[English] 日本語
Yorodumi
- PDB-2x69: X-ray Structure of Macrophage Inflammatory Protein-1 alpha polymer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x69
TitleX-ray Structure of Macrophage Inflammatory Protein-1 alpha polymer
ComponentsC-C MOTIF CHEMOKINE 3
KeywordsIMMUNE SYSTEM / INFLAMMATORY RESPONSE / CYTOKINE / CHEMOTAXIS
Function / homology
Function and homology information


granulocyte chemotaxis / lymphocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / signaling / regulation of behavior / astrocyte cell migration / CCR5 chemokine receptor binding / eosinophil degranulation ...granulocyte chemotaxis / lymphocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / signaling / regulation of behavior / astrocyte cell migration / CCR5 chemokine receptor binding / eosinophil degranulation / regulation of sensory perception of pain / negative regulation of bone mineralization / CCR chemokine receptor binding / positive regulation of microglial cell activation / cell activation / T cell chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / response to cholesterol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / chemokine activity / phospholipase activator activity / macrophage chemotaxis / positive regulation of calcium ion import / chemoattractant activity / exocytosis / negative regulation of osteoclast differentiation / monocyte chemotaxis / Interleukin-10 signaling / cellular response to interleukin-1 / negative regulation by host of viral transcription / cytoskeleton organization / positive regulation of calcium-mediated signaling / neutrophil chemotaxis / positive regulation of interleukin-1 beta production / calcium-mediated signaling / response to toxic substance / cellular response to type II interferon / intracellular calcium ion homeostasis / positive regulation of inflammatory response / osteoblast differentiation / chemotaxis / calcium ion transport / positive regulation of neuron apoptotic process / MAPK cascade / positive regulation of tumor necrosis factor production / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / cellular response to tumor necrosis factor / kinase activity / regulation of cell shape / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / positive regulation of cell migration / inflammatory response / negative regulation of gene expression / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding / cytosol / cytoplasm
Similarity search - Function
CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
C-C motif chemokine 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGuo, Q. / Ren, M. / Tang, W.
CitationJournal: Embo J. / Year: 2010
Title: Polymerization of Mip-1 Chemokine (Ccl3 and Ccl4) and Clearance of Mip-1 by Insulin-Degrading Enzyme.
Authors: Ren, M. / Guo, Q. / Guo, L. / Lenz, M. / Qian, F. / Koenen, R.R. / Xu, H. / Schilling, A.B. / Weber, C. / Ye, R.D. / Dinner, A.R. / Tang, W.
History
DepositionFeb 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-C MOTIF CHEMOKINE 3
B: C-C MOTIF CHEMOKINE 3
C: C-C MOTIF CHEMOKINE 3
D: C-C MOTIF CHEMOKINE 3
E: C-C MOTIF CHEMOKINE 3


Theoretical massNumber of molelcules
Total (without water)38,9685
Polymers38,9685
Non-polymers00
Water23413
1
B: C-C MOTIF CHEMOKINE 3
C: C-C MOTIF CHEMOKINE 3


Theoretical massNumber of molelcules
Total (without water)15,5872
Polymers15,5872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-11.7 kcal/mol
Surface area8310 Å2
MethodPISA
2
A: C-C MOTIF CHEMOKINE 3

A: C-C MOTIF CHEMOKINE 3


Theoretical massNumber of molelcules
Total (without water)15,5872
Polymers15,5872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area1330 Å2
ΔGint-9.9 kcal/mol
Surface area8300 Å2
MethodPISA
3
D: C-C MOTIF CHEMOKINE 3
E: C-C MOTIF CHEMOKINE 3


Theoretical massNumber of molelcules
Total (without water)15,5872
Polymers15,5872
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-9.5 kcal/mol
Surface area8590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.541, 181.541, 76.845
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

-
Components

#1: Protein
C-C MOTIF CHEMOKINE 3 / SMALL-INDUCIBLE CYTOKINE A3 / MACROPHAGE INFLAMMATORY PROTEIN 1-ALPHA / TONSILLAR LYMPHOCYTE LD78 ...SMALL-INDUCIBLE CYTOKINE A3 / MACROPHAGE INFLAMMATORY PROTEIN 1-ALPHA / TONSILLAR LYMPHOCYTE LD78 ALPHA PROTEIN / G0/G1 SWITCH REGULATORY PROTEIN 19-1 / SIS- BETA / PAT 464.1 / MIP-1-ALPHA(4-69) / LD78-ALPHA(4-69) / MIP- 1-ALPHA


Mass: 7793.664 Da / Num. of mol.: 5 / Fragment: RESIDUES 23-92 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P10147
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 4.69 Å3/Da / Density % sol: 73.78 % / Description: NONE

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 22235 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Biso Wilson estimate: 52.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 40.7
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 11 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 5.2 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→157.22 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.907 / SU B: 9.787 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26461 1133 5.1 %RANDOM
Rwork0.2227 ---
obs0.23483 21083 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.689 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å2-0 Å2
2--0.08 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.65→157.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 0 13 2618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222675
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0991.9463640
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5365325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53324.4125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.74315430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.211515
X-RAY DIFFRACTIONr_chiral_restr0.1590.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212045
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0441.51660
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.04522705
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.99631015
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1374.5935
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.647→2.716 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 95 -
Rwork0.314 1504 -
obs--99.94 %

+
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