[English] 日本語
Yorodumi
- PDB-4x0r: Crystal structure of human MxB stalk domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x0r
TitleCrystal structure of human MxB stalk domain
ComponentsInterferon-induced GTP-binding protein Mx2
KeywordsANTIVIRAL PROTEIN / myxovirus resistance protein 2 / anti-HIV dynamin-like protein / Stalk domain / dimer
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, 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 Mx2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.905 Å
AuthorsYu, X.-F. / Xie, W.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Structural insight into the assembly of human anti-HIV dynamin-like protein MxB/Mx2.
Authors: Xu, B. / Kong, J. / Wang, X. / Wei, W. / Xie, W. / Yu, X.F.
History
DepositionNov 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Interferon-induced GTP-binding protein Mx2
A: Interferon-induced GTP-binding protein Mx2


Theoretical massNumber of molelcules
Total (without water)56,4372
Polymers56,4372
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-16 kcal/mol
Surface area23550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.612, 154.612, 103.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Interferon-induced GTP-binding protein Mx2 / Interferon-regulated resistance GTP-binding protein MxB / Myxovirus resistance protein 2 / p78-related protein


Mass: 28218.484 Da / Num. of mol.: 2 / Fragment: MxB Stalk domain / Mutation: Y75A, R76A, G77A, K78A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MX2 / Production host: Escherichia coli (E. coli) / Strain (production host): XL10 Gold / References: UniProt: P20592

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.32 Å3/Da / Density % sol: 80.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1mol/L sodium acetate at pH 4.5 with 6% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.905→38.65 Å / Num. obs: 31652 / % possible obs: 99.77 % / Redundancy: 16.2 % / Net I/σ(I): 18.74

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LJB

3ljb


Resolution: 2.905→38.65 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2411 1596 5.05 %
Rwork0.2184 --
obs0.2195 31629 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.905→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3491 0 0 0 3491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093547
X-RAY DIFFRACTIONf_angle_d1.254751
X-RAY DIFFRACTIONf_dihedral_angle_d16.0591360
X-RAY DIFFRACTIONf_chiral_restr0.075525
X-RAY DIFFRACTIONf_plane_restr0.006604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9051-2.99880.36491270.31522638X-RAY DIFFRACTION97
2.9988-3.1060.33491300.30472717X-RAY DIFFRACTION100
3.106-3.23030.28861430.28962725X-RAY DIFFRACTION100
3.2303-3.37720.30911390.2512720X-RAY DIFFRACTION100
3.3772-3.55510.28931720.22932666X-RAY DIFFRACTION100
3.5551-3.77770.24661520.22342717X-RAY DIFFRACTION100
3.7777-4.06910.2171360.19842741X-RAY DIFFRACTION100
4.0691-4.4780.19151510.17692723X-RAY DIFFRACTION100
4.478-5.12470.17631320.17022779X-RAY DIFFRACTION100
5.1247-6.45170.29051540.25992763X-RAY DIFFRACTION100
6.4517-38.65640.22191600.20952844X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 167.3732 Å / Origin y: 73.7939 Å / Origin z: 120.5859 Å
111213212223313233
T0.4971 Å20.0398 Å20.0083 Å2-0.7795 Å2-0.0953 Å2--0.5078 Å2
L2.2322 °20.4019 °20.9532 °2-1.7193 °20.5835 °2--2.1461 °2
S0.2574 Å °-0.1163 Å °0.0111 Å °-0.0237 Å °0.0654 Å °-0.0669 Å °0.2672 Å °0.2945 Å °-0.2488 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB3 - 239
2X-RAY DIFFRACTION1allA3 - 239

+
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://pdbjlc1.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