SAXSdb — 2ky6

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

Mediator of RNA polymerase II transcription subunit 25

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 391–553	Fragment：VP16-binding-domain (VBD) Activator-interacting domain (ACID) (UNP Residues 391-553)	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure ambient NMR sample composition：50-1000 uM [U-99% 15N] ARC92VBD, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：1.0 mM ARC92VBD, 100% D2O \| 100% D2O NMR sample composition：200-1000 uM [U-99% 13C; U-99% 15N] ARC92VBD, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：700 uM [U-100% 13C; U-100% 15N; U-80% 2H] ARC92VBD, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：700 uM [ILV-100% 13C1H; U-100% 15N; U-100% 2H] ARC92VBD, 100% D2O \| 100% D2O	Resolution not provided

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.

Other PDB	Difference from Current Entry 2KY6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2L23 NMR structure of the ACID (ACtivator Interacting Domain) of the human mediator Med25 protein Deposited 2010-08-10	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 126–283（158 aa） Fragment：ACID domain, UNP residues 391-548	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.75；293 K；Ionic strength (raw mmCIF value) 120；Pressure AMBIENT NMR sample composition 0.3-0.5 MM [U-98% 13C U-98% 15N] MED25, 10 MM SODIUM PHOSPHATE, 100 MM SODIUM CHLORIDE, 5 MM DTT, 90% H2O/ 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3-0.5 MM [U-100% 15N] MED25, 10 MM SODIUM PHOSPHATE, 100 MM SODIUM CHLORIDE, 5 MM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3-0.5 MM [U-95% 13C] MED25, 10 MM SODIUM PHOSPHATE, 100 MM SODIUM CHLORIDE, 5 MM DTT, 100% D2O \| 100% D2O NMR sample composition 0.2 MM [U-100% 15N] MED25, 10 MM SODIUM PHOSPHATE, 100 MM SODIUM CHLORIDE, 5 MM DTT, 100% D2O \| 100% D2O	Resolution not provided
2L6U Solution NMR Structure of Med25(391-543) Comprising the Activator-Interacting Domain (ACID) of Human Mediator Subuniti 25. Northeast Structural Genomics Consortium Target HR6188A Deposited 2010-11-24	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 391–543（153 aa） Fragment：ACID domain residues 391-543	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Pressure AMBIENT NMR sample composition 0.7 MM [U-100% 13C U-100% 15N] HR6188A, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.4 MM [U-5% 13C U-100% 15N] HR6188A, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2XNF The Mediator Med25 activator interaction domain: Structure and cooperative binding of VP16 subdomains Deposited 2010-08-02	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 394–543（150 aa） Fragment：MED25 ACID DOMAIN, RESIDUES 394-543	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；295 K；Ionic strength (raw mmCIF value) 100；Pressure 1.0 NMR measurement conditions pH 6.5；295 K；Ionic strength (raw mmCIF value) 100；Pressure 1.0 NMR sample composition 90%WATER/10% D2O	Resolution not provided
7EMF Human Mediator (deletion of MED1-IDR) in a Tail-extended conformation Deposited 2021-04-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain Y 1–747（747 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric	Chain 3 1–747（747 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric	Chain y 1–747（747 aa）	Not recorded	ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.04 Å
8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric	Chain y 1–747（747 aa）	Not recorded	ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.16 Å
8T9D CryoEM structure of TR-TRAP Deposited 2023-06-23	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric	Chain T 1–747（747 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.66 Å
9CCV Crystal structure of human respiratory syncytial virus NS1 bound to human MED25 ACID Deposited 2024-06-23	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 389–543（155 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.15 M ammonium tartrate, 0.1 M MES pH 5.6, 12% PEG 3350	Resolution 2.53 Å R-free 0.262

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MED25_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–166； UniProt 391–553

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	2ky6
Deposition date deposition_date	2010-05-14
Structure title title	Structure of ARC92VBD/MED25ACID
Keywords keywords	Mediator, ARC, VP16 binding domain, ACID, TRANSCRIPTION REGULATOR; TRANSCRIPTION REGULATOR
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	17.19 Å
Radius of gyration Rg (electron density) rg_electron	16.60 Å
Forward intensity I(0) i0	2924090000.00
Molecular weight molecular_weight	474080.0 kDa
Excluded volume excluded_volume	599130 Å³
Envelope volume envelope_volume	43830 Å³
Hydration-shell volume shell_volume	19629 Å³
Envelope diameter envelope_diameter	72.6 Å
Shell Rg shell_rg	25.31 Å
Envelope Rg envelope_rg	19.26 Å
Shape Rg shape_rg	16.60 Å
Total Rg total_rg	16.69 Å
Total atoms total_atoms	67325
Residues n_residues	4150
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	63.2 Å
Rg (real space) rg_real	17.16 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	2.9240e+09
I(0) uncertainty (real space) i0_real_error	3.3410e+07
Rg (reciprocal space) rg_reciprocal	17.16 Å
I(0) (reciprocal space) i0_reciprocal	2924000000.0000
Solution quality estimate total_estimate	0.8118
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	61.6 Å
Skewness Skewness skewness	0.338
Kurtosis Kurtosis kurtosis	0.152
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	642900.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.535; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.994

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2ky6A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	290 — Ku70; Chain: A; Domain 2
Homologous superfamily homologous superfamily	30 — Mediator complex subunit 25, ACID domain

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8. Citations (1)

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Description description	Mediator of RNA polymerase II transcription subunit 25
Molecular weight formula_weight	18979.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	67325

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/ky/2ky6/2ky6.fit
pddf	/app/data/pr_computation/ky/2ky6/2ky6.pr.out
profile	/app/data/saxs_computation/ky/2ky6/2ky6.dat

Structure of ARC92VBD/MED25ACID

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

Mediator of RNA polymerase II transcription subunit 25

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)