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- PDB-5eki: Crystal Structure of Truncated CCL21 -

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Basic information

Entry
Database: PDB / ID: 5eki
TitleCrystal Structure of Truncated CCL21
ComponentsC-C motif chemokine 21
KeywordsIMMUNE SYSTEM / Cytokine / Chemokine / Chemotaxis / Inflammation
Function / homology
Function and homology information


mesangial cell-matrix adhesion / CCL21-activated CCR7 signaling pathway / dendritic cell dendrite assembly / negative regulation of dendritic cell dendrite assembly / CCR7 chemokine receptor binding / positive regulation of phospholipase C/protein kinase C signal transduction / chemokine (C-C motif) ligand 21 signaling pathway / positive regulation of dendritic cell antigen processing and presentation / positive regulation of myeloid dendritic cell chemotaxis / negative regulation of leukocyte tethering or rolling ...mesangial cell-matrix adhesion / CCL21-activated CCR7 signaling pathway / dendritic cell dendrite assembly / negative regulation of dendritic cell dendrite assembly / CCR7 chemokine receptor binding / positive regulation of phospholipase C/protein kinase C signal transduction / chemokine (C-C motif) ligand 21 signaling pathway / positive regulation of dendritic cell antigen processing and presentation / positive regulation of myeloid dendritic cell chemotaxis / negative regulation of leukocyte tethering or rolling / positive regulation of glycoprotein biosynthetic process / establishment of T cell polarity / chemokine receptor binding / immunological synapse formation / positive regulation of T cell chemotaxis / CCR chemokine receptor binding / positive regulation of pseudopodium assembly / positive regulation of chemotaxis / negative regulation of dendritic cell apoptotic process / cellular response to chemokine / chemokine-mediated signaling pathway / eosinophil chemotaxis / ruffle organization / positive regulation of neutrophil chemotaxis / chemokine activity / positive regulation of cell adhesion mediated by integrin / Chemokine receptors bind chemokines / positive regulation of filopodium assembly / dendritic cell chemotaxis / positive regulation of cell motility / positive regulation of cell-matrix adhesion / positive regulation of actin filament polymerization / positive regulation of T cell migration / cell maturation / T cell costimulation / release of sequestered calcium ion into cytosol / cell chemotaxis / positive regulation of JNK cascade / positive regulation of receptor-mediated endocytosis / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / cellular response to prostaglandin E stimulus / G alpha (i) signalling events / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / immune response / positive regulation of cell migration / G protein-coupled receptor signaling pathway / inflammatory response / extracellular space / extracellular region
Similarity search - Function
Chemokine CC, DCCL motif-cointaining 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
C-C motif chemokine 21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLewandowski, E.M. / Smith, E.W. / Chen, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM097381 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA159202-01 United States
CitationJournal: Biochemistry / Year: 2016
Title: Crystallographic Structure of Truncated CCL21 and the Putative Sulfotyrosine-Binding Site.
Authors: Smith, E.W. / Lewandowski, E.M. / Moussouras, N.A. / Kroeck, K.G. / Volkman, B.F. / Veldkamp, C.T. / Chen, Y.
History
DepositionNov 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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-C motif chemokine 21
B: C-C motif chemokine 21
C: C-C motif chemokine 21
D: C-C motif chemokine 21
E: C-C motif chemokine 21
F: C-C motif chemokine 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,66611
Polymers53,1866
Non-polymers4805
Water3,369187
1
A: C-C motif chemokine 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9602
Polymers8,8641
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C-C motif chemokine 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9602
Polymers8,8641
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: C-C motif chemokine 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9602
Polymers8,8641
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: C-C motif chemokine 21


Theoretical massNumber of molelcules
Total (without water)8,8641
Polymers8,8641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: C-C motif chemokine 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9602
Polymers8,8641
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: C-C motif chemokine 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9602
Polymers8,8641
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-146 kcal/mol
Surface area24130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.752, 58.244, 66.054
Angle α, β, γ (deg.)90.00, 119.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
C-C motif chemokine 21 / 6Ckine / Beta-chemokine exodus-2 / Secondary lymphoid-tissue chemokine / SLC / Small-inducible cytokine A21


Mass: 8864.284 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL21, SCYA21, UNQ784/PRO1600 / Production host: Escherichia coli (E. coli) / References: UniProt: O00585
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.903→57.24 Å / Num. obs: 34110 / % possible obs: 99.9 % / Redundancy: 7 % / Net I/σ(I): 16.54
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data scaling
SCALEPACKdata scaling
DENZOdata reduction
BALBESphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→57.24 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.433 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26219 1335 4.6 %RANDOM
Rwork0.21023 ---
obs0.21267 27663 84.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.489 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å2-0.15 Å2
2--1 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→57.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 25 187 3639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193537
X-RAY DIFFRACTIONr_bond_other_d0.0050.023529
X-RAY DIFFRACTIONr_angle_refined_deg1.8362.0144781
X-RAY DIFFRACTIONr_angle_other_deg0.99838205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2485421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52423.571140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55715688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3361530
X-RAY DIFFRACTIONr_chiral_restr0.110.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0223787
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02719
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_it1.9372.0961702
X-RAY DIFFRACTIONr_mcbond_other1.9362.0951701
X-RAY DIFFRACTIONr_mcangle_it3.1713.1212117
X-RAY DIFFRACTIONr_mcangle_other3.1713.1222118
X-RAY DIFFRACTIONr_scbond_it2.4252.4151835
X-RAY DIFFRACTIONr_scbond_other2.4272.4121832
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8883.462659
X-RAY DIFFRACTIONr_long_range_B_refined6.12124.5793896
X-RAY DIFFRACTIONr_long_range_B_other6.10324.5583890
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 56 -
Rwork0.241 1206 -
obs--49.78 %

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