[English] 日本語
Yorodumi
- PDB-1iri: Crystal structure of human autocrine motility factor complexed wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1iri
TitleCrystal structure of human autocrine motility factor complexed with an inhibitor
Componentsautocrine motility factor
KeywordsISOMERASE / cytokine
Function / homology
Function and homology information


: / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / monosaccharide binding / fructose 6-phosphate metabolic process / Glycolysis ...: / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / monosaccharide binding / fructose 6-phosphate metabolic process / Glycolysis / erythrocyte homeostasis / ciliary membrane / positive regulation of immunoglobulin production / response to testosterone / humoral immune response / mesoderm formation / response to immobilization stress / response to cadmium ion / response to muscle stretch / positive regulation of endothelial cell migration / response to progesterone / cytokine activity / gluconeogenesis / TP53 Regulates Metabolic Genes / glycolytic process / growth factor activity / glucose homeostasis / response to estradiol / secretory granule lumen / in utero embryonic development / negative regulation of neuron apoptotic process / ficolin-1-rich granule lumen / carbohydrate metabolic process / learning or memory / ubiquitin protein ligase binding / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / cytosol
Similarity search - Function
Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. ...Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ERYTHOSE-4-PHOSPHATE / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsTanaka, N. / Haga, A. / Uemura, H. / Akiyama, H. / Funasaka, T. / Nagase, H. / Raz, A. / Nakamura, K.T.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Inhibition mechanism of cytokine activity of human autocrine motility factor examined by crystal structure analyses and site-directed mutagenesis studies.
Authors: Tanaka, N. / Haga, A. / Uemura, H. / Akiyama, H. / Funasaka, T. / Nagase, H. / Raz, A. / Nakamura, K.T.
History
DepositionOct 8, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: autocrine motility factor
B: autocrine motility factor
C: autocrine motility factor
D: autocrine motility factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,7208
Polymers252,9204
Non-polymers8004
Water7,782432
1
A: autocrine motility factor
B: autocrine motility factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,8604
Polymers126,4602
Non-polymers4002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13900 Å2
ΔGint-78 kcal/mol
Surface area36730 Å2
MethodPISA
2
C: autocrine motility factor
D: autocrine motility factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,8604
Polymers126,4602
Non-polymers4002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-77 kcal/mol
Surface area36820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.651, 107.771, 270.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer. Two dimers exist in an asymmetric unit.

-
Components

#1: Protein
autocrine motility factor / glucose phosphate isomerase


Mass: 63229.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P / Production host: Escherichia coli (E. coli) / References: UniProt: P06744, glucose-6-phosphate isomerase
#2: Sugar
ChemComp-E4P / ERYTHOSE-4-PHOSPHATE


Type: saccharide / Mass: 200.084 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H9O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: cacodylate, sodium acetate, PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 47 %
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 mg/mlprotein1drop
20.05 M1dropNaCl
320 %(v/v)glycerol1drop
40.02 MTris1droppH7.5
528 %(w/v)PEG80001reservoir
60.2 Msodium acetate1reservoir
720 %(v/v)glycerol1reservoir
80.1 Msodium cacodylate1reservoirpH6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. all: 92870 / Num. obs: 92870 / % possible obs: 100 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.3
Reflection shellResolution: 2→2.53 Å / Redundancy: 6 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 25 Å / % possible obs: 100 % / Num. measured all: 550782 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 2.4 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.357

-
Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1JIQ

1jiq


Resolution: 2.4→25 Å
RfactorNum. reflection% reflection
Rfree0.241 4595 5.205 %
Rwork0.193 --
obs-88274 -
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17780 0 52 432 18264
Refine LS restraintsType: p_bond_d / Dev ideal: 0.013
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor obs: 0.193 / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.528
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.46 Å

+
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