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- PDB-3szr: Crystal structure of modified nucleotide-free human MxA -

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Basic information

Entry
Database: PDB / ID: 3szr
TitleCrystal structure of modified nucleotide-free human MxA
ComponentsInterferon-induced GTP-binding protein Mx1
KeywordsPROTEIN BINDING / Interferon-induced antiviral GTPase / membrane associated
Function / homology
Function and homology information


interleukin-27-mediated signaling pathway / response to type I interferon / negative regulation of viral genome replication / antiviral innate immune response / response to virus / ISG15 antiviral mechanism / defense response / Interferon alpha/beta signaling / microtubule binding / nuclear membrane ...interleukin-27-mediated signaling pathway / response to type I interferon / negative regulation of viral genome replication / antiviral innate immune response / response to virus / ISG15 antiviral mechanism / defense response / Interferon alpha/beta signaling / microtubule binding / nuclear membrane / microtubule / defense response to virus / innate immune response / GTPase activity / apoptotic process / endoplasmic reticulum membrane / GTP binding / perinuclear region of cytoplasm / signal transduction / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Dynamin, middle 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, middle 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Interferon-induced GTP-binding protein Mx1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsGao, S. / Daumke, O.
CitationJournal: Immunity / Year: 2011
Title: Structure of myxovirus resistance protein a reveals intra- and intermolecular domain interactions required for the antiviral function.
Authors: Gao, S. / von der Malsburg, A. / Dick, A. / Faelber, K. / Schroder, G.F. / Haller, O. / Kochs, G. / Daumke, O.
History
DepositionJul 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon-induced GTP-binding protein Mx1


Theoretical massNumber of molelcules
Total (without water)69,1771
Polymers69,1771
Non-polymers00
Water00
1
A: Interferon-induced GTP-binding protein Mx1

A: Interferon-induced GTP-binding protein Mx1


Theoretical massNumber of molelcules
Total (without water)138,3542
Polymers138,3542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_553-x,y,-z-21
MethodPISA
2
A: Interferon-induced GTP-binding protein Mx1

A: Interferon-induced GTP-binding protein Mx1


Theoretical massNumber of molelcules
Total (without water)138,3542
Polymers138,3542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
MethodPISA
Unit cell
Length a, b, c (Å)156.820, 134.080, 58.100
Angle α, β, γ (deg.)90.00, 106.34, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE BIOLOGICALLY RELEVANT ASSEMBLY IS LINEAR OLIGOMER CREATED BY CRYSTALLOGRAPHIC SYMMETRY ALONG THE C-AXIS OF THE CRYSTAL.THERE ARE TWO INTERFACES INVOLVED IN THE BUILDING OF THE OLIGOMER WHICH IS SEEN IN THE ASSEMBLIES GIVEN IN REMARK 350.

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Components

#1: Protein Interferon-induced GTP-binding protein Mx1 / Interferon-induced protein p78 / IFI-78K / Interferon-regulated resistance GTP-binding protein MxA ...Interferon-induced protein p78 / IFI-78K / Interferon-regulated resistance GTP-binding protein MxA / Myxoma resistance protein 1 / Myxovirus resistance protein 1 / Interferon-induced GTP-binding protein Mx1 / N-terminally processed


Mass: 69176.812 Da / Num. of mol.: 1 / Fragment: UNP residues 33-662 / Mutation: Y440A,R441A,G442A,R443A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MX1 / Plasmid: pSKB-LNB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Rosetta / References: UniProt: P20591

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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: 4.24 Å3/Da / Density % sol: 70.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 7% PEG3350, 100 mM HEPES (pH 7.6), 80 mM NaCl, 2.5% 2-methyl-2,4-pentandiol (MPD), 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 30, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.5→35 Å / Num. all: 14649 / Num. obs: 10349 / % possible obs: 70.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.06 % / Rsym value: 0.097 / Net I/σ(I): 9.33
Reflection shellResolution: 3.5→4.15 Å / Redundancy: 3.03 % / Mean I/σ(I) obs: 2.25 / Num. unique all: 1699 / Rsym value: 0.595 / % possible all: 29

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Processing

Software
NameVersionClassification
REFMAC5.6.0086refinement
PHASERphasing
CNS1.3refinement
iMOSFLMdata reduction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2AKA chain B and PDB entry 3LJB chain B

2aka

3ljb


Resolution: 3.5→34.98 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.838 / SU B: 85.978 / SU ML: 0.584 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R Free: 0.799 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2954 520 5 %RANDOM
Rwork0.2616 ---
all0.26324 14578 --
obs0.26324 9831 71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 140.837 Å2
Baniso -1Baniso -2Baniso -3
1--2.29 Å20 Å2-1.4 Å2
2---0.49 Å20 Å2
3---1.99 Å2
Refinement stepCycle: LAST / Resolution: 3.5→34.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4507 0 0 0 4507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224572
X-RAY DIFFRACTIONr_bond_other_d0.0030.023184
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.9726148
X-RAY DIFFRACTIONr_angle_other_deg1.17737800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5065552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34125.067223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24415897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9781529
X-RAY DIFFRACTIONr_chiral_restr0.0780.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024968
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02858
LS refinement shellResolution: 3.502→3.592 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 5 -
Rwork0.501 51 -
obs--5.23 %
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)
14.6063-0.94851.56115.60961.55118.719-0.3805-0.4068-1.03680.23310.3862-0.57980.91850.4325-0.00571.05280.9510.08461.10550.26220.6738.918-21.47430.724
26.6127-1.7997-0.70087.8728-4.72427.019-0.3022-0.3413-0.50390.24290.55750.33070.91521.1491-0.25530.55180.61680.01840.8321-0.09370.157823.213-3.98112.535
33.92651.4794-2.86316.2095-7.469814.4673-0.2304-0.48630.5749-0.14450.3086-0.0810.28910.753-0.07820.2480.03310.06460.3448-0.21970.362624.48412.613-45.562
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A64 - 340
2X-RAY DIFFRACTION2A1 - 63
3X-RAY DIFFRACTION2A341 - 365
4X-RAY DIFFRACTION2A638 - 662
5X-RAY DIFFRACTION3A366 - 637

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