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- PDB-4p4t: GDP-bound stalkless-MxA -

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Basic information

Entry
Database: PDB / ID: 4p4t
TitleGDP-bound stalkless-MxA
ComponentsInterferon-induced GTP-binding protein Mx1
KeywordsANTIVIRAL PROTEIN/HYDROLASE / GTPase / dynamin-related protein / antiviral / mechano-enzyme / HYDROLASE / GTP-BINDING PROTEIN / ANTIVIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


synaptic vesicle budding from presynaptic endocytic zone membrane / interleukin-27-mediated signaling pathway / response to type I interferon / negative regulation of viral genome replication / antiviral innate immune response / defense response / response to virus / receptor internalization / ISG15 antiviral mechanism / Interferon alpha/beta signaling ...synaptic vesicle budding from presynaptic endocytic zone membrane / interleukin-27-mediated signaling pathway / response to type I interferon / negative regulation of viral genome replication / antiviral innate immune response / defense response / response to virus / receptor internalization / ISG15 antiviral mechanism / Interferon alpha/beta signaling / presynapse / microtubule binding / nuclear membrane / defense response to virus / microtubule / innate immune response / GTPase activity / apoptotic process / synapse / endoplasmic reticulum membrane / GTP binding / perinuclear region of cytoplasm / signal transduction / identical protein binding / nucleus / plasma membrane / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Interferon-induced GTP-binding protein Mx1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRennie, M.L. / McKelvie, S.A. / Bulloch, E.M. / Kingston, R.L.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Maurice Wilkins Centre, Auckland Medical Research Foundation New Zealand
CitationJournal: Structure / Year: 2014
Title: Transient Dimerization of Human MxA Promotes GTP Hydrolysis, Resulting in a Mechanical Power Stroke.
Authors: Rennie, M.L. / McKelvie, S.A. / Bulloch, E.M. / Kingston, R.L.
History
DepositionMar 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Structure summary
Revision 1.2Jul 20, 2016Group: Data collection
Revision 1.3Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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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 Mx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7605
Polymers40,0291
Non-polymers7314
Water1,56787
1
A: Interferon-induced GTP-binding protein Mx1
hetero molecules

A: Interferon-induced GTP-binding protein Mx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,52010
Polymers80,0572
Non-polymers1,4638
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area4970 Å2
ΔGint-68 kcal/mol
Surface area32030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.020, 77.590, 212.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-819-

HOH

21A-821-

HOH

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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


Mass: 40028.719 Da / Num. of mol.: 1 / Fragment: UNP residues 37-366 and 637-662 via LINKER GSGS / Mutation: C42S, C322S, C336S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MX1 / Production host: Escherichia coli (E. coli) / References: UniProt: P20591
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsChimera protein is stalkless-MxA made of UNP residues 37-366 and 637-662 via LINKER GSGS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.1 / Details: 2.0-2.5M Ammonium sulfate, 0.2M AMPSO/KOH pH 9.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.3→32.05 Å / Num. obs: 17794 / % possible obs: 99.9 % / Redundancy: 7.1 % / Net I/σ(I): 28.9
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P4U

4p4u


Resolution: 2.3→32.05 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 18.641 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25378 890 5 %RANDOM
Rwork0.2163 ---
obs0.21831 16884 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.592 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2---0.46 Å20 Å2
3----0.92 Å2
Refinement stepCycle: 1 / Resolution: 2.3→32.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2641 0 43 87 2771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192733
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1282.0133698
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9015337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05824.833120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68115529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1871521
X-RAY DIFFRACTIONr_chiral_restr0.0710.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211971
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0162.8181342
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7824.2141672
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.23.0671389
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.74424.1134146
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.342 Å / Total num. of bins used: 28
RfactorNum. reflection% reflection
Rfree0.333 45 -
Rwork0.304 877 -
obs--99.25 %
Refinement TLS params.Method: refined / Origin x: 7.0046 Å / Origin y: -0.3062 Å / Origin z: 80.0314 Å
111213212223313233
T0.1418 Å2-0.1079 Å2-0.0007 Å2-0.1466 Å20.0263 Å2--0.0577 Å2
L1.4196 °2-0.548 °2-0.4959 °2-4.2695 °21.6372 °2--2.428 °2
S0.0065 Å °-0.0813 Å °-0.079 Å °-0.2993 Å °0.1313 Å °-0.3941 Å °0.0659 Å °0.2074 Å °-0.1379 Å °

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