[English] 日本語
Yorodumi
- PDB-7scv: Crystal Structure of the Tick Evasin EVA-AAM1001 Complexed to Hum... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7scv
TitleCrystal Structure of the Tick Evasin EVA-AAM1001 Complexed to Human Chemokine CCL17
Components
  • C-C motif chemokine 17
  • Evasin P1243
KeywordsIMMUNE SYSTEM / Inflammation / Chemokine / Ticks / Evasin
Function / homology
Function and homology information


negative regulation of chemokine activity / chemokine binding / C-C chemokine binding / chemokine activity / Chemokine receptors bind chemokines / chemotaxis / cell-cell signaling / immune response / inflammatory response / signaling receptor binding ...negative regulation of chemokine activity / chemokine binding / C-C chemokine binding / chemokine activity / Chemokine receptors bind chemokines / chemotaxis / cell-cell signaling / immune response / inflammatory response / signaling receptor binding / extracellular space / extracellular region
Similarity search - Function
Evasins Class A / Evasins Class A / 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
Similarity search - Domain/homology
Evasin P1243 / C-C motif chemokine 17
Similarity search - Component
Biological speciesAmblyomma americanum (Lone Star tick)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsDevkota, S.R. / Bhusal, R.P. / Aryal, P. / Wilce, M.C.J. / Stone, M.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
Citation
Journal: Nat Commun / Year: 2023
Title: Engineering broad-spectrum inhibitors of inflammatory chemokines from subclass A3 tick evasins.
Authors: Devkota, S.R. / Aryal, P. / Pokhrel, R. / Jiao, W. / Perry, A. / Panjikar, S. / Payne, R.J. / Wilce, M.C.J. / Bhusal, R.P. / Stone, M.J.
#1: Journal: Res Sq / Year: 2023
Title: Engineering Broad-spectrum Inhibitors of Inflammatory Chemokines from a New Family of Tick Evasins
Authors: Devkota, S. / Aryal, P. / Jiao, W. / Perry, A. / Panjikar, S. / Payne, R. / Wilce, M. / Bhusal, R. / Stone, M.
History
DepositionSep 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Evasin P1243
B: C-C motif chemokine 17


Theoretical massNumber of molelcules
Total (without water)19,2112
Polymers19,2112
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-15 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.900, 87.900, 54.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-259-

HOH

-
Components

#1: Protein Evasin P1243


Mass: 11114.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amblyomma americanum (Lone Star tick) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C9S461
#2: Protein C-C motif chemokine 17 / CC chemokine TARC / Small-inducible cytokine A17 / Thymus and activation-regulated chemokine


Mass: 8096.292 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL17, SCYA17, TARC / Production host: Escherichia coli (E. coli) / References: UniProt: Q92583
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na Acet 4.6 pH (Buffer),2 M NaCl (Precipitant)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.01→44.56 Å / Num. obs: 16587 / % possible obs: 99.9 % / Redundancy: 20 % / Biso Wilson estimate: 40.89 Å2 / CC1/2: 1 / Net I/σ(I): 24.7
Reflection shellResolution: 2.01→2.06 Å / Num. unique obs: 1196 / CC1/2: 0.869

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SCS

7scs


Resolution: 2.01→44.56 Å / SU ML: 0.2007 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.3704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2512 914 5.51 %
Rwork0.2367 15662 -
obs0.2375 16576 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.41 Å2
Refinement stepCycle: LAST / Resolution: 2.01→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 0 88 1177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00241109
X-RAY DIFFRACTIONf_angle_d0.60651501
X-RAY DIFFRACTIONf_chiral_restr0.0395171
X-RAY DIFFRACTIONf_plane_restr0.0026191
X-RAY DIFFRACTIONf_dihedral_angle_d4.6486159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.120.2981440.26892205X-RAY DIFFRACTION99.91
2.12-2.250.29451200.25152208X-RAY DIFFRACTION99.91
2.25-2.420.25471380.26632189X-RAY DIFFRACTION100
2.43-2.670.30381220.27862238X-RAY DIFFRACTION100
2.67-3.050.28791170.26782248X-RAY DIFFRACTION100
3.05-3.850.22771270.22342247X-RAY DIFFRACTION100
3.85-44.560.23511460.21482327X-RAY DIFFRACTION99.96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.460626032591.16052131785-1.756460324.326850207163.37918658216.206664077220.268187155844-0.238207041725-0.040445430069-1.98400809993-0.1753394258730.6491072480810.38391059164-1.30340472477-0.1713669798310.735766785152-0.185308897986-0.1266906284640.4799649732630.04586612168080.504591611215-11.674884390956.597122576621.1916779027
25.758040489140.0676042726267-1.221060676195.817789125630.1279952742828.819686626530.19212736699-0.367584045118-0.6909683413610.759286906839-0.213208379702-0.7952546515461.522542533080.9662486401530.03386252303660.582405872761-0.00529942191511-0.09615425359950.307232774010.03389040595290.498812263786.8575016903358.103459203232.8158739327
34.285368709780.7112536181650.360302552824.47113710684-2.120687155695.66450745541-0.2287692678870.5095197547940.0637888565607-0.250947160350.154966267978-0.195067771584-0.2371708756320.2313212298190.161438341130.439533168283-0.05496313200740.03281674631460.2597653601780.01713365509830.255368642061-0.90115091955863.406232691425.0857701232
44.38902061080.927279989547-0.5758325581485.46117975572-0.6029274414544.99351520863-0.1778683649650.03682568124520.114481488373-0.210215759228-0.0601616782881-0.2236531746670.2399959262110.1791823617230.2077750938250.452992945806-0.02765279627510.03444240828930.2534690615170.02575027175750.3674909418332.394382099466.843270506525.462156344
53.88502137874-5.009551720234.053410351587.12384471846-5.338243341464.75572439387-0.886840713384-1.023610539611.247701995740.09950574765550.0806602261343-3.54267511233-0.2085047859750.6806488891790.5852974063820.4468512552630.0650334357641-0.0854002166810.6880697700040.001313011742980.82185406742116.802922614860.254457512927.0939806999
65.23227313877-0.0548534236021-0.08879691470654.846553938220.8010888693232.97132618821-0.145155148503-0.0634559513157-0.1177417011560.773896687335-0.0411648495794-0.1476245158560.06760602841230.1665627085970.2314572019670.584581741677-0.0674904225444-0.04097925946890.3165006956260.00681396679410.3929211853344.3932527236370.430902327433.684393606
72.12708466791.926766873172.393387710121.787963490631.576602831159.739896820250.30211228110.1381435118430.1102407568410.79688158397-0.444735476092-1.689952392171.160691007950.2867853048290.2666811500590.4882853900840.0973514395084-0.1004170805090.4427297491480.07609526037810.56335893201411.740379850757.344356860127.3785189723
85.827065021953.576935563182.082315375914.198674897840.7243773659262.946905896020.4926146564280.351623561363-0.134465525903-0.116703407379-0.2155134221450.4864400470630.117526604142-0.139733113533-0.1887914748910.4840446720120.01160910124040.01616828947760.339236994173-0.02045132925490.377477948967-10.243199288353.868363499727.0207096073
94.615862647074.000986860642.790423736625.195294693892.102105869263.657254330510.08034339066790.0326070919996-0.5449216827170.07842584968710.237925422266-0.477432325840.01763200754150.0145420810274-0.2616586015890.388127781515-0.07683821933640.0337104561190.3669415551980.00150660624180.408431332207-8.3528571593347.323438353727.3278192218
105.259163014111.719245419111.714641013237.216597414660.8086730557435.734779762410.0715943743503-0.0265706477142-0.431710262828-0.02911042378130.128162692410.5834272977710.0128108040147-0.243722951719-0.1892905527680.303107703838-0.106838339598-0.02085762282630.45415333069-0.004594944540170.441602445413-14.041520526943.444296899527.5271208317
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 17 through 26 )AA17 - 261 - 10
22chain 'A' and (resid 27 through 36 )AA27 - 3611 - 20
33chain 'A' and (resid 37 through 46 )AA37 - 4621 - 30
44chain 'A' and (resid 47 through 69 )AA47 - 6931 - 53
55chain 'A' and (resid 70 through 76 )AA70 - 7654 - 60
66chain 'A' and (resid 77 through 96 )AA77 - 9661 - 80
77chain 'A' and (resid 97 through 101 )AA97 - 10181 - 85
88chain 'B' and (resid 7 through 20 )BB7 - 201 - 14
99chain 'B' and (resid 21 through 43 )BB21 - 4315 - 37
1010chain 'B' and (resid 44 through 69 )BB44 - 6938 - 63

+
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