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- PDB-7sta: X-ray Crystal Structure of Truncated Human Chemokine CCL19 (7-70) -

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Basic information

Entry
Database: PDB / ID: 7sta
TitleX-ray Crystal Structure of Truncated Human Chemokine CCL19 (7-70)
ComponentsC-C motif chemokine 19
KeywordsSIGNALING PROTEIN / CCL19 / Chemokine
Function / homology
Function and homology information


positive regulation of dendritic cell dendrite assembly / myeloid dendritic cell chemotaxis / CCR7 chemokine receptor binding / mature conventional dendritic cell differentiation / CCR10 chemokine receptor binding / positive regulation of dendritic cell antigen processing and presentation / response to prostaglandin E / positive regulation of T-helper 1 cell differentiation / establishment of T cell polarity / positive regulation of glycoprotein biosynthetic process ...positive regulation of dendritic cell dendrite assembly / myeloid dendritic cell chemotaxis / CCR7 chemokine receptor binding / mature conventional dendritic cell differentiation / CCR10 chemokine receptor binding / positive regulation of dendritic cell antigen processing and presentation / response to prostaglandin E / positive regulation of T-helper 1 cell differentiation / establishment of T cell polarity / positive regulation of glycoprotein biosynthetic process / chemokine receptor binding / regulation of cell projection assembly / immunological synapse formation / CCR chemokine receptor binding / lymphocyte chemotaxis / cell communication / positive regulation of chemotaxis / negative regulation of dendritic cell apoptotic process / chemokine-mediated signaling pathway / positive regulation of neutrophil chemotaxis / positive regulation of cell motility / Chemokine receptors bind chemokines / chemokine activity / dendritic cell chemotaxis / response to nitric oxide / positive regulation of endocytosis / Interleukin-10 signaling / monocyte chemotaxis / positive regulation of protein kinase activity / cellular response to interleukin-1 / positive regulation of T cell proliferation / release of sequestered calcium ion into cytosol / positive regulation of JUN kinase activity / cell maturation / T cell costimulation / positive regulation of interleukin-12 production / neutrophil chemotaxis / positive regulation of GTPase activity / positive regulation of interleukin-1 beta production / positive regulation of JNK cascade / response to virus / cellular response to virus / cellular response to type II interferon / positive regulation of receptor-mediated endocytosis / intracellular calcium ion homeostasis / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / G alpha (i) signalling events / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / inflammatory response / immune response / G protein-coupled receptor signaling pathway / extracellular space / extracellular region
Similarity search - Function
Chemokine CC, DCCL motif-cointaining domain / 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
C-C motif chemokine 19
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLewandowski, E.M. / Kroeck, K. / Chen, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097381 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)OD20000 United States
CitationJournal: Biochemistry / Year: 2022
Title: Structural Insights into Molecular Recognition by Human Chemokine CCL19.
Authors: Lewandowski, E.M. / Kroeck, K.G. / Jacobs, L.M.C. / Fenske, T.G. / Witt, R.N. / Hintz, A.M. / Ramsden, E.R. / Zhang, X. / Peterson, F. / Volkman, B.F. / Veldkamp, C.T. / Chen, Y.
History
DepositionNov 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-C motif chemokine 19
B: C-C motif chemokine 19
C: C-C motif chemokine 19
D: C-C motif chemokine 19


Theoretical massNumber of molelcules
Total (without water)29,3954
Polymers29,3954
Non-polymers00
Water181
1
A: C-C motif chemokine 19


Theoretical massNumber of molelcules
Total (without water)7,3491
Polymers7,3491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: C-C motif chemokine 19


Theoretical massNumber of molelcules
Total (without water)7,3491
Polymers7,3491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: C-C motif chemokine 19


Theoretical massNumber of molelcules
Total (without water)7,3491
Polymers7,3491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: C-C motif chemokine 19


Theoretical massNumber of molelcules
Total (without water)7,3491
Polymers7,3491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.940, 148.180, 29.000
Angle α, β, γ (deg.)90.000, 90.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
C-C motif chemokine 19 / Beta-chemokine exodus-3 / CK beta-11 / Epstein-Barr virus-induced molecule 1 ligand chemokine / ...Beta-chemokine exodus-3 / CK beta-11 / Epstein-Barr virus-induced molecule 1 ligand chemokine / EBI1 ligand chemokine / ELC / Macrophage inflammatory protein 3 beta / MIP-3-beta / Small-inducible cytokine A19


Mass: 7348.646 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL19, ELC, MIP3B, SCYA19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99731
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 20% PEG 3350, 0.2 M Sodium Nitrate, final pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.02 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.5→49.39 Å / Num. obs: 8480 / % possible obs: 100 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 5 / Num. unique obs: 4601 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MP1

2mp1


Resolution: 2.5→37.07 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.883 / SU B: 33.091 / SU ML: 0.328 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 388 4.6 %RANDOM
Rwork0.2335 ---
obs0.2351 8065 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.61 Å2 / Biso mean: 54.145 Å2 / Biso min: 29.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20.3 Å2
2---1.52 Å20 Å2
3---1.33 Å2
Refinement stepCycle: final / Resolution: 2.5→37.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 0 1 2014
Biso mean---36.84 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132119
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172069
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.672895
X-RAY DIFFRACTIONr_angle_other_deg1.2181.5774765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.065254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.9417.742124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.39515361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1141532
X-RAY DIFFRACTIONr_chiral_restr0.0720.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022354
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02494
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 28 -
Rwork0.293 621 -
all-649 -
obs--100 %
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)
17.36491.4489-0.73385.7520.83832.24260.21540.0051-0.1633-0.1971-0.1320.4164-0.50230.0318-0.08330.3678-0.0083-0.02670.1980.03680.077814.3837.6816.174
25.35534.3604-2.10294.8215-1.13054.28390.12520.0596-0.7192-0.0193-0.0830.1379-0.4254-0.0151-0.04220.1107-0.0095-0.16020.15940.00550.94335.48419.41519.389
32.09520.35360.2134.6639-0.87627.0506-0.1204-0.0090.41180.3331-0.12720.1730.1676-0.03830.24770.15750.0389-0.01210.25320.0150.40991.6690.6180.105
45.1901-0.12430.73443.8826-3.82155.4986-0.06070.04340.53880.1092-0.1669-0.06130.84980.02030.22760.94470.01780.15270.14130.01280.09014.906-17.5849.011
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 70
2X-RAY DIFFRACTION2B8 - 68
3X-RAY DIFFRACTION3C7 - 70
4X-RAY DIFFRACTION4D8 - 68

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