PDB-9ccv: Crystal structure of human respiratory syncytial virus NS1 bound ...

ID or keywords:

Entry

Database: PDB / ID: 9ccv

Title

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

Components

Mediator of RNA polymerase II transcription subunit 25
Non-structural protein 1

Keywords

VIRAL PROTEIN / complex / host nuclear protein

Function / homology

Function and homology information

symbiont-mediated suppression of host adaptive immune response / positive regulation of mediator complex assembly / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated perturbation of host apoptosis / core mediator complex / nuclear retinoic acid receptor binding / mediator complex / Generic Transcription Pathway / positive regulation of chromatin binding / : ...
Similarity search - Function

Biological species

Human respiratory syncytial virus A

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.53 Å

Authors

Kalita, P. / Borek, D.M. / Amarasinghe, G.K. / Leung, D.W.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI159678	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI140758	United States

Citation

Journal: Nat Commun / Year: 2025
Title: Molecular basis for human respiratory syncytial virus transcriptional regulator NS1 interactions with MED25.
Authors: Kalita, P. / Khatavkar, O. / Uwase, G. / Korshunova, Y. / Hu, Y. / Wagner, N.D. / Xu, J. / Pan, J. / Nix, J.C. / Gross, M.L. / Brody, S.L. / Borek, D. / Amarasinghe, G.K. / Payton, J.E. / Leung, D.W.

History

Deposition	Jun 23, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 9, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ccv.cif.gz	127.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9ccv.ent.gz	99.1 KB	Display	PDB format
PDBx/mmJSON format	9ccv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cc/9ccv ftp://data.pdbj.org/pub/pdb/validation_reports/cc/9ccv	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#134 - Feb 2011 Integrin similarity (1) #166 - Oct 2013 Proteasome similarity (1) #55 - Jul 2004 DNA Ligase similarity (1)

Deposited unit

A: Non-structural protein 1

B: Mediator of RNA polymerase II transcription subunit 25

36.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	104.953, 104.953, 63.450
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Non-structural protein 1 / Non-structural protein 1C Mass: 15776.216 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human respiratory syncytial virus A / Strain: A/WI / Gene: NS1 / Production host: Escherichia coli (E. coli) / References: UniProt: E0WLW8
#2: Protein	Mediator of RNA polymerase II transcription subunit 25 / Activator interaction domain-containing protein 1 / Activator-recruited cofactor 92 kDa component / ...Activator interaction domain-containing protein 1 / Activator-recruited cofactor 92 kDa component / ARC92 / Mediator complex subunit 25 / p78 Mass: 20971.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MED25, ACID1, ARC92, PTOV2, TCBAP0758 / Production host: Escherichia coli (E. coli) / References: UniProt: Q71SY5
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.4 % / Description: single crystal
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.15 M ammonium tartrate, 0.1 M MES pH 5.6, 12% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00002 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 10, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00002 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. obs: 12815 / % possible obs: 100 % / Redundancy: 25 % / CC_1/2: 0.996 / R_merge(I) obs: 0.073 / Net I/σ(I): 54
Reflection shell	Resolution: 2.5→2.54 Å / R_merge(I) obs: 0.0475 / Num. unique obs: 622 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0415	refinement
HKL-3000	718	data reduction
HKL-3000	718	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.53→48.23 Å / Cor.coef. F_o:F_c: 0.901 / Cor.coef. F_o:F_c free: 0.897 / SU B: 22.899 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.783 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26211	537	5 %	RANDOM
R_work	0.24246	-	-	-
obs	0.24343	10304	87.92 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 41.322 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.4 Å²	-0 Å²	-0 Å²
2-	-	-0.4 Å²	-0 Å²
3-	-	-	0.81 Å²

Refinement step

Cycle: 1 / Resolution: 2.53→48.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2137	0	0	33	2170

