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- PDB-5c6w: anti-CXCL13 scFv - E10 -

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Basic information

Entry
Database: PDB / ID: 5c6w
Titleanti-CXCL13 scFv - E10
ComponentsProtein IGHV1-69-2,Ig lambda chain V-II region NIG-84
KeywordsIMMUNE SYSTEM / anti-CXCL13 / scFv
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / antigen binding / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Immunoglobulin heavy variable 1-69D / Immunoglobulin lambda variable 2-14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsTu, C. / Bard, J. / Mosyak, L.
CitationJournal: To Be Published
Title: Optimization of a scFv-based biotherapeutic by CDR side-chain clash repair
Authors: Tu, C. / Terraube, V. / Tam, A. / Stochaj, W. / Fennell, B. / Lin, L. / Stahl, M. / LaVallie, E. / Somers, W. / Finlay, W. / Mosyak, L. / Bard, J. / Cunningham, O.
History
DepositionJun 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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
H: Protein IGHV1-69-2,Ig lambda chain V-II region NIG-84
J: Protein IGHV1-69-2,Ig lambda chain V-II region NIG-84
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,68744
Polymers54,9822
Non-polymers2,70542
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-12 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.980, 80.360, 119.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDimer confirmed by SEC

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Components

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Antibody , 1 types, 2 molecules HJ

#1: Antibody Protein IGHV1-69-2,Ig lambda chain V-II region NIG-84


Mass: 27490.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK 293 / Gene: IGHV1-69-2 / Production host: Mammalia (mammals) / References: UniProt: A0A0B4J2H0, UniProt: P04209

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Non-polymers , 5 types, 601 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 3.03 Å3/Da / Density % sol: 59 % / Description: very nice bi-pyramid
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris pH 8.5, 2000 mM (NH4)2SO4 / PH range: 8.5

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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: Nov 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 98395 / % possible obs: 98.8 % / Redundancy: 8.8 % / Biso Wilson estimate: 22.29 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 26
Reflection shellResolution: 1.54→1.63 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.4 / % possible all: 92.2

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JUY

3juy


Resolution: 1.54→50 Å / Cor.coef. Fo:Fc: 0.9691 / Cor.coef. Fo:Fc free: 0.9688 / SU R Cruickshank DPI: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.059 / SU Rfree Blow DPI: 0.056 / SU Rfree Cruickshank DPI: 0.054
RfactorNum. reflection% reflectionSelection details
Rfree0.1635 4903 4.99 %RANDOM
Rwork0.1539 ---
obs0.1544 98308 98.32 %-
Displacement parametersBiso mean: 26.97 Å2
Baniso -1Baniso -2Baniso -3
1--2.108 Å20 Å20 Å2
2--0.4663 Å20 Å2
3---1.6416 Å2
Refine analyzeLuzzati coordinate error obs: 0.155 Å
Refinement stepCycle: 1 / Resolution: 1.54→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3717 0 161 559 4437
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013960HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.095390HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1325SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes609HARMONIC5
X-RAY DIFFRACTIONt_it3960HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.32
X-RAY DIFFRACTIONt_other_torsion14.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion529SEMIHARMONIC5
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_contact5031SEMIHARMONIC4
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2315 296 5.01 %
Rwork0.1986 5615 -
all0.2002 5911 -
obs--98.32 %
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)
10.99590.28650.69440.55420.6211.69430.041-0.12480.0016-0.01020.01520.0454-0.0017-0.2184-0.05620.116-0.0033-0.02290.15090.00040.1187heavy chain-28.4043-6.1094-53.4505
21.3634-0.02180.33441.2363-0.09110.4741-0.0002-0.02180.0148-0.1416-0.02180.01710.00990.03340.0220.0812-0.00690.00350.1061-0.00490.085light chain-9.5765-15.1522-56.4033
30.71620.15050.19150.75080.13410.79440.0149-0.00960.0142-0.04990.04280.0377-0.1085-0.0201-0.05770.1096-0.007-0.00660.0533-0.00730.0633heavy chain-6.62118.1409-30.9871
40.6179-0.03320.26222.1047-0.11811.4636-0.0253-0.0741-0.0071-0.0225-0.0044-0.04040.1239-0.05810.02970.1101-0.01060.00370.06640.00770.0889light chain-3.3117-12.642-29.6258
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ H|1 - H|127 }
2X-RAY DIFFRACTION2{ H|1001 - H|1122 }
3X-RAY DIFFRACTION3{ J|1 - J|127 }
4X-RAY DIFFRACTION4{ J|1001 - J|1122 }

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