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- PDB-5vj2: Structure of human respiratory syncytial virus non-structural pro... -

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Basic information

Entry
Database: PDB / ID: 5vj2
TitleStructure of human respiratory syncytial virus non-structural protein 1 (NS1)
ComponentsNon-structural protein 1
KeywordsVIRAL PROTEIN / RSV / immune modulator
Function / homology
Function and homology information


symbiont-mediated suppression of host adaptive immune response / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell nucleus / cytoplasm
Similarity search - Function
Pneumovirus NS1 protein / Pneumovirus NS1 protein
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Non-structural protein 1
Similarity search - Component
Biological speciesRespiratory syncytial virus type A
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.22 Å
AuthorsLeung, D.W. / Borek, D.M. / Amarasinghe, G.K.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI107056 , U191099565 , United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI123926 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI114654 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U191099565, U19AI109945 , U19AI109664 , U19AI070489 , RO1AI111605 , R01 AI087798, U19 AI095227 T32-CA09547 United States
CitationJournal: Nat Microbiol / Year: 2017
Title: Structural basis for human respiratory syncytial virus NS1-mediated modulation of host responses.
Authors: Chatterjee, S. / Luthra, P. / Esaulova, E. / Agapov, E. / Yen, B.C. / Borek, D.M. / Edwards, M.R. / Mittal, A. / Jordan, D.S. / Ramanan, P. / Moore, M.L. / Pappu, R.V. / Holtzman, M.J. / ...Authors: Chatterjee, S. / Luthra, P. / Esaulova, E. / Agapov, E. / Yen, B.C. / Borek, D.M. / Edwards, M.R. / Mittal, A. / Jordan, D.S. / Ramanan, P. / Moore, M.L. / Pappu, R.V. / Holtzman, M.J. / Artyomov, M.N. / Basler, C.F. / Amarasinghe, G.K. / Leung, D.W.
History
DepositionApr 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_assembly ...pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 1
B: Non-structural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,31913
Polymers31,5522
Non-polymers76711
Water93752
1
A: Non-structural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2928
Polymers15,7761
Non-polymers5157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-structural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0275
Polymers15,7761
Non-polymers2514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.977, 100.682, 122.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 5 - 139 / Label seq-ID: 7 - 141

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Non-structural protein 1 / Nonstructural protein 1


Mass: 15776.216 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus type A / Gene: NS1 / Production host: Escherichia coli (E. coli) / References: UniProt: X5FN71
#2: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.1, 1.5 M ammonium sulfate, and 10% dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.22→26.27 Å / Num. obs: 13278 / % possible obs: 98.82 % / Redundancy: 5.6 % / Net I/σ(I): 24.12

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.22→26.27 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 12.509 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.219 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23689 691 4.9 %RANDOM
Rwork0.18566 ---
obs0.18814 13276 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.569 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0 Å2
2---0.03 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.22→26.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 46 52 2198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192186
X-RAY DIFFRACTIONr_bond_other_d0.0010.022154
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9782949
X-RAY DIFFRACTIONr_angle_other_deg0.79434979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.255272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8326.55287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47715400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.728152
X-RAY DIFFRACTIONr_chiral_restr0.0690.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022396
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02454
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.462.81082
X-RAY DIFFRACTIONr_mcbond_other3.4152.7941081
X-RAY DIFFRACTIONr_mcangle_it4.8894.1761350
X-RAY DIFFRACTIONr_mcangle_other4.9084.181351
X-RAY DIFFRACTIONr_scbond_it5.163.3311104
X-RAY DIFFRACTIONr_scbond_other5.1593.3311104
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4864.7551598
X-RAY DIFFRACTIONr_long_range_B_refined9.69634.1572203
X-RAY DIFFRACTIONr_long_range_B_other9.7134.0812193
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 7866 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.221→2.279 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 55 -
Rwork0.236 936 -
obs--96.49 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.2122-7.30897.854711.6106-10.161212.9903-0.01110.4177-0.08970.5157-0.0640.3090.21910.7610.07510.29480.14740.02840.32640.04970.096813.156-11.89976.684
20.0780.0266-0.189611.26090.34820.60890.0333-0.0089-0.0963-0.2686-0.322-0.1366-0.0163-0.06870.28860.0701-0.0188-0.00380.118-0.0150.14596.8992.27769.105
35.93620.00631.83273.65817.302815.1760.08690.09140.0198-0.1764-0.24240.0934-0.2907-0.41830.15540.11410.011-0.04150.0859-0.01860.06555.69711.79166.361
41.9742-4.33884.19049.7934-8.839510.19980.0751-0.0044-0.1325-0.10730.06890.2971-0.1090.1899-0.14390.1699-0.0387-0.02660.07480.01170.115512.921-2.62971.087
514.8085.93133.83394.9904-0.14912.07820.31440.1922-0.17570.402-0.3465-0.19-0.09730.32290.03210.1277-0.00920.00610.10630.05650.054413.617-12.21785.787
69.2412-6.68-5.796811.9837-0.77547.6245-0.3497-0.1147-0.2090.43220.17930.13420.1975-0.09550.17040.1221-0.0342-0.00140.05440.02320.047.981-4.9884.751
77.6336.7294-6.16126.9076-5.40096.0918-0.0004-0.17370.1319-0.0485-0.0590.16270.0724-0.04030.05940.0857-0.0287-0.01190.12350.00910.08038.3045.54579.65
83.3561-0.1342-2.15751.1196-1.98898.8992-0.0983-0.0431-0.1193-0.06070.0093-0.11410.02920.17410.0890.0873-0.00980.01580.0793-0.00380.123822.8077.7372.077
97.42544.5221-3.90723.4839-3.03792.66380.0583-0.30490.24120.2263-0.08240.0035-0.18410.09780.02410.1588-0.0061-0.00850.14560.0120.06539.95.04484.885
1010.87730.61891.94497.4251.11792.3969-0.8484-0.80610.38170.88130.6678-0.09960.0936-0.03820.18070.46180.1041-0.10710.2080.02230.076315.248-1.5889.21
110.2245-0.0860.47462.9296-2.43043.6726-0.03220.0907-0.09330.0399-0.1131-0.2892-0.01940.19350.14530.1115-0.01650.00380.1049-0.00020.105517.39-0.90570.772
125.5034-0.661-1.9932.94262.40562.36120.19830.33960.2862-0.28-0.0337-0.1135-0.2678-0.1235-0.16460.11260.0085-0.03270.0970.05370.076115.97212.63869.084
134.80841.7129-2.357310.3431-1.4561.1960.12520.1022-0.13660.0651-0.16750.1892-0.0615-0.0330.04230.0651-0.0292-0.02970.0812-0.0130.07585.0841.51272.125
1424.0917-11.9427-1.63239.31482.13760.63460.00110.1189-0.9552-0.1715-0.07990.5187-0.0444-0.02330.07870.1357-0.0384-0.00640.014-0.00270.098111.356-14.62674.018
159.807510.1617-0.504311.1974-1.84110.2619-0.18020.3989-0.5399-0.32160.2816-0.88220.68680.4902-0.10140.09080.04510.02260.10070.01110.265722.163-7.73770.411
167.1028-3.755-8.8815.16792.832712.1961-0.1612-0.2930.10510.18270.1534-0.28430.1530.370.00790.07270.0026-0.04350.09140.00520.082318.482.41381.247
178.5561-9.1068-0.46725.16680.85070.06480.07160.3607-0.35420.6568-0.12560.41570.032-0.04530.05410.0797-0.00490.02030.1311-0.03690.05318.712.02889.662
180.95160.71293.34724.4153.144711.8807-0.0185-0.00420.07590.2165-0.3140.4595-0.0213-0.04840.33250.0836-0.0190.03450.138-0.01970.05816.0419.29584.534
194.9410.06262.46730.2008-1.952320.9216-0.4090.0650.2806-0.01810.0105-0.0198-0.0675-0.05550.39850.07160.0103-0.01510.0563-0.00410.09392.03618.79775.309
2011.1603-1.391212.109810.084-7.408716.66080.0176-0.3782-0.05470.45090.09830.1642-0.2623-0.4374-0.11590.050.004-0.01350.11250.01720.13210.22111.34978.84
214.7052-7.4647-2.194712.9282.15482.67360.1630.16560.1198-0.1812-0.2374-0.2484-0.1646-0.1040.07440.0722-0.0373-0.0240.05390.0080.164518.16540.3971.595
222.9170.47720.41435.3946-1.32194.1794-0.1291-0.01940.216-0.62470.1378-0.49870.47390.2675-0.00870.25830.0119-0.01230.1664-0.0050.118124.38620.76968.859
231.0294-3.3532-0.038911.54530.78511.25510.19330.1270.1796-0.6866-0.3564-0.3557-0.082-0.15940.16310.1699-0.0333-0.02030.13390.06580.173319.44430.71565.862
240.78332.68571.77759.26226.08866.60760.1632-0.0177-0.05440.615-0.0561-0.29380.5083-0.1519-0.10710.08480.0198-0.09680.0556-0.02330.219512.58644.59877.602
255.0924-0.8975-0.427218.9109-1.97210.2595-0.3979-0.35350.1910.36540.4116-0.0273-0.0004-0.0098-0.01370.15530.033-0.08470.047-0.03710.084416.95142.34982.717
2610.45685.0147.84046.99314.25165.9317-0.2682-0.3227-0.0966-0.0290.4646-1.2094-0.1978-0.1756-0.19640.21320.038-0.05650.2871-0.17160.302421.69233.84182.901
274.7170.37433.75670.68761.02156.5538-0.01330.04740.00870.06320.03790.09840.0588-0.0009-0.02460.0731-0.0137-0.02640.05610.02340.10429.89224.55371.265
282.44121.93265.58981.99334.216112.90030.0279-0.02250.06190.0566-0.17250.02820.07570.02830.14460.11890.0059-0.03680.1028-0.01450.073516.6329.07283.883
2915.7764-3.354110.34582.8778-1.17277.2999-0.4599-0.81330.05460.27470.37120.0516-0.2412-0.48370.08870.12650.0529-0.00940.1371-0.03390.021910.61836.1985.975
304.6535-0.9166-6.7973.36040.568211.84020.01410.17250.08270.28850.00720.1062-0.139-0.2219-0.02130.08060.011-0.05080.02440.02250.11768.98339.59974.082
3110.2553-6.3485-12.55116.48976.696315.82510.20690.5135-0.2265-0.2469-0.50460.174-0.2166-0.5370.29760.0787-0.0439-0.03960.09690.01930.089316.36428.58262.698
327.7465-0.2122-0.72746.5038-4.43473.1224-0.37660.85580.01350.2130.2232-0.2199-0.1084-0.24690.15340.1114-0.0723-0.04410.1319-0.01460.074212.35720.61463.241
336.96961.90072.58674.6788-0.23432.284-0.2132-0.0312-0.1269-0.00820.0811-0.1416-0.1216-0.01910.1320.0757-0.00060.0060.09960.00540.068221.7125.22971.935
341.0063-3.5732-0.557615.00492.82570.61770.10080.04170.0546-0.0627-0.22850.23610.0524-0.0520.12770.1102-0.03780.04480.0553-0.00750.18823.71640.55373.197
350.851-3.3177-1.82613.05598.130212.64220.2030.04230.2086-0.8572-0.1569-0.7806-0.91260.0498-0.04610.16170.0053-0.00470.09310.10330.216312.62345.18767.302
360.5061-0.13552.06190.1301-0.2899.6584-0.0147-0.052-0.05860.02610.06980.1304-0.1292-0.0007-0.05520.12590.01410.00110.07120.03910.22728.59531.86675.786
377.2336-2.06223.011715.02-3.62651.7848-0.3825-0.02120.1085-0.00390.2809-0.3243-0.1361-0.06280.10160.15560.01930.00590.1162-0.00820.008416.67222.89189.737
382.80980.4997-5.7060.1846-0.931911.6682-0.14290.0299-0.1433-0.0491-0.0201-0.17730.2605-0.11710.16290.1527-0.00390.01640.15640.02050.25620.87814.51386.044
3912.11366.751-1.62429.30923.39853.55720.10020.17390.04070.15470.0112-0.12180.0648-0.0891-0.11150.0811-0.0192-0.01170.10480.02970.053526.79115.0677.492
403.4879-2.2374-4.61175.9119-3.703416.13770.07410.0013-0.10480.3411-0.17920.1095-0.79190.19690.10510.15770.0138-0.04610.11020.00960.053626.97422.46981.603
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 10
2X-RAY DIFFRACTION2A11 - 15
3X-RAY DIFFRACTION3A16 - 20
4X-RAY DIFFRACTION4A21 - 29
5X-RAY DIFFRACTION5A30 - 34
6X-RAY DIFFRACTION6A35 - 41
7X-RAY DIFFRACTION7A42 - 48
8X-RAY DIFFRACTION8A49 - 57
9X-RAY DIFFRACTION9A58 - 64
10X-RAY DIFFRACTION10A65 - 70
11X-RAY DIFFRACTION11A71 - 83
12X-RAY DIFFRACTION12A84 - 89
13X-RAY DIFFRACTION13A90 - 95
14X-RAY DIFFRACTION14A96 - 103
15X-RAY DIFFRACTION15A104 - 108
16X-RAY DIFFRACTION16A109 - 114
17X-RAY DIFFRACTION17A115 - 119
18X-RAY DIFFRACTION18A120 - 127
19X-RAY DIFFRACTION19A128 - 133
20X-RAY DIFFRACTION20A134 - 139
21X-RAY DIFFRACTION21B5 - 13
22X-RAY DIFFRACTION22B14 - 19
23X-RAY DIFFRACTION23B20 - 26
24X-RAY DIFFRACTION24B27 - 32
25X-RAY DIFFRACTION25B33 - 38
26X-RAY DIFFRACTION26B39 - 44
27X-RAY DIFFRACTION27B45 - 57
28X-RAY DIFFRACTION28B58 - 64
29X-RAY DIFFRACTION29B65 - 70
30X-RAY DIFFRACTION30B71 - 76
31X-RAY DIFFRACTION31B77 - 81
32X-RAY DIFFRACTION32B82 - 87
33X-RAY DIFFRACTION33B88 - 93
34X-RAY DIFFRACTION34B94 - 98
35X-RAY DIFFRACTION35B99 - 106
36X-RAY DIFFRACTION36B107 - 114
37X-RAY DIFFRACTION37B115 - 119
38X-RAY DIFFRACTION38B120 - 128
39X-RAY DIFFRACTION39B129 - 134
40X-RAY DIFFRACTION40B135 - 139

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