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.012	2207
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2159
X-RAY DIFFRACTION	r_angle_refined_deg	0.805	1.645	2987
X-RAY DIFFRACTION	r_angle_other_deg	0.277	1.574	4971
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.588	5	269
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	3.697	5	7
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.232	10	410
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.035	0.2	346
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	2522
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	494
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.295	2.361	1082
X-RAY DIFFRACTION	r_mcbond_other	1.295	2.361	1082
X-RAY DIFFRACTION	r_mcangle_it	2.446	4.223	1349
X-RAY DIFFRACTION	r_mcangle_other	2.446	4.225	1350
X-RAY DIFFRACTION	r_scbond_it	0.645	2.398	1125
X-RAY DIFFRACTION	r_scbond_other	0.645	2.4	1126
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.369	4.403	1639
X-RAY DIFFRACTION	r_long_range_B_refined	4.013	20.96	2281
X-RAY DIFFRACTION	r_long_range_B_other	4.013	20.97	2281
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.53→2.595 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.256	8	-
R_work	0.328	112	-
obs	-	-	13.5 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	9.2617	1.338	8.4752	2.4878	1.7947	7.9085	-0.0449	-0.1658	0.1334	-0.1552	-0.0741	0.1307	-0.0618	-0.1866	0.119	0.2065	-0.0021	-0.0435	0.2317	0.0793	0.0942	34.3511	2.8058	-20.9524
2	7.7594	-0.0765	2.2265	1.8391	0.9859	3.5926	0.0613	0.1477	0.0425	-0.2911	0.1856	-0.2099	-0.2149	0.2035	-0.2469	0.2046	-0.0116	0.0303	0.1254	0.0236	0.0567	47.0026	2.3689	-7.2932
3	0.7145	-0.9642	-1.3832	1.3207	1.8839	2.6968	0.0832	0.0657	0.0301	-0.1661	-0.0473	-0.0048	-0.2029	-0.0637	-0.0358	0.1667	-0.0612	-0.1075	0.3724	0.0769	0.1278	29.3042	3.0787	-20.0355
4	0.5716	-1.9374	1.9796	6.6048	-6.7423	6.8865	0.0112	-0.1009	-0.0998	0.0113	0.3881	0.4256	-0.0167	-0.3749	-0.3993	0.1741	0.0631	0.0062	0.2421	0.2083	0.368	28.7895	11.1472	-19.1065
5	1.6291	-1.503	3.8525	6.0517	-1.1909	10.3608	-0.0138	0.141	0.1589	-0.2317	-0.1301	-0.3829	-0.1646	0.286	0.1439	0.1101	0.002	0.0406	0.0936	0.1171	0.2661	35.9177	12.725	-11.033
6	2.1319	-0.2623	-1.1386	7.287	-2.9534	1.9273	-0.0744	-0.0281	-0.0233	-0.054	0.1478	0.2035	0.0649	-0.0502	-0.0734	0.1379	0.0106	-0.0257	0.1621	-0.0023	0.1077	34.8429	-1.8719	-2.1166
7	0.067	-0.3151	-0.0312	10.5195	-3.0298	1.1311	0.1099	0.0298	0.1541	-0.2474	0.1095	-0.296	-0.1496	-0.1024	-0.2194	0.2878	0.0672	0.1797	0.0723	0.0755	0.45	29.813	15.5076	-8.4863
8	12.997	-9.9596	8.0092	7.7205	-6.5207	6.827	-0.1201	0.4936	-0.2322	0.162	-0.1777	0.1414	-0.4659	-0.3036	0.2978	0.1004	0.048	-0.1377	0.7585	0.2222	0.3618	24.183	4.4956	-13.0075
9	3.4682	0.8176	-1.5017	0.9567	-0.2136	1.8998	0.0012	0.0714	0.1615	-0.2843	0.1644	0.0703	0.0041	-0.0031	-0.1655	0.2064	-0.0004	-0.0247	0.1459	0.0265	0.0357	41.5778	0.1072	-8.9327
10	4.3775	0.5245	5.1878	7.1307	-4.2104	9.5305	-0.4091	-0.0855	-0.3148	-0.9096	0.3056	-0.8042	0.214	-0.4625	0.1035	0.4414	-0.0989	0.1082	0.4208	0.0563	0.3536	33.5363	-3.0721	-26.0221
11	1.5645	-1.6803	-2.0584	2.0644	3.9535	14.7045	0.0959	0.0356	-0.3745	-0.0784	-0.0563	0.3421	0.1794	-0.3556	-0.0396	0.1768	-0.0215	-0.1105	0.211	0.024	0.1842	31.5584	-5.6317	-12.3064
