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- PDB-3upa: A general strategy for the generation of human antibody variable ... -

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Basic information

Entry
Database: PDB / ID: 3upa
TitleA general strategy for the generation of human antibody variable domains with increased aggregation resistance
Componentskappa light chain variable domain
KeywordsIMMUNE SYSTEM / immunoglobulin fold
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 / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / 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 / blood microparticle / 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
Immunoglobulin kappa variable 1-39
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsDudgeon, K. / Rouet, R. / Kokmeijer, I. / Langley, D.B. / Christ, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: General strategy for the generation of human antibody variable domains with increased aggregation resistance
Authors: Dudgeon, K. / Rouet, R. / Kokmeijer, I. / Schofield, P. / Stolp, J. / Langley, D. / Stock, D. / Christ, D.
History
DepositionNov 17, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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

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Assembly

Deposited unit
A: kappa light chain variable domain
B: kappa light chain variable domain


Theoretical massNumber of molelcules
Total (without water)23,2822
Polymers23,2822
Non-polymers00
Water1,69394
1
A: kappa light chain variable domain


Theoretical massNumber of molelcules
Total (without water)11,6411
Polymers11,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: kappa light chain variable domain


Theoretical massNumber of molelcules
Total (without water)11,6411
Polymers11,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.040, 45.040, 173.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-123-

HOH

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Components

#1: Antibody kappa light chain variable domain


Mass: 11640.765 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHEN1 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P01597*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 1.89 Å3/Da / Density % sol: 34.81 % / Mosaicity: 1.57 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 26% PEG 10000, 100mM Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2011
RadiationMonochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.8→43.591 Å / Num. all: 17458 / Num. obs: 17458 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Rsym value: 0.14 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.912.50.8210.7880.93074924610.2270.8210.788399.6
1.9-2.0112.40.5140.4931.52900523380.1430.5140.4934.599.7
2.01-2.1512.30.3260.3132.42735222250.0910.3260.3136.799.9
2.15-2.3212.20.2580.24732509220590.0720.2580.2478.699.9
2.32-2.55120.2080.1993.72323319320.0590.2080.1999.899.9
2.55-2.8511.80.1570.154.82070417590.0450.1570.1512.799.9
2.85-3.2911.40.1210.1165.81782315610.0350.1210.11617.899.9
3.29-4.0210.70.1050.16.71466413650.0310.1050.123.399.8
4.02-5.69100.0720.0689.21081810800.0220.0720.06825.299.4
5.69-45.0410.50.040.0381571006780.0120.040.03821.399.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å43.59 Å
Translation3.5 Å43.59 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Iceicedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F6L

1f6l


Resolution: 1.8→43.59 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.89 / WRfactor Rfree: 0.2777 / WRfactor Rwork: 0.2227 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8421 / SU B: 6.487 / SU ML: 0.106 / SU R Cruickshank DPI: 0.1676 / SU Rfree: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.283 885 5.1 %RANDOM
Rwork0.2288 ---
all0.23136 17403 --
obs0.2314 17403 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 42.52 Å2 / Biso mean: 20.592 Å2 / Biso min: 6.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 0 94 1597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211555
X-RAY DIFFRACTIONr_bond_other_d0.0010.02950
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.9562141
X-RAY DIFFRACTIONr_angle_other_deg0.87832345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5245220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52725.09453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93615195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.231153
X-RAY DIFFRACTIONr_chiral_restr0.0860.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211815
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02308
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 53 -
Rwork0.268 1014 -
all-1067 -
obs--99.16 %
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)
12.08281.1071-0.82611.7525-0.11031.29830.0285-0.0279-0.12580.2434-0.0557-0.10020.08410.04740.02720.09240.0017-0.00150.0131-0.00010.048720.3566-18.300316.5852
21.4649-0.2206-0.27821.82780.85722.10150.08730.17830.0412-0.016-0.1182-0.0537-0.0357-0.14480.03080.01670.03370.00920.08130.03630.044414.9164-0.92064.1609
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 105
2X-RAY DIFFRACTION2B1 - 106

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