[English] 日本語
Yorodumi
- PDB-1ml0: VIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS68... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ml0
TitleVIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS68 IN COMPLEX WITH THE P8A VARIANT OF CC-CHEMOKINE MCP-1
Components
  • M3 Protein
  • Small Inducible Cytokine
KeywordsIMMUNE SYSTEM / HERPESVIRUS / VIRAL IMMUNE EVASION / CHEMOKINE BINDING PROTEIN / DECOY RECEPTOR
Function / homology
Function and homology information


helper T cell extravasation / CCR2 chemokine receptor binding / negative regulation of natural killer cell chemotaxis / positive regulation of NMDA glutamate receptor activity / chemokine binding / negative regulation of glial cell apoptotic process / astrocyte cell migration / ATF4 activates genes in response to endoplasmic reticulum stress / positive regulation of apoptotic cell clearance / CCR chemokine receptor binding ...helper T cell extravasation / CCR2 chemokine receptor binding / negative regulation of natural killer cell chemotaxis / positive regulation of NMDA glutamate receptor activity / chemokine binding / negative regulation of glial cell apoptotic process / astrocyte cell migration / ATF4 activates genes in response to endoplasmic reticulum stress / positive regulation of apoptotic cell clearance / CCR chemokine receptor binding / cellular homeostasis / positive regulation of endothelial cell apoptotic process / NFE2L2 regulating inflammation associated genes / eosinophil chemotaxis / cellular response to fibroblast growth factor stimulus / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / negative regulation of vascular endothelial cell proliferation / negative regulation of G1/S transition of mitotic cell cycle / macrophage chemotaxis / positive regulation of calcium ion import / positive regulation of nitric-oxide synthase biosynthetic process / monocyte chemotaxis / Interleukin-10 signaling / cell surface receptor signaling pathway via JAK-STAT / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / humoral immune response / cellular response to interleukin-1 / cytoskeleton organization / sensory perception of pain / viral genome replication / positive regulation of synaptic transmission, glutamatergic / animal organ morphogenesis / response to bacterium / cellular response to type II interferon / cytokine-mediated signaling pathway / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of T cell activation / cellular response to tumor necrosis factor / regulation of cell shape / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / angiogenesis / negative regulation of neuron apoptotic process / cell surface receptor signaling pathway / cell adhesion / protein kinase activity / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / protein phosphorylation / signaling receptor binding / signal transduction / extracellular space / extracellular region
Similarity search - Function
Immunoglobulin-like - #1330 / Chemokine-binding protein M3-like / Chemokine-binding M3, viral / Chemokine-binding M3, subdomain 1, viral / Chemokine-binding M3, subdomain 2, viral / Chemokine-binding M3 superfamily / M3 / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta ...Immunoglobulin-like - #1330 / Chemokine-binding protein M3-like / Chemokine-binding M3, viral / Chemokine-binding M3, subdomain 1, viral / Chemokine-binding M3, subdomain 2, viral / Chemokine-binding M3 superfamily / M3 / 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) / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
M3 / C-C motif chemokine 2
Similarity search - Component
Biological speciesMurid herpesvirus 4 (Murine herpesvirus 68)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAlexander, J.M. / Fremont, D.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Structural Basis of Chemokine Sequestration by a Herpesvirus Decoy Receptor
Authors: Alexander, J.M. / Nelson, C.A. / van Berkel, V. / Lau, E.K. / Studts, J.M. / Brett, T.J. / Speck, S.H. / Handel, T.M. / Virgin, H.W. / Fremont, D.H.
History
DepositionAug 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: M3 Protein
D: Small Inducible Cytokine


Theoretical massNumber of molelcules
Total (without water)50,4812
Polymers50,4812
Non-polymers00
Water77543
1
A: M3 Protein
D: Small Inducible Cytokine

A: M3 Protein
D: Small Inducible Cytokine


Theoretical massNumber of molelcules
Total (without water)100,9624
Polymers100,9624
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area6840 Å2
ΔGint-41 kcal/mol
Surface area37310 Å2
MethodPISA
2
A: M3 Protein
D: Small Inducible Cytokine
x 6


Theoretical massNumber of molelcules
Total (without water)302,88712
Polymers302,88712
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)99.200, 99.200, 78.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

-
Components

#1: Protein M3 Protein


Mass: 41826.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68)
Genus: Rhadinovirus / Gene: M3 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O41925
#2: Protein Small Inducible Cytokine / CCL2 / Monocyte chemotactic protein 1 / MCP-1 / Monocyte chemotactic protein 1 / MCP-1 / Monocyte ...CCL2 / Monocyte chemotactic protein 1 / MCP-1 / Monocyte chemotactic protein 1 / MCP-1 / Monocyte chemoattractant protein-1 / Monocyte chemotactic and activating factor / MCAF / Monocyte secretory protein JE / HC11


Mass: 8654.971 Da / Num. of mol.: 1 / Mutation: P8A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MONOCYTE CHEMOATTRACTANT PROTEIN 1 / Plasmid: PAED-4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYS S / References: UniProt: P13500
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.21 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 14% PEG4000 200MM, SODIUM ACETATE, 100MM MAGNESIUM CHLORIDE, pH 4.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 4.1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
214 %PEG40001reservoir
3200 mMsodium acetate1reservoirpH4.1
4100 mM1reservoirMgCl2

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 / Wavelength: 1.000, 0.9796, 0.9789, 0.9599
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2000
RadiationMonochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
211
30.97961
40.97891
50.95991
ReflectionResolution: 2.8→20 Å / Num. all: 11156 / Num. obs: 11156 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Biso Wilson estimate: 70.9 Å2 / Rsym value: 0.088 / Net I/σ(I): 14.5
Reflection shellResolution: 2.8→2.97 Å / Mean I/σ(I) obs: 4.8 / Rsym value: 0.422 / % possible all: 97.9
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Num. obs: 16718 / % possible obs: 96.3 % / Num. measured all: 41932 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.19 Å / % possible obs: 94.4 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3.2

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MKF

1mkf


Resolution: 2.8→19.37 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 36852.37 / Data cutoff high rms absF: 36852.37 / 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
Rfree0.282 569 5.2 %RANDOM
Rwork0.201 ---
all-10904 --
obs-10904 96 %-
Solvent computationBsol: 43.4831 Å2 / ksol: 0.316929 e/Å3
Displacement parametersBiso mean: 62.8 Å2
Baniso -1Baniso -2Baniso -3
1--14.22 Å25.3 Å20 Å2
2---14.22 Å20 Å2
3---28.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.33 Å
Luzzati d res low-6 Å
Luzzati sigma a0.6 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 0 43 3411
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_deg1.4
X-RAY DIFFRACTIONo_dihedral_angle_d25.7
X-RAY DIFFRACTIONo_improper_angle_d0.87
X-RAY DIFFRACTIONo_mcbond_it1.361.5
X-RAY DIFFRACTIONo_mcangle_it2.422
X-RAY DIFFRACTIONo_scbond_it1.82
X-RAY DIFFRACTIONo_scangle_it2.792.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 91 5.5 %
Rwork0.324 1564 -
obs-1564 89.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 19.37 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg25.7
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg0.87
LS refinement shell
*PLUS
Highest resolution: 2.8 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://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