12	4.2531	-4.3906	-2.3459	9.0117	3.779	7.634	0.0321	0.2369	0.1938	-0.5287	0.4178	0.1849	-0.3148	-0.0357	-0.45	0.1546	0.0271	-0.0511	0.2183	0.0845	0.1794	29.0704	8.0696	-6.0892
13	2.5981	-1.1338	-5.2758	1.6392	0.2326	14.5673	0.1408	-0.0771	0.3364	0.0867	-0.0594	-0.4065	-0.4456	0.3483	-0.0814	0.1834	-0.014	0.0535	0.0409	0.0442	0.3479	31.0569	17.8339	6.3361
14	1.1774	0.3804	-3.6326	0.2211	-1.0054	11.504	0.0534	-0.0166	0.0723	0.0579	-0.1823	0.2143	-0.0853	-0.2394	0.1289	0.1611	-0.0231	0.1334	0.3482	-0.2995	0.4579	27.4959	13.1908	14.7782
15	22.9625	4.5569	1.589	10.2805	7.7263	10.065	-0.2417	-0.4897	-0.1109	0.5639	0.2712	0.3203	0.0495	-0.4035	-0.0295	0.1851	-0.0014	0.1292	0.2272	-0.0113	0.0915	28.0664	7.4255	20.3958
16	1.3981	0.4497	-1.0085	6.9239	-0.1546	1.3544	0.0914	-0.1734	0.092	0.1771	-0.0327	-0.1378	0.1477	-0.385	-0.0587	0.1291	-0.1533	0.065	0.455	0.0149	0.1919	19.4463	-9.0017	13.5749
17	17.6152	10.6454	-0.0471	27.6245	-2.8397	3.7115	0.5526	-0.6182	1.3811	-0.0824	-0.5523	1.2883	-0.3106	-0.4576	-0.0004	0.105	0.091	0.0811	0.1731	-0.0139	0.2967	13.7226	7.7745	12.1008
18	12.4194	-2.6158	-0.4039	2.0921	-0.6424	0.3585	0.1668	-0.044	-0.2745	-0.2888	-0.209	0.0154	0.1205	0.0962	0.0422	0.156	-0.0135	0.0142	0.1459	0.012	0.1432	21.5534	-14.3884	10.7838
19	13.2138	-3.2426	-3.9664	1.5365	4.5659	18.6234	-0.5539	-1.0839	0.0059	0.3644	0.3133	0.0447	1.3117	0.5614	0.2406	0.2995	0.0157	-0.0166	0.1552	0.101	0.1646	28.8653	-17.0086	19.2856
20	9.8428	-6.464	4.3807	5.7878	-4.3649	9.4888	-0.1699	-0.411	-0.2898	0.4307	0.186	0.4798	-0.2011	-0.2199	-0.0161	0.1111	-0.0548	0.0679	0.1512	-0.0188	0.1214	20.8148	-7.3691	21.8121
21	3.9322	2.0801	-1.718	1.486	-1.7639	2.7745	0.0752	0.1574	0.5519	0.0434	0.1009	0.2701	-0.0211	0.0258	-0.1761	0.1583	0.0108	0.0531	0.1983	-0.0579	0.1934	29.7883	4.7909	8.2346
22	29.0977	21.4306	2.3953	16.1445	0.6443	3.9806	-1.0701	0.3085	0.7635	-0.8291	0.1507	0.3337	0.0089	0.4712	0.9194	0.1337	0.0056	-0.0395	0.1848	0.1233	0.2837	40.3616	-3.8139	9.986
23	11.3636	1.2389	1.2468	2.4917	-0.6806	1.7843	-0.0695	-0.1298	-0.4561	-0.008	0.0859	0.1176	0.2019	-0.0549	-0.0163	0.1598	-0.0256	0.0233	0.1394	0.0204	0.0819	24.0632	-10.9646	9.2972
24	19.769	5.4705	-10.5276	54.8199	-23.2671	13.3804	-0.1106	-0.0114	-0.4786	0.9573	0.3991	1.2536	-0.3122	-0.1651	-0.2885	0.1961	0.0755	-0.0828	0.3592	-0.0236	0.2101	8.3932	-5.9176	5.857
25	11.8847	-0.2283	-0.4628	1.5975	-1.1897	0.9305	0.337	0.2297	0.1541	0.0592	-0.0651	0.2871	-0.0617	0.0131	-0.272	0.1135	0.031	-0.0156	0.126	0.0668	0.2815	16.0481	0.191	2.058
26	4.1468	-1.5938	-3.4213	0.703	1.3546	2.8401	0.3564	-0.0376	0.5221	-0.0907	-0.011	0.0309	-0.2851	0.0273	-0.3454	0.1126	-0.0841	0.1694	0.2296	-0.0063	0.6621	24.6371	1.4194	11.1322
27	59.0413	-12.723	-8.3516	2.7715	1.7911	1.1959	-0.017	-1.2953	0.817	0.0017	0.1742	-0.1746	-0.0109	0.2044	-0.1572	0.2513	-0.0749	0.0295	0.4257	0.0108	0.1407	28.1621	-4.3368	28.7153
28	1.0027	0.7903	-0.8789	0.7583	-1.0759	6.4881	-0.0147	-0.0042	0.0879	-0.0001	0.0036	0.2001	0.0264	0.1674	0.011	0.0873	0.0011	0.0006	0.157	0.0145	0.1825	27.6103	-4.2398	7.32
29	6.0732	1.3409	3.1974	2.4055	-0.7451	4.5093	0.1104	0.1355	-0.1893	-0.1065	-0.1281	0.0926	0.4475	0.5006	0.0177	0.1073	0.0009	0.0365	0.1559	0.0066	0.1008	29.9235	-7.0447	9.1452
30	3.2177	-1.938	-0.2423	14.7501	-3.0312	1.4845	0.1454	-0.2245	0.1552	0.3047	-0.1297	0.0351	-0.1022	-0.0116	-0.0157	0.117	-0.0389	0.0216	0.1934	-0.0567	0.0886	36.6613	7.7417	15.86

