[English] 日本語
Yorodumi
- PDB-4whj: Myxovirus Resistance Protein 2 (MxB) -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more