[English] 日本語
Yorodumi
- PDB-2d58: Human microglia-specific protein Iba1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2d58
TitleHuman microglia-specific protein Iba1
ComponentsAllograft inflammatory factor 1
KeywordsMETAL BINDING PROTEIN / EF-hand
Function / homology
Function and homology information


negative regulation of smooth muscle cell chemotaxis / positive regulation of smooth muscle cell chemotaxis / parallel actin filament bundle assembly / positive regulation of fibroblast growth factor production / actin crosslink formation / ruffle assembly / positive regulation of chemotaxis / positive regulation of mononuclear cell migration / positive regulation of monocyte chemotaxis / phagocytosis, engulfment ...negative regulation of smooth muscle cell chemotaxis / positive regulation of smooth muscle cell chemotaxis / parallel actin filament bundle assembly / positive regulation of fibroblast growth factor production / actin crosslink formation / ruffle assembly / positive regulation of chemotaxis / positive regulation of mononuclear cell migration / positive regulation of monocyte chemotaxis / phagocytosis, engulfment / Rac protein signal transduction / glial cell projection / phagocytic cup / actin filament bundle assembly / positive regulation of T cell migration / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of T cell proliferation / positive regulation of chemokine production / ruffle / actin filament polymerization / actin filament / negative regulation of smooth muscle cell proliferation / positive regulation of smooth muscle cell proliferation / microglial cell activation / ruffle membrane / cellular response to type II interferon / positive regulation of interleukin-6 production / actin filament binding / lamellipodium / cellular response to oxidative stress / regulation of gene expression / positive regulation of cell migration / inflammatory response / calcium ion binding / positive regulation of cell population proliferation / perinuclear region of cytoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Allograft inflammatory factor 1 / : / Allograft inflammatory factor 1 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
NICKEL (II) ION / Allograft inflammatory factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKamitori, S.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: X-ray Structures of the Microglia/Macrophage-specific Protein Iba1 from Human and Mouse Demonstrate Novel Molecular Conformation Change Induced by Calcium binding
Authors: Yamada, M. / Ohsawa, K. / Imai, Y. / Kohsaka, S. / Kamitori, S.
History
DepositionOct 31, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Allograft inflammatory factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3972
Polymers12,3381
Non-polymers591
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.748, 36.617, 44.024
Angle α, β, γ (deg.)90.00, 99.71, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Allograft inflammatory factor 1 / / AIF-1 / Ionized calcium-binding adapter molecule 1 / G1 protein


Mass: 12338.285 Da / Num. of mol.: 1 / Fragment: residues 17-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P55008
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.66 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 7.3
Details: 20% (w/v) polyethylene glycol (PEG) 4000, 10% (w/v) 2-propanol, 0.01M NiCl2 in 100mM of Tris-HCl (pH 7.3), VAPOR DIFFUSION, temperature 300K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2004
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→31.24 Å / Num. all: 7462 / Num. obs: 7462 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.76
Reflection shellResolution: 1.9→2.02 Å / % possible all: 90.1

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→31.24 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 116478.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 798 10.7 %RANDOM
Rwork0.195 ---
obs0.195 7462 97.4 %-
all-7462 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.6003 Å2 / ksol: 0.350076 e/Å3
Displacement parametersBiso mean: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å22.66 Å2
2---2.3 Å20 Å2
3---1.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.9→31.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms861 0 1 107 969
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.811.5
X-RAY DIFFRACTIONc_mcangle_it2.712
X-RAY DIFFRACTIONc_scbond_it2.952
X-RAY DIFFRACTIONc_scangle_it4.262.5
LS refinement shellResolution: 1.9→2.02 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.21 1142 -
obs--90.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4water_rep.param

+
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