[English] 日本語
Yorodumi
- PDB-5wk3: CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CCL17 AND M116 FAB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wk3
TitleCRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CCL17 AND M116 FAB
Components
  • C-C motif chemokine 17Chemokine
  • M116 HEAVY CHAIN
  • M116 LIGHT CHAIN
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


CCR chemokine receptor binding / lymphocyte chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / monocyte chemotaxis / cellular response to interleukin-1 / neutrophil chemotaxis / cellular response to type II interferon / chemotaxis ...CCR chemokine receptor binding / lymphocyte chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / monocyte chemotaxis / cellular response to interleukin-1 / neutrophil chemotaxis / cellular response to type II interferon / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / positive regulation of ERK1 and ERK2 cascade / inflammatory response / G protein-coupled receptor signaling pathway / signaling receptor binding / extracellular space / extracellular region
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) / Immunoglobulins ...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) / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
C-C motif chemokine 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTeplyakov, A. / Obmolova, G. / Gilliland, G.L.
CitationJournal: Biochem Biophys Rep / Year: 2018
Title: Structural insights into chemokine CCL17 recognition by antibody M116.
Authors: Teplyakov, A. / Obmolova, G. / Gilliland, G.L.
History
DepositionJul 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
P: M116 LIGHT CHAIN
Q: M116 HEAVY CHAIN
R: M116 LIGHT CHAIN
S: M116 HEAVY CHAIN
T: M116 LIGHT CHAIN
U: M116 HEAVY CHAIN
V: M116 LIGHT CHAIN
W: M116 HEAVY CHAIN
A: C-C motif chemokine 17
B: C-C motif chemokine 17
C: C-C motif chemokine 17
D: C-C motif chemokine 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,02316
Polymers227,65512
Non-polymers3684
Water18,3751020
1
P: M116 LIGHT CHAIN
Q: M116 HEAVY CHAIN
A: C-C motif chemokine 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0064
Polymers56,9143
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
R: M116 LIGHT CHAIN
S: M116 HEAVY CHAIN
B: C-C motif chemokine 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0064
Polymers56,9143
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
T: M116 LIGHT CHAIN
U: M116 HEAVY CHAIN
C: C-C motif chemokine 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0064
Polymers56,9143
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
V: M116 LIGHT CHAIN
W: M116 HEAVY CHAIN
D: C-C motif chemokine 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0064
Polymers56,9143
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.510, 81.930, 130.500
Angle α, β, γ (deg.)93.96, 99.21, 104.19
Int Tables number1
Space group name H-MP1

-
Components

#1: Antibody
M116 LIGHT CHAIN


Mass: 24067.729 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
M116 HEAVY CHAIN


Mass: 24705.621 Da / Num. of mol.: 4 / Fragment: FD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein
C-C motif chemokine 17 / Chemokine / CC chemokine TARC / Small-inducible cytokine A17 / Thymus and activation-regulated chemokine


Mass: 8140.344 Da / Num. of mol.: 4 / Fragment: UNP residues 24-94
Source method: isolated from a genetically manipulated source
Details: G7T mutant of human CCL17 / Source: (gene. exp.) Homo sapiens (human) / Gene: CCL17, SCYA17, TARC / Production host: Escherichia coli (E. coli) / References: UniProt: Q92583
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1020 / 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: 2.34 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 15% PEG 3350, 0.2 M POTASSIUM SODIUM TARTRATE / PH range: 7.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 153743 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.3
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 10386 / % possible all: 87.9

-
Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
REFMAC5.6.0117refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1nr4

1nr4


Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.431 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.146
RfactorNum. reflection% reflectionSelection details
Rfree0.23147 1536 1 %RANDOM
Rwork0.18044 ---
obs0.18094 152202 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.24 Å21.29 Å2
2---0.84 Å20.22 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15220 0 24 1020 16264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0215621
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.95421268
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13851990
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92824.705593
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.753152516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4031551
X-RAY DIFFRACTIONr_chiral_restr0.0830.22396
X-RAY DIFFRACTIONr_gen_planes_refined00.02111675
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 102 -
Rwork0.241 10130 -
obs--87.88 %

+
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