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 12
2	X-RAY DIFFRACTION	2	A	13 - 25
3	X-RAY DIFFRACTION	3	A	26 - 32
4	X-RAY DIFFRACTION	4	A	33 - 38
5	X-RAY DIFFRACTION	5	A	39 - 46
6	X-RAY DIFFRACTION	6	A	47 - 59
7	X-RAY DIFFRACTION	7	A	60 - 67
8	X-RAY DIFFRACTION	8	A	68 - 73
9	X-RAY DIFFRACTION	9	A	74 - 97
10	X-RAY DIFFRACTION	10	A	98 - 104
11	X-RAY DIFFRACTION	11	A	105 - 110
12	X-RAY DIFFRACTION	12	A	111 - 115
13	X-RAY DIFFRACTION	13	A	116 - 123
14	X-RAY DIFFRACTION	14	A	124 - 130
15	X-RAY DIFFRACTION	15	A	131 - 135
16	X-RAY DIFFRACTION	16	B	398 - 409
17	X-RAY DIFFRACTION	17	B	410 - 426
18	X-RAY DIFFRACTION	18	B	427 - 436
19	X-RAY DIFFRACTION	19	B	437 - 442
20	X-RAY DIFFRACTION	20	B	443 - 448
21	X-RAY DIFFRACTION	21	B	449 - 462
22	X-RAY DIFFRACTION	22	B	463 - 468
23	X-RAY DIFFRACTION	23	B	469 - 476
24	X-RAY DIFFRACTION	24	B	477 - 481
25	X-RAY DIFFRACTION	25	B	482 - 490
26	X-RAY DIFFRACTION	26	B	491 - 501
27	X-RAY DIFFRACTION	27	B	502 - 507
28	X-RAY DIFFRACTION	28	B	508 - 519
29	X-RAY DIFFRACTION	29	B	520 - 530
30	X-RAY DIFFRACTION	30	B	531 - 543

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About Yorodumi

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Yorodumi