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- PDB-7jny: Crystal structure of CXCL13 -

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Basic information

Entry
Database: PDB / ID: 7jny
TitleCrystal structure of CXCL13
ComponentsC-X-C motif chemokine 13
KeywordsCYTOKINE / Chemokine / CXCL13
Function / homology
Function and homology information


lymphocyte chemotaxis across high endothelial venule / CXCR5 chemokine receptor binding / endothelial cell chemotaxis to fibroblast growth factor / negative regulation of endothelial cell chemotaxis to fibroblast growth factor / CCR10 chemokine receptor binding / B cell chemotaxis / CXCR3 chemokine receptor binding / regulation of humoral immune response / chronic inflammatory response / positive regulation of cell-cell adhesion mediated by integrin ...lymphocyte chemotaxis across high endothelial venule / CXCR5 chemokine receptor binding / endothelial cell chemotaxis to fibroblast growth factor / negative regulation of endothelial cell chemotaxis to fibroblast growth factor / CCR10 chemokine receptor binding / B cell chemotaxis / CXCR3 chemokine receptor binding / regulation of humoral immune response / chronic inflammatory response / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of T cell chemotaxis / CXCR chemokine receptor binding / positive regulation of integrin activation / germinal center formation / chemokine-mediated signaling pathway / activation of GTPase activity / Chemokine receptors bind chemokines / chemokine activity / fibroblast growth factor binding / regulation of angiogenesis / neutrophil chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / heparin binding / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / cellular response to lipopolysaccharide / receptor ligand activity / cell surface receptor signaling pathway / defense response to bacterium / inflammatory response / immune response / extracellular space / extracellular region
Similarity search - Function
CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / 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
C-X-C motif chemokine 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsRosenberg Jr., E.M. / Rajasekaran, D. / Murphy, J.W. / Pantouris, G. / Lolis, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI113606 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: The N-terminal length and side-chain composition of CXCL13 affect crystallization, structure and functional activity.
Authors: Rosenberg Jr., E.M. / Herrington, J. / Rajasekaran, D. / Murphy, J.W. / Pantouris, G. / Lolis, E.J.
History
DepositionAug 5, 2020Deposition site: RCSB / Processing site: RCSB
SupersessionOct 7, 2020ID: 4ZAI
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-X-C motif chemokine 13


Theoretical massNumber of molelcules
Total (without water)10,4671
Polymers10,4671
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.967, 48.967, 80.278
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein C-X-C motif chemokine 13 / Angie / B cell-attracting chemokine 1 / BCA-1 / B lymphocyte chemoattractant / CXC chemokine BLC / ...Angie / B cell-attracting chemokine 1 / BCA-1 / B lymphocyte chemoattractant / CXC chemokine BLC / Small-inducible cytokine B13


Mass: 10466.571 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL13, BCA1, BLC, SCYB13 / Production host: Escherichia coli (E. coli) / References: UniProt: O43927
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M Sodium chloride 0.1 M BIS-TRIS propane pH 9.0, 25% w/v Polyethylene glycol 1,500. Crystals formed within a couple days

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 9412 / % possible obs: 99.4 % / Redundancy: 4.8 % / CC1/2: 1 / Rpim(I) all: 0.027 / Net I/σ(I): 20.12
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
1.88-1.914110.7541
1.91-1.954610.8331
1.95-1.984340.8651
1.98-2.034650.8741
2.03-2.074670.9411
2.07-2.124780.9351
2.12-2.174500.9521
2.17-2.234760.9731
2.23-2.294670.9791
2.29-2.374480.9821
2.37-2.454870.9881
2.45-2.554620.9931
2.55-2.674670.9931
2.67-2.814770.9951
2.81-2.984770.9961
2.98-3.214750.9981
3.21-3.544860.9991
3.54-4.054870.9981
4.05-5.14910.9991
5.1-505460.9991

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXdev_3946refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZAI

4zai
PDB Unreleased entry


Resolution: 1.88→42.41 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 1756 10.28 %
Rwork0.1874 15321 -
obs0.1911 9388 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.32 Å2 / Biso mean: 39.7731 Å2 / Biso min: 14.22 Å2
Refinement stepCycle: final / Resolution: 1.88→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms661 0 0 75 736
Biso mean---37.81 -
Num. residues----80
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.88-1.930.3631210.3101103890
1.93-1.990.32781310.2653113995
1.99-2.050.29981370.2506119498
2.06-2.130.26731380.2337119698
2.13-2.210.24671340.2025116599
2.21-2.310.20211360.1934118798
2.31-2.440.24441370.2136121299
2.44-2.590.27051350.20751201100
2.59-2.790.24321360.20361183100
2.79-3.070.20491490.19841204100
3.07-3.510.22571320.16851205100
3.51-4.420.17291440.15041186100
4.43-42.410.20091260.1553121199
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)
11.42870.5631.1011.48162.58175.95920.0419-0.0909-0.05640.3342-0.1615-0.16530.01930.30480.130.3105-0.0635-0.02350.17410.01460.27829.2793.3403-4.5933
23.2776-0.2598-0.92344.2169-1.40944.7097-0.2605-0.42750.15240.6406-0.3094-0.2098-0.20130.2962-0.42680.836-0.0674-0.07440.17160.03150.283725.451918.898-8.6927
32.8580.5361-0.15712.2257-1.53315.99070.2221-0.0216-0.05150.4723-0.2834-0.0548-0.75710.55220.12920.3424-0.1141-0.01560.18070.00330.248527.46318.5599-7.9843
41.7830.36281.81872.2237-0.39422.1062-0.45890.4250.3450.432-0.0022-0.0781-0.98430.4720.02750.6769-0.2181-0.06370.24080.02610.242328.882914.7952-9.242
51.5604-0.1977-1.25365.55134.6794.756-0.08350.0846-0.07530.1823-0.35370.4804-0.665-0.67940.35090.34790.1181-0.0240.1703-0.00870.298517.34767.7909-18.6401
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 14 )A0 - 14
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 22 )A15 - 22
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 47 )A23 - 47
4X-RAY DIFFRACTION4chain 'A' and (resid 48 through 59 )A48 - 59
5X-RAY DIFFRACTION5chain 'A' and (resid 60 through 79 )A60 - 79

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