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- PDB-5cba: 3B4 in complex with CXCL13 - 3B4-CXCL13 -

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Basic information

Entry
Database: PDB / ID: 5cba
Title3B4 in complex with CXCL13 - 3B4-CXCL13
Components
  • 3b4 heavy chain
  • 3b4 light chain
  • C-X-C motif chemokine 13
KeywordsIMMUNE SYSTEM / anti-CXCL13 / CXCL13 / scFv
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 / CD22 mediated BCR regulation / activation of GTPase activity / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / fibroblast growth factor binding / immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / regulation of angiogenesis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / neutrophil chemotaxis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / heparin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cellular response to lipopolysaccharide / Potential therapeutics for SARS / adaptive immune response / receptor ligand activity / cell surface receptor signaling pathway / defense response to bacterium / immune response / inflammatory response / extracellular space / extracellular exosome / extracellular region / plasma membrane
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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 ...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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Immunoglobulin heavy variable 1-69D / C-X-C motif chemokine 13 / Immunoglobulin lambda variable 2-14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTu, C. / Bard, J. / Mosyak, L.
CitationJournal: J. Biol. Chem. / Year: 2016
Title: A Combination of Structural and Empirical Analyses Delineates the Key Contacts Mediating Stability and Affinity Increases in an Optimized Biotherapeutic Single-chain Fv (scFv).
Authors: Tu, C. / Terraube, V. / Tam, A.S. / Stochaj, W. / Fennell, B.J. / Lin, L. / Stahl, M. / LaVallie, E.R. / Somers, W. / Finlay, W.J. / Mosyak, L. / Bard, J. / Cunningham, O.
History
DepositionJun 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: 3b4 heavy chain
B: 3b4 light chain
C: 3b4 heavy chain
D: 3b4 light chain
E: C-X-C motif chemokine 13
F: C-X-C motif chemokine 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,77511
Polymers75,4206
Non-polymers3545
Water2,126118
1
A: 3b4 heavy chain
B: 3b4 light chain
E: C-X-C motif chemokine 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0037
Polymers37,7103
Non-polymers2924
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-12 kcal/mol
Surface area14560 Å2
MethodPISA
2
C: 3b4 heavy chain
D: 3b4 light chain
F: C-X-C motif chemokine 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7724
Polymers37,7103
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-13 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.350, 55.680, 112.770
Angle α, β, γ (deg.)90.00, 120.56, 90.00
Int Tables number5
Space group name H-MC121
DetailsTrimer confirmed by gel filtration

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Components

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Protein , 1 types, 2 molecules EF

#3: 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.: 2
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

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody 3b4 heavy chain


Mass: 14663.956 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV1-69-2
Cell line (production host): Expi293F human embryonic kidney cells
Production host: Homo sapiens (human) / References: UniProt: A0A0B4J2H0
#2: Antibody 3b4 light chain


Mass: 12579.694 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Cell line (production host): Expi293F human embryonic kidney cells
Production host: Homo sapiens (human) / References: UniProt: P04209

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Non-polymers , 3 types, 123 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.14 Å3/Da / Density % sol: 42.5 % / Description: long needles/rods
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM Tris pH 8, 100 mM NaCl, 8 % PEG 20000 / PH range: 8

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→48.7 Å / Num. obs: 22217 / % possible obs: 99.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 59.79 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 12.3
Reflection shellResolution: 2.5→2.511 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.9 / % possible all: 87

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B4 and 3GV3/2R3Z/4HSV/3IL8

3gv3

2r3z

4hsv

3il8


Resolution: 2.5→48.7 Å / Cor.coef. Fo:Fc: 0.9295 / Cor.coef. Fo:Fc free: 0.9016 / SU R Cruickshank DPI: 0.599 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.582 / SU Rfree Blow DPI: 0.269 / SU Rfree Cruickshank DPI: 0.274
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 1129 5.08 %RANDOM
Rwork0.1973 ---
obs0.1994 22212 99.34 %-
Displacement parametersBiso mean: 58.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.6711 Å20 Å210.6255 Å2
2--0.5913 Å20 Å2
3---0.0798 Å2
Refine analyzeLuzzati coordinate error obs: 0.351 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4607 0 23 118 4748
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074735HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.056421HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1582SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes693HARMONIC5
X-RAY DIFFRACTIONt_it4735HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion19.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion628SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5126SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.62 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2627 122 4.26 %
Rwork0.2278 2740 -
all0.2293 2862 -
obs--99.34 %
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
12.10370.63351.60514.76920.60943.0222-0.05580.07480.1419-0.31250.07980.50440.1148-0.0229-0.024-0.1789-0.0136-0.1705-0.33830.0486-0.0977chain A heavy chain-8.0271-4.4821-38.4182
21.5445-1.22370.01165.0809-1.17671.5772-0.00360.1256-0.0092-0.10770.0603-0.07840.06910.1446-0.0566-0.10860.0173-0.149-0.20960.0015-0.1454chain B light chain8.1413-14.6211-31.0342
31.9484-0.69031.28554.85391.02845.38330.0065-0.0438-0.3052-0.20990.0523-0.12290.28170.1596-0.0588-0.23580.0705-0.1346-0.2674-0.0116-0.0633chain C heavy chain-20.8013-26.2782-17.7391
44.7142-1.31892.21853.157-0.9191.6001-0.0559-0.04010.00690.00380.03390.0594-0.004-0.01340.022-0.21090.0295-0.0331-0.2487-0.0324-0.1702chain D light chain-33.6409-10.3683-19.945
53.4862-0.83231.27545.26790.32122.70360.0048-0.43120.05360.74170.0230.2694-0.0768-0.1984-0.0278-0.06740.00310.0309-0.3103-0.0111-0.2193chain E CXCL13-1.043214.5216-19.1857
61.2169-0.47322.25490.38013.16289.00520.00490.0401-0.10770.45540.06670.06830.07480.0619-0.07160.06080.0013-0.2977-0.2584-0.0723-0.0237chain F CXCL13-12.765-12.64425.824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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