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- PDB-3ljb: Structural basis of oligomerisation in the MxA stalk -

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Basic information

Entry
Database: PDB / ID: 3ljb
TitleStructural basis of oligomerisation in the MxA stalk
ComponentsInterferon-induced GTP-binding protein Mx1
KeywordsANTIVIRAL PROTEIN / FOUR-HELIX-BUNDLE / GTP-binding
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) / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Interferon-induced GTP-binding protein Mx1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGao, S. / Daumke, O.
CitationJournal: Nature / Year: 2010
Title: Structural basis of oligomerization in the stalk region of dynamin-like MxA.
Authors: Gao, S. / von der Malsburg, A. / Paeschke, S. / Behlke, J. / Haller, O. / Kochs, G. / Daumke, O.
History
DepositionJan 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,8192
Polymers64,8192
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-16 kcal/mol
Surface area23710 Å2
MethodPISA
2
A: Interferon-induced GTP-binding protein Mx1

B: Interferon-induced GTP-binding protein Mx1


Theoretical massNumber of molelcules
Total (without water)64,8192
Polymers64,8192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area1330 Å2
ΔGint-8 kcal/mol
Surface area24130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.147, 57.366, 57.491
Angle α, β, γ (deg.)65.82, 88.47, 74.87
Int Tables number1
Space group name H-MP1
DetailsAuthors state that the biological assembly is an oligomer generated from the dimer in the asymmetric unit by a translation along the y-axis.

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Components

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


Mass: 32409.748 Da / Num. of mol.: 2 / Fragment: Stalk region (UNP residues 366 to 636)
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 5% PEG3350, 100 mM MES (pH 6.8), 100 mM MgCl2 and 0.01 mM Hexammine cobalt (III) chloride, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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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: Aug 7, 2008
Details: Double crystal monochromator with 2 sets of mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. obs: 21393 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.52 % / Rmerge(I) obs: 0.103 / Rsym value: 0.062 / Net I/σ(I): 14.91
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.54 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 3.76 / Num. unique all: 1547 / Rsym value: 0.387 / % possible all: 96.7

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Initial model derived from a low-resolution SeMet data set

Resolution: 2.4→19.95 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 17.228 / SU ML: 0.182 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.406 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25681 1084 5.1 %RANDOM
Rwork0.19314 ---
all0.19634 20811 --
obs0.19634 20309 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.808 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.02 Å20.55 Å2
2---1.49 Å2-0.84 Å2
3---1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 0 102 3741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223751
X-RAY DIFFRACTIONr_bond_other_d0.0010.022612
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.9335037
X-RAY DIFFRACTIONr_angle_other_deg0.88136354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9215436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.09924.698215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93515745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6471524
X-RAY DIFFRACTIONr_chiral_restr0.0690.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02780
X-RAY DIFFRACTIONr_mcbond_it0.6571.52156
X-RAY DIFFRACTIONr_mcbond_other0.1041.5870
X-RAY DIFFRACTIONr_mcangle_it1.27423500
X-RAY DIFFRACTIONr_scbond_it1.66531595
X-RAY DIFFRACTIONr_scangle_it2.8034.51531
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 67 -
Rwork0.236 1454 -
obs--96.88 %
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)
10.3972-0.4027-0.03585.1744-1.97331.47380.08180.05490.14010.0395-0.0010.19160.0123-0.1399-0.08080.05180.00960.06670.245-0.02180.1169-17.564-13.4186.67
22.0662.44030.98355.14732.34672.074-0.10140.0970.0328-0.24490.0594-0.11010.02040.06630.04190.05830.02840.04710.202-0.02290.08765.695-1.002-2.492
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A365 - 633
2X-RAY DIFFRACTION2B367 - 637

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