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- PDB-4p4s: GMPPCP-bound stalkless-MxA -

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Basic information

Entry
Database: PDB / ID: 4p4s
TitleGMPPCP-bound stalkless-MxA
Components(Interferon-induced GTP-binding protein Mx1) x 2
KeywordsANTIVIRAL PROTEIN/HYDROLASE / GTPase / dynamin-related protein / antiviral / SIGNALING 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 / receptor internalization / ISG15 antiviral mechanism / response to virus / 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 / receptor internalization / ISG15 antiviral mechanism / response to virus / Interferon alpha/beta signaling / presynapse / nuclear membrane / microtubule binding / 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 / cytoplasm / cytosol
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
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Interferon-induced GTP-binding protein Mx1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 1.1Jul 20, 2016Group: Data collection
Revision 1.2Sep 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_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim
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_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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


Theoretical massNumber of molelcules
Total (without water)72,2316
Polymers71,1402
Non-polymers1,0914
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-43 kcal/mol
Surface area28850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.290, 66.760, 170.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Refine code: _

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1UNKUNKUNKUNKAA52 - 3591 - 302
2LEULEULYSLYSBB59 - 35917 - 317

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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: 32600.695 Da / Num. of mol.: 1 / Fragment: UNP residues 43-361, 636-662 / Mutation: C42S,C322S,C336S, T636G, S637D, D638P, R640A
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: 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: 38539.195 Da / Num. of mol.: 1 / Fragment: UNP residues 43-361, 636-662 / Mutation: C42S,C322S,C336S, T636G, S637D, D638P, R640A
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
#3: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Sequence detailsAuthor states that chain A and chain B are from the same protein construct. However, in chain A ...Author states that chain A and chain B are from the same protein construct. However, in chain A where they were unable to determine the sequence register for some N-terminal and C-terminal residues, these residues were modeled as UNKs. The C-terminal UNKs are likely represent UNP residues 343-360.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 23-27% PEG 4000, 0.2 M EPPS/KOH pH 7.9, 0.5M glycerol

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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: Oct 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 3.3→49.26 Å / Num. obs: 10950 / % possible obs: 99.9 % / Redundancy: 9 % / Net I/σ(I): 19
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 2.9 / % 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: 3.3→49.26 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.85 / SU B: 85.04 / SU ML: 0.686 / Cross valid method: THROUGHOUT / ESU R Free: 0.71 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30531 529 4.9 %RANDOM
Rwork0.2306 ---
obs0.23441 10362 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.846 Å2
Baniso -1Baniso -2Baniso -3
1-8.89 Å20 Å20 Å2
2---4.18 Å20 Å2
3----4.7 Å2
Refinement stepCycle: 1 / Resolution: 3.3→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4879 0 66 17 4962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195018
X-RAY DIFFRACTIONr_bond_other_d0.0040.025013
X-RAY DIFFRACTIONr_angle_refined_deg1.6052.0086785
X-RAY DIFFRACTIONr_angle_other_deg1.022311566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2875636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98625.354198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.06515930
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3161529
X-RAY DIFFRACTIONr_chiral_restr0.0790.2812
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215528
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02979
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_it3.0534.4982553
X-RAY DIFFRACTIONr_mcbond_other3.0544.4982552
X-RAY DIFFRACTIONr_mcangle_it4.9456.7453186
X-RAY DIFFRACTIONr_mcangle_other4.9446.7453187
X-RAY DIFFRACTIONr_scbond_it3.3534.7392465
X-RAY DIFFRACTIONr_scbond_other3.3534.7392465
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.456.9973597
X-RAY DIFFRACTIONr_long_range_B_refined9.74942.92821023
X-RAY DIFFRACTIONr_long_range_B_other9.74842.92821024
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17744 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.3→3.396 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.361 31 -
Rwork0.338 816 -
obs--96.58 %
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)
10.22780.163-1.74770.1411-1.2613.6054-0.14780.04830.0081-0.06080.02380.12960.9006-0.32980.12390.54350.133-0.05980.4352-0.03970.91615.76432.4262-27.1188
23.8557-0.6621-1.1841.72170.11118.06870.2940.3106-0.027-0.4425-0.2811-0.0256-0.6101-0.4921-0.01280.16010.1183-0.01510.1058-0.05440.125823.6725-0.6807-6.6876
34.92190.19391.44510.02530.08890.53420.0440.18950.74040.0768-0.06330.00820.2056-0.00150.01930.61160.0475-0.14060.69670.03050.686728.090514.1495-40.2302
49.5452-4.8085-5.41053.5594.97838.4463-0.09-0.0382-0.1249-0.2612-0.3190.4126-0.0615-0.24630.4090.52470.1645-0.26910.5197-0.11090.46639.317510.351545.9479
52.3542-0.93070.39394.05180.92715.03770.0015-0.48450.26810.6902-0.1021-0.0389-0.679-0.05780.10050.3056-0.1087-0.01010.2859-0.05820.144427.62166.642426.1886
69.44832.0698-6.50874.67211.050712.3817-0.44850.0067-0.9975-0.43950.3670.0341.01271.02690.08150.24410.0586-0.2160.44220.07370.514643.70529.929158.4894
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 70
2X-RAY DIFFRACTION2A71 - 340
3X-RAY DIFFRACTION3A341 - 360
4X-RAY DIFFRACTION4B51 - 70
5X-RAY DIFFRACTION5B71 - 340
6X-RAY DIFFRACTION6B341 - 360

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