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- PDB-5cbe: E10 in complex with CXCL13 -

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Basic information

Entry
Database: PDB / ID: 5cbe
TitleE10 in complex with CXCL13
Components
  • C-X-C motif chemokine 13
  • E10 heavy chain
  • E10 light chain
KeywordsIMMUNE SYSTEM / anti-CXCL13 / E10 / 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
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: 2.4 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 1, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
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
Revision 1.4Sep 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: E10 heavy chain
B: E10 light chain
C: E10 heavy chain
D: E10 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)76,0137
Polymers75,9516
Non-polymers621
Water1,67593
1
A: E10 heavy chain
B: E10 light chain
E: C-X-C motif chemokine 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0384
Polymers37,9753
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-19 kcal/mol
Surface area15260 Å2
MethodPISA
2
C: E10 heavy chain
D: E10 light chain
F: C-X-C motif chemokine 13


Theoretical massNumber of molelcules
Total (without water)37,9753
Polymers37,9753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-24 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.000, 125.000, 98.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsTrimer confirmed by gel filtration

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Components

#1: Antibody E10 heavy chain


Mass: 14663.956 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293 / Gene: IGHV1-69-2 / Cell line (production host): HEK293F / Production host: Mammalia (mammals) / References: UniProt: A0A0B4J2H0
#2: Antibody E10 light chain


Mass: 12844.972 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Mammalia (mammals) / References: UniProt: P04209
#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
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57 % / Description: long rod
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM KH2PO4, 100 mM NaH2PO4, 100 mM MES pH 6, 2000 mM NaCl
PH range: 6

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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: Apr 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 34874 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 59.02 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 30.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: E10 and 3GV3/2R3Z/4HSV/3IL8

3gv3

2r3z

4hsv

3il8


Resolution: 2.4→40.92 Å / Cor.coef. Fo:Fc: 0.9049 / Cor.coef. Fo:Fc free: 0.8838 / SU R Cruickshank DPI: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.316 / SU Rfree Blow DPI: 0.237 / SU Rfree Cruickshank DPI: 0.242
RfactorNum. reflection% reflectionSelection details
Rfree0.2746 1751 5.02 %RANDOM
Rwork0.2481 ---
obs0.2495 34852 99.85 %-
Displacement parametersBiso mean: 82.67 Å2
Baniso -1Baniso -2Baniso -3
1--4.6629 Å20 Å20 Å2
2---4.6629 Å20 Å2
3---9.3259 Å2
Refine analyzeLuzzati coordinate error obs: 0.609 Å
Refinement stepCycle: 1 / Resolution: 2.4→40.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4599 0 4 93 4696
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084711HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.066401HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1566SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes689HARMONIC5
X-RAY DIFFRACTIONt_it4711HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.48
X-RAY DIFFRACTIONt_other_torsion20.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion631SEMIHARMONIC5
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_contact5074SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.47 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2684 135 4.61 %
Rwork0.2506 2795 -
all0.2514 2930 -
obs--99.85 %
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)
13.5723-1.11950.59831.77930.9623.5191-0.0198-0.50940.23570.2863-0.4321.4955-0.0709-0.43060.4518-0.4499-0.02980.041-0.4521-0.21660.772E10 heavy chain-42.031288.531-18.4422
22.49270.34030.61296.98552.10184.76450.08120.3026-0.1253-0.8378-0.38490.9965-0.23670.30810.3037-0.14850.0465-0.2343-0.22490.07730.053E10 light chain-27.41284.8883-33.0132
32.098-0.1369-0.3434.12954.0315.6197-0.00360.1802-0.271-0.1954-0.0493-0.03670.1499-0.0790.0529-0.1304-0.33790.03870.2402-0.106-0.459E10 heavy chain-14.391832.9913-19.101
43.66560.47012.4343.49583.15821.1317-0.41080.6386-0.015-0.28680.54420.4531-0.1975-0.4539-0.1334-0.2797-0.3793-0.02060.80850.1239-0.5335E10 light chain-32.864735.7885-8.9025
53.0695-0.18162.41040.0464-3.22536.5379-0.0467-0.2690.08170.45880.06210.14290.0822-0.1274-0.01540.38150.03330.1966-0.33810.1301-0.2617CXCL13-21.921476.0432-1.1157
6-0.7218-1.3248-1.23267.1051-5.31161.8669-0.16570.47940.4586-0.17550.199-0.0091-0.4422-0.0697-0.03330.03050.0163-0.08640.16060.1151-0.2846CXCL13-9.66959.0684-7.4758
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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