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- PDB-3m8a: Crystal Structure of Swine Flu Virus NS1 N-Terminal RNA Binding D... -

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Basic information

Entry
Database: PDB / ID: 3m8a
TitleCrystal Structure of Swine Flu Virus NS1 N-Terminal RNA Binding Domain from H1N1 Influenza A/California/07/2009
ComponentsNonstructural protein 1
KeywordsVIRAL PROTEIN / NS1 / N-terminal RNA binding Domain / Influenza A virus / H1N1 / Host cytoplasm / Host nucleus / Host-virus interaction / Interferon antiviral system evasion / RNA-binding / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / host cell nucleus / RNA binding
Similarity search - Function
Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / S15/NS1, RNA-binding / Helix Hairpins / S15/NS1, RNA-binding / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / MALONATE ION / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBrunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Swine Flu Virus NS1 N-Terminal RNA Binding Domain from H1N1 Influenza A/California/07/2009
Authors: Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nonstructural protein 1
B: Nonstructural protein 1
C: Nonstructural protein 1
D: Nonstructural protein 1
E: Nonstructural protein 1
F: Nonstructural protein 1
G: Nonstructural protein 1
H: Nonstructural protein 1
I: Nonstructural protein 1
J: Nonstructural protein 1
K: Nonstructural protein 1
L: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,78626
Polymers103,84612
Non-polymers94014
Water17,655980
1
A: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7132
Polymers8,6541
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7562
Polymers8,6541
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7793
Polymers8,6541
Non-polymers1252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7562
Polymers8,6541
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7132
Polymers8,6541
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7132
Polymers8,6541
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7562
Polymers8,6541
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7132
Polymers8,6541
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6772
Polymers8,6541
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7793
Polymers8,6541
Non-polymers1252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)8,6541
Polymers8,6541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7793
Polymers8,6541
Non-polymers1252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.847, 156.795, 73.523
Angle α, β, γ (deg.)90.00, 109.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nonstructural protein 1


Mass: 8653.802 Da / Num. of mol.: 12 / Fragment: N-terminal RNA Binding Domain (UNP residues 1-73)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/CALIFORNIA/07/2009(H1N1) / References: UniProt: C3W611
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 980 / 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: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Tacsimate 35%, ph 7, KCl 0.1M, MgCl2 0.1M, 0.3M NDSB211, TCEP 2mM, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 4, 2010 / Details: Be Lenes
RadiationMonochromator: Single Crystal Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 75867 / Num. obs: 75867 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 28.36 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 18.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 3.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
MrBUMPphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z0A

2z0a


Resolution: 2.1→29.25 Å / Cor.coef. Fo:Fc: 0.9429 / Cor.coef. Fo:Fc free: 0.9229 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 3809 5.04 %RANDOM
Rwork0.1703 ---
obs0.172 75521 --
Displacement parametersBiso mean: 31.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.539 Å20 Å2-1.7559 Å2
2--7.8192 Å20 Å2
3----7.2801 Å2
Refine analyzeLuzzati coordinate error obs: 0.216 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6935 0 62 980 7977
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017323HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.919862HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2712SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes209HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1074HARMONIC5
X-RAY DIFFRACTIONt_it7287HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2495 244 4.4 %
Rwork0.2084 5305 -
all0.2101 5549 -

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