SAXSdb — 9ccv

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

Non-structural protein 1

Human respiratory syncytial virus A

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 1–139	Not recorded	Mediator of RNA polymerase II transcription subunit 25 × 1 （Q71SY5）	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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	E0WLW8_HRSV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–141； UniProt 1–139

Mediator of RNA polymerase II transcription subunit 25

Homo sapiens

UniProt Q71SY5

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 389–543	Not recorded	Non-structural protein 1 × 1 （E0WLW8）	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

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 9CCV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KY6 Structure of ARC92VBD/MED25ACID Deposited 2010-05-14	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 391–553（163 aa） Fragment：VP16-binding-domain (VBD) Activator-interacting domain (ACID) (UNP Residues 391-553)	Not recorded	No recorded non-water small molecule	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
2L23 NMR structure of the ACID (ACtivator Interacting Domain) of the human mediator Med25 protein Deposited 2010-08-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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

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	2
Chains and sequence ranges	Author chain B； PDBConstruct 31–185； UniProt 389–543

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	9ccv
Deposition date deposition_date	2024-06-23
最后修订 last_revision	2025-04-09
Structure title title	Crystal structure of human respiratory syncytial virus NS1 bound to human MED25 ACID
Keywords keywords	complex, viral protein, host nuclear protein; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	20.54 Å
Radius of gyration Rg (electron density) rg_electron	19.29 Å
Forward intensity I(0) i0	15347400.00
Molecular weight molecular_weight	30485.0 kDa
Excluded volume excluded_volume	38619 Å³
Envelope volume envelope_volume	45482 Å³
Hydration-shell volume shell_volume	19785 Å³
Envelope diameter envelope_diameter	66.5 Å
Shell Rg shell_rg	25.52 Å
Envelope Rg envelope_rg	19.54 Å
Shape Rg shape_rg	19.27 Å
Total Rg total_rg	20.26 Å
Total atoms total_atoms	2137
Residues n_residues	268
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	67.8 Å
Rg (real space) rg_real	20.47 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	1.5350e+07
I(0) uncertainty (real space) i0_real_error	2.1250e+05
Rg (reciprocal space) rg_reciprocal	20.49 Å
I(0) (reciprocal space) i0_reciprocal	15350000.0000
Solution quality estimate total_estimate	0.7999
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.6 Å
Skewness Skewness skewness	0.247
Kurtosis Kurtosis kurtosis	-0.369
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3107000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 0.991; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Non-structural protein 1
Molecular weight formula_weight	15776.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2196

GHMGSNSLSMIKVRLQNLFDNDEVALLKITCYTDKLIHLTNALAKAVIHTIKLNGIVFVHVITSSDICPNNNIVVKSNFTTMPVLQNGGYIWEMMELTHCSQPNGLIDDNCEIKFSKKLSDSTMTNYMNQLSELLGFDLNP

来源 Source

来源生物 organism	Human respiratory syncytial virus A
NCBI Class编号 ncbi_taxonomy_id	208893
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Mediator of RNA polymerase II transcription subunit 25
Molecular weight formula_weight	20971.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGSSHHHHHHSSGLVPRGSHIENLYFQGHMLGGQQSVSNKLLAWSGVLEWQEKPKPASVDANTKLTRSLPCQVYVNHGENLKTEQWPQKLIMQLIPQQLLTTLGPLFRNSRMVQFHFTNKDLESLKGLYRIMGNGFAGCVHFPHTAPCEVRVLMLLYSSKKKIFMGLIPYDQSGFVNGIRQVITN

来源 Source

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	33

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8. Citations (1)

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Unit-cell length a length_a	104.953 Å
Unit-cell length b length_b	104.953 Å
Unit-cell length c length_c	63.450 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.530 Å
Low-resolution limit resolution_low	48.230 Å
R factor r_factor	0.2434
R_work r_work	0.2425
R_free r_free	0.2621

fit	/app/data/saxs_computation/cc/9ccv/9ccv.fit
pddf	/app/data/pr_computation/cc/9ccv/9ccv.pr.out
profile	/app/data/saxs_computation/cc/9ccv/9ccv.dat

Crystal structure of human respiratory syncytial virus NS1 bound to human MED25 ACID

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

Non-structural protein 1

State in the Current Structure

Other States of the Same Protein in the Database

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)