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology140 — q64v53_bacfr protein fold
Homologous superfamily homologous superfamily20
Domain ID domain_id2hzmF00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology320 — Hypothetical Protein Pfu-838710-001
Homologous superfamily homologous superfamily10 — Hypothetical Protein Pfu-838710-001
Domain ID domain_id2hzmG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily180
Domain ID domain_id2hzmG02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology140 — q64v53_bacfr protein fold
Homologous superfamily homologous superfamily20
Domain ID domain_id2hzmH00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology320 — Hypothetical Protein Pfu-838710-001
Homologous superfamily homologous superfamily10 — Hypothetical Protein Pfu-838710-001

8. Citations (1)

9. Files and Curves (10)