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- PDB-4whj: Myxovirus Resistance Protein 2 (MxB) -

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Basic information

Entry
Database: PDB / ID: 4whj
TitleMyxovirus Resistance Protein 2 (MxB)
ComponentsInterferon-induced GTP-binding protein Mx2
KeywordsANTIVIRAL PROTEIN / HYDROLASE / Dimer / 4-helix bundle / GTPase
Function / homology
Function and homology information


response to interferon-alpha / regulation of nucleocytoplasmic transport / mRNA transport / nuclear pore / response to virus / ISG15 antiviral mechanism / defense response / Interferon alpha/beta signaling / protein transport / microtubule binding ...response to interferon-alpha / regulation of nucleocytoplasmic transport / mRNA transport / nuclear pore / response to virus / ISG15 antiviral mechanism / defense response / Interferon alpha/beta signaling / protein transport / microtubule binding / defense response to virus / microtubule / regulation of cell cycle / innate immune response / GTPase activity / GTP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain ...Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Interferon-induced GTP-binding protein Mx2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsXiong, Y. / Fribourgh, J.L. / Nguyen, H.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Collaboration Development Pilot Program award from the Pittsburgh Center for HIV Protein Interactions United States
CitationJournal: Cell Host Microbe / Year: 2014
Title: Structural Insight into HIV-1 Restriction by MxB.
Authors: Fribourgh, J.L. / Nguyen, H.C. / Matreyek, K.A. / Alvarez, F.J. / Summers, B.J. / Dewdney, T.G. / Aiken, C. / Zhang, P. / Engelman, A. / Xiong, Y.
History
DepositionSep 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.name
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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: Interferon-induced GTP-binding protein Mx2
B: Interferon-induced GTP-binding protein Mx2


Theoretical massNumber of molelcules
Total (without water)147,7782
Polymers147,7782
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-16 kcal/mol
Surface area60230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.185, 80.782, 183.666
Angle α, β, γ (deg.)90.000, 95.730, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 93 - 711 / Label seq-ID: 24 - 642

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Interferon-induced GTP-binding protein Mx2 / Interferon-regulated resistance GTP-binding protein MxB / Myxovirus resistance protein 2 / p78-related protein


Mass: 73888.781 Da / Num. of mol.: 2 / Fragment: UNP residues 84-715 / Mutation: YRGK487-490AAAA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MX2 / Production host: Escherichia coli (E. coli) / References: UniProt: P20592

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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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 298 K / Method: microbatch
Details: 0.1 M MES, 5% PEG4000, 10% 2-Propanol, 0.05 M magnesium chloride
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 24322 / % possible obs: 94.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 102.78 Å2 / Rmerge(I) obs: 0.089 / Χ2: 1.134 / Net I/av σ(I): 15.627 / Net I/σ(I): 8.9 / Num. measured all: 132310
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
3.2-3.265.111261.08889.9
3.26-3.315.411621.11588
3.31-3.385.411131.10289.5
3.38-3.455.311411.08890.9
3.45-3.525.311821.12191.60.815
3.52-3.65.311671.11792.50.691
3.6-3.695.311921.16993.10.478
3.69-3.795.212191.11594.60.386
3.79-3.915.311661.12593.90.329
3.91-4.035.212301.152940.282
4.03-4.185.212171.13195.20.227
4.18-4.345.311981.17595.60.18
4.34-4.545.312351.15495.50.131
4.54-4.785.312501.0997.20.108
4.78-5.085.312521.17298.20.102
5.08-5.475.612761.13599.10.105
5.47-6.025.813021.22499.90.113
6.02-6.89612871.2631000.089
6.89-8.67612971.00799.50.047
8.67-50613101.108970.04

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SZR

3szr


Resolution: 3.2→43.929 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 0.94 / Phase error: 37.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2993 2294 5.05 %
Rwork0.2649 43163 -
obs0.2667 45457 90.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 439.09 Å2 / Biso mean: 162.6098 Å2 / Biso min: 37.34 Å2
Refinement stepCycle: final / Resolution: 3.2→43.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9082 0 0 0 9082
Num. residues----1130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029218
X-RAY DIFFRACTIONf_angle_d0.6312418
X-RAY DIFFRACTIONf_chiral_restr0.0231430
X-RAY DIFFRACTIONf_plane_restr0.0031594
X-RAY DIFFRACTIONf_dihedral_angle_d9.6613572
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5474X-RAY DIFFRACTION9.455TORSIONAL
12B5474X-RAY DIFFRACTION9.455TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.26680.45161020.41622187228972
3.2668-3.34280.45911240.39042586271084
3.3428-3.42630.45861480.38372484263287
3.4263-3.5190.47561270.3582646277387
3.519-3.62250.39861330.33122588272187
3.6225-3.73930.35141460.32682609275588
3.7393-3.87290.32251430.30892687283089
3.8729-4.02780.30841370.2962648278590
4.0278-4.2110.30551380.27762705284390
4.211-4.43280.3071560.24822733288991
4.4328-4.71030.28221670.23562730289793
4.7103-5.07350.26241570.23022805296294
5.0735-5.58310.28221490.25952904305398
5.5831-6.38890.34221550.29942960311599
6.3889-8.04130.27431550.28022988314399
8.0413-43.93360.24031570.1982903306097
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)
16.3417-1.85421.33197.7418-2.03277.81430.28460.37570.39440.7269-0.6213-0.08-0.6040.85740.31410.8832-0.0157-0.01630.4844-0.07380.6317-26.667-16.603515.0188
29.0326-0.02073.25887.0564-0.08796.8455-0.287-0.09671.0469-0.36240.15090.4698-1.5173-1.1424-0.12252.26630.1913-0.18992.83430.47541.512-162.52869.8838-88.8445
34.0858-3.98185.32743.9765-3.97855.51420.67950.8181-1.0663-0.88740.0790.7581.09350.3273-1.00931.37180.4154-0.17230.9884-0.02481.0556-36.3571-19.3897-8.6416
40.38120.78820.19212.50631.52121.06250.45370.6062-0.9253-1.14551.371-0.41150.0663-0.5465-1.29192.0294-0.7863-0.56723.44631.08641.5314-153.8892-2.2561-67.8131
58.44372.7171.82022.29670.7273.29410.0275-0.4941-0.94970.32790.2422-0.14770.5055-0.446-0.27170.81180.31160.050.63030.12030.6414-87.4793-24.6963-32.2833
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 93:368)A93 - 368
2X-RAY DIFFRACTION2chain 'B' and (resseq 93:368)B93 - 368
3X-RAY DIFFRACTION3chain 'A' and ((resseq 369:408) or (resseq 681:711))A0
4X-RAY DIFFRACTION4chain 'B' and ((resseq 369:408) or (resseq 681:711))B0
5X-RAY DIFFRACTION5chain 'A' and (resseq 409:680)A409 - 680

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