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- PDB-7ldk: Structure of human respiratory syncytial virus nonstructural prot... -

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Basic information

Entry
Database: PDB / ID: 7ldk
TitleStructure of human respiratory syncytial virus nonstructural protein 2 (NS2)
ComponentsNon-structural protein 2
KeywordsVIRAL PROTEIN / nonstructural protein / interferon antagonist
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / 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 TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway
Similarity search - Function
Respiratory synctial virus non-structural protein NS2 / Respiratory synctial virus non-structural protein NS2
Similarity search - Domain/homology
D(-)-TARTARIC ACID / Non-structural protein 2
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsChatterjee, S. / Borek, D. / Otwinowski, Z. / Amarasinghe, G.K. / Leung, D.W.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI107056 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI40758 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI20943 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structural basis for IFN antagonism by human respiratory syncytial virus nonstructural protein 2.
Authors: Pei, J. / Wagner, N.D. / Zou, A.J. / Chatterjee, S. / Borek, D. / Cole, A.R. / Kim, P.J. / Basler, C.F. / Otwinowski, Z. / Gross, M.L. / Amarasinghe, G.K. / Leung, D.W.
History
DepositionJan 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Non-structural protein 2
A: Non-structural protein 2
C: Non-structural protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1529
Polymers44,5963
Non-polymers5576
Water1,04558
1
B: Non-structural protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0513
Polymers14,8651
Non-polymers1862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Non-structural protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2365
Polymers14,8651
Non-polymers3714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Non-structural protein 2


Theoretical massNumber of molelcules
Total (without water)14,8651
Polymers14,8651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.646, 157.646, 47.291
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13A
23C

NCS domain segments:

Component-ID: 0 / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERBA22 - 12323 - 124
21SERSERAB22 - 12323 - 124
12PROPROBA20 - 12321 - 124
22PROPROCC20 - 12321 - 124
13SERSERAB22 - 12323 - 124
23SERSERCC22 - 12323 - 124

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Non-structural protein 2 / NS2 / Non-structural protein 1B


Mass: 14865.252 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A / Strain: Long / Gene: 1B, NS2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86305
#2: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.84 Å3/Da / Density % sol: 67.97 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: 0.4 M potassium-sodium-tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 16685 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.033 / Rrim(I) all: 0.09 / Χ2: 0.908 / Net I/σ(I): 24.8
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 5.9 % / Rmerge(I) obs: 2.154 / Mean I/σ(I) obs: 0.82 / Num. unique obs: 740 / CC1/2: 0.432 / CC star: 0.777 / Rpim(I) all: 0.842 / Rrim(I) all: 2.154 / Χ2: 0.86 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
BUCCANEERmodel building
Cootmodel building
PARROTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house Se-Met-labeled NS2 model, solved by SAD phasing

Resolution: 2.82→45.55 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.888 / SU B: 27.617 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 0.649 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 695 4.9 %RANDOM
Rwork0.2118 ---
obs0.21394 13610 86.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.564 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 2.82→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2633 0 33 58 2724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132752
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172616
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.6683729
X-RAY DIFFRACTIONr_angle_other_deg1.2291.5766055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9045315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14721.493134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.92415500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2191514
X-RAY DIFFRACTIONr_chiral_restr0.0730.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022974
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02622
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_it1.0712.1581260
X-RAY DIFFRACTIONr_mcbond_other1.0692.1561259
X-RAY DIFFRACTIONr_mcangle_it1.9233.2251572
X-RAY DIFFRACTIONr_mcangle_other1.9233.2281573
X-RAY DIFFRACTIONr_scbond_it1.2032.3291492
X-RAY DIFFRACTIONr_scbond_other1.2032.3291492
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0963.4552156
X-RAY DIFFRACTIONr_long_range_B_refined4.75825.093053
X-RAY DIFFRACTIONr_long_range_B_other4.74625.0893052
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B31490.13
12A31490.13
21B32130.14
22C32130.14
31A31280.15
32C31280.15
LS refinement shellResolution: 2.82→2.89 Å
RfactorNum. reflection% reflection
Rfree0.35 9 -
Rwork0.265 172 -
obs--15.01 %
Refinement TLS params.

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

IDL11 (°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)
16.9675-2.6095-0.99155.77780.783.22950.0368-0.6687-0.08740.19410.33360.2766-0.195-0.401-0.37040.09580.0545-0.06140.17320.05060.201868.27457.52113.712
24.29490.37571.57495.7747-0.0744.77220.1161-0.524-0.3930.4112-0.0071-0.09580.2591-0.4521-0.1090.09720.09420.0210.35010.12740.217145.33358.047.978
310.33921.6092.00062.54690.21122.9614-0.32610.62951.1748-0.48330.18440.1883-0.84780.11930.14170.4018-0.03280.02380.3004-0.01840.318180.61176.6646.228
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B19 - 124
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1B401
4X-RAY DIFFRACTION2A22 - 124
5X-RAY DIFFRACTION2A302
6X-RAY DIFFRACTION3C20 - 